eLife Assessment

Bonnifet et al. present data on the expression and interacting partners of the transposable element L1 in the mammalian brain. The work includes important findings addressing the potential role of L1 in aging and neurodegenerative disease. The reviewers conclude that several aspects of the study are well done. However, the experimental evidence presented supporting the L1 increase with aging is not fully conclusive and this finding remains incomplete in its current form.

eLife Assessment

This fundamental study describes patterns of anatomical connectivity between the cortex and the thalamus using magnetic resonance imaging data in humans and non-human primates. The measures are related to numerous other modalities to develop a robust understanding of the organisation of the system. The authors provide convincing evidence that there is a difference between sensory and association cortices in terms of their connectivity with the thalamus, which may have downstream effects on brain function. This work will be of interest to neuroscientists interested in the organization and dynamics of cortico-thalamic circuits.

eLife Assessment

The manuscript reports fundamental findings supported by convincing data that supports the biological mechanism for optimal nodulation in soybean. The results are of relevance to understanding the signaling pathways (specifically those dependent on RIN4/RPM1-interacting protein 4) underpinning beneficial rhizobia symbiosis, while repressing the immune response.

eLife Assessment

This paper shows that it is possible to optogenetically activate single retinal ganglion cells in vivo in monkeys. This is an important step towards towards causal tests of the role of specific ganglion cell types in visual perception. The paper presents convincing evidence for the promise of the approach but further work will be needed to full explore its limitations and specificity.

eLife Assessment

The study reports an important finding on the role of the global metabolic regulator Crp/cAMP in the formation of antibiotic persister Escherichia coli. The evidence supporting the claims is solid including metabolomic analysis and characterization of many mutant strains.

eLife Assessment

This study introduces a valuable spring-bead model for epithelial cell layers, designed to improve previous cell-resolved approaches and to understand the connection between the biophysics of cell-cell contacts and the tissue mechanics. While the model is not entirely new and does not fully settle open questions such as the role of adhesion in tissue fluidity, it provides solid evidence and stands out as simple and efficient. A more comprehensive comparison with previous cell-revolved approaches and, in particular, with experimental data, would further strengthen the proposed model as a conceptual and practical tool.

eLife Assessment

This important study utilizes the nematode C. elegans and mammalian cell culture to investigate the role of MML-1/Mondo in conserved regulation of metabolism and aging. The evidence supporting the conclusions is convincing and covers a range of areas including localization, upstream pathways, and conservation. The paper will be of interest to a broad range of biologists studying aging, metabolism, and transcriptional regulation.

eLife Assessment

This Research Advance manuscript further elucidates the roles of SMC5/6 loader proteins and associated factors in the silencing of extrachromosomal circular DNA by the SMC5/6 complex. While the findings are largely in line with expectations, they are useful, representing a meaningful advance beyond the recent study (reference 33), contributing to a growing foundation for further comparative and mechanistic investigations. Solid evidence is presented for a role for SIMC1/SLF2 in the localization of the SMC5/6 complex to plasmid DNA, and the distinct requirements, as compared to the recruitment of SMC5/6 to chromosomal DNA lesions.

eLife Assessment

This study provides an important understanding of the contribution of different striatal subregions, the anterior Dorsal Lateral Striatum (aDLS) and the posterior Ventrolateral Striatum (pVLS), to auditory discrimination learning. The authors have included robust behavior combined with multiple observational and perturbation techniques. The data provided are convincing of the relevance of task-related activity in these two subregions during learning.

eLife Assessment

This valuable paper used a longitudinal cohort of individuals initiating ART to suggest that CD8+ T cells may contribute to the clearance of intact HIV DNA during long-term antiretroviral therapy (ART) for HIV, which is relevant to our understanding of the mechanisms driving reservoir persistence in people living with HIV. The reviewers concluded that the evidence presented is incomplete to fully support these claims, as the cohort sampling is relatively infrequent, and the association direction could be bi-directional or due to other confounding variables.

eLife Assessment

This paper examines selection on induced epigenetic variation ("Lamarckian evolution") in response to herbivory in Arabidopsis thaliana. The authors find weak evidence for such adaptation, which contrasts with a recently published study that reported extensive heritable variation induced by the environment. The authors convincingly demonstrate that the findings of the previous study were confounded by mix-ups of genetically distinct material, so that standing genetic variation was mistaken for acquired (epigenetic) variation. Given the controversy surrounding the influence of heritable epigenetic variation on phenotypic variation and adaptation, this study is an important, clarifying contribution; it serves as a timely reminder that sequence-based verification of genetic material should be prioritized when either genetic identity or divergence is of importance to the conclusions.

eLife Assessment

Using a combination of connectomics, optogenetics, behavioral analysis, and modeling, this study provides important findings on the role of two populations of inhibitory neurons in the generation of leg grooming movements in Drosophila. The data as presented provide incomplete evidence that the identified neuronal populations contribute to the alternation of flexion and extension by inhibiting specific sets of motor neurons while disinhibiting their counterparts. While the manuscript provides comprehensive details about the 13A/B neuronal populations involved in grooming control, updates on statistics, and explicit mentioning of experimental/modeling caveats would strengthen the study. The work will interest neuroscientists, and particularly those working on motor control.

eLife Assessment

This study presents a valuable finding on the perturbed pyruvate metabolism in models of repetitive traumatic brain injury. The evidence supporting the main claims of the authors is solid, but much of the accompanying analysis and interpretation relies on incomplete evidence. The work will be of interest to those working on the imaging of traumatic brain injury.

eLife Assessment

This is a valuable and rigorous study that addresses the question of what determines the spatial organization of endocytic zones at synapses. The authors use compelling approaches, in both Drosophila and rodent model systems, to define the role of activity and active zone structure on the organization of the peri-active zone. While the findings are primarily negative, they are carefully executed and contribute to the field by refining existing models of presynaptic organization.

eLife Assessment

The authors conducted a valuable study that investigates a molecular pathway mediating the transformation of a cell aggregate into a sheet known as the nucleus laminaris, a crucial site for auditory processing. While the study offers a comprehensive view of the sequence of developmental events and suggests possible roles for FGF signaling, the transcription factor Mafb, and the cell surface adhesive molecule Cadherin-23 in this process, the current data were considered incomplete.

eLife Assessment

This manuscript provides valuable information on the neurodynamics of emotional processing while participants were watching movie clips. The methods and results were solid in deciphering the temporal-spatial dynamics of emotional processing. This work will be of interest to affective neuroscientists.

eLife Assessment

This important study looks into the effect of exogenous CoA on the response of TLR4-activated macrophages. Specifically, CoA enhances the LPS response by examining metabolomics, 13C tracing, and assessments of transcription and acetylation. Together, these provide a compelling series of findings that show exogenous CoA is taken up by macrophages, and this facilitates histone acetylation and transcription associated with activation and antimicrobial activity.

eLife Assessment

Karimian et al. present a valuable new model to explain how gamma-band synchrony (30-80 Hz) can support human visual feature binding by selectively grouping image elements, countering recent criticisms that the stimulus dependence of gamma oscillations limits their functional role. Grounded in the theory of weakly coupled oscillators and informed by primate electrophysiology, the model captures behavioural patterns observed in human psychophysics, offering support for the potential role of synchrony-based mechanisms, but incomplete evidence for a specific role of gamma oscillations. This work could be strengthened by more direct evidence for the proposed mechanism, and expanding beyond figure-only model inputs with limited ecological validity.

eLife Assessment

The authors present an important multi-scale computational platform, which aims to automate the workflow for coarse-grained simulations of biomolecules in the framework of the popular MARTINI model. The capability of the platform has been convincingly demonstrated by the application to a large number of proteins as well as macrocycles and polymers. This work will be of interest to both computational biophysicists and chemists.

eLife Assessment

This study provides a fundamental analysis of the EmrE efflux pump, highlighting the role of the C-terminal domain in influencing uncoupled proton leak. The integration of biophysical techniques with molecular dynamics simulations offers solid support for the key findings and adds substantial evidence toward a definitive understanding of EmrE transport mechanism.

eLife Assessment

This fundamental study investigates the role of polyunsaturated fatty acids (PUFAs) in physiology and membrane biology, using a unique model to perform a thorough genetic screen that demonstrates that PUFA synthesis defects cannot be compensated for by mutations in other pathways. These findings are supported by compelling evidence from a high quality genetic screen, functional validation of their hits, and lipid analyses. This study will appeal to researchers in membrane biology, lipid metabolism, and C. elegans genetics.

eLife Assessment

The authors design and implement an elegant strategy to delete genomic sequences encoding the dopamine receptor dop1R2 from specific subsets of mushroom body neurons (ab, a'b' and gamma) and show that while none of these manipulations affect short term appetitive or aversive memory, loss of dop1R2 from ab or a'b' block the ability of flies to display measurable forms of longer forms of memory. These findings are important in confirming and extending prior observations, and well supported by convincing evidence that build on precise techniques for genetic perturbation.

eLife Assessment

This important study presents an alternative platform for nanobody discovery using phage-displayed synthetic libraries. The evidence supporting the platform, which is used to isolate and validate nanobodies targeting Drosophila secreted proteins, is compelling. By making the library openly accessible, this provides an excellent resource to the wider scientific community. The paper presents a detailed protocol for nanobody screening; as this protocol is refined and optimized over time, this will increase the success rate for discovering nanobodies with improved properties using this alternative platform.

eLife Assessment

This study reveals a neural signature of a common behavioural phenomenon: serial dependence, whereby estimates of a visual feature (here motion direction) are attracted towards the recent history of encoded and reported stimuli. The study provides solid evidence that this phenomenon arises primarily during working memory maintenance. The pervasiveness of serial dependencies across modalities and species makes these findings important for researchers interested in perceptual decision-making across subfields.

eLife Assessment

In this valuable study, Nold et al. examined exercise-induced pain modulation in a pharmacological within-subject fMRI study using the opioid-antagonist naloxone and different levels of aerobic exercise intensity and pain. This investigation provides solid evidence to show that the intensity of exercise does not seem to impact the hypoalgesic effect. Moreover, exploratory analysis identified that fitness level and sex may potentially play a role in exercise-induced hypoalgesia, and that further confirmatory studies are required in order to verify these findings.

eLife Assessment

This valuable manuscript investigates the localisation of nutrient receptors in bloodstream stage trypanosomes, with implications for both nutrient uptake and immune evasion. Results after direct fixation of the cells in culture medium provide convincing evidence that the amounts of receptors on the surface of the cell, as opposed to the flagellar pocket, have previously been severely underestimated. Some results were essentially confirmatory, and there are questions regarding the quantitation of ligand binding by transferring receptors.

eLife Assessment

The study is a timely and important contribution to our knowledge of the circuit mechanisms of fear analgesia. The novel cue-induced analgesia paradigm allowed a compelling identification of a brainstem circuit element, i.e., somatostatin-expressing neurons within the ventrolateral periaqueductal grey that project to the rostroventral medulla, in mediating fear analgesia. The vlPAG is a known region of pain modulation, and this study adds key insight to the circuit involved in fear-associated analgesia. This work will be of interest to systems and behavioral neuroscientists, especially those interested in emotional behavior, pain, and/or brainstem function.

eLife Assessment

This valuable study addresses the structural basis of voltage-activation of BK channels using atomistic simulations of several microseconds, to assess conformational changes that underlie both voltage-sensing and gating of the pore. The findings, including movement of specific charged residues, combined with the degree to which these movements are coupled to pore movements, provide a solid basis for understanding voltage-gating mechanisms in this class of channels. This paper will likely be of interest to ion channel biologists and biophysicists focused on voltage-dependent channel gating mechanisms.

eLife Assessment

Sanchez-Vasquez et al establish an innovative approach to induce aneuploidy in preimplantation embryos. This important study extends the author's previous publications evaluating the consequences of aneuploidy in the mammalian embryo. In this work, the authors investigate the developmental potential of aneuploid embryos and characterize changes in gene expression profiles under normoxic and hypoxic culture conditions. Using a solid methodology they identify sensitivity to Hif1alpha loss in aneuploid embryos, and in further convincing experiments they assess how levels of DNA damage and DNA repair are altered under hypoxic and normoxic conditions.

eLife Assessment

This study provides a comprehensive analysis of gene expression and bioinformatics data, offering important insights into the roles of fibroblasts in cardiac development. The large and well-analyzed single-cell RNA sequencing (scRNA-seq) dataset is compelling and a significant contribution to the field, and will be of broad interest to the scientific community.

eLife Assessment

This paper identifies a crucial step in the regulation of tight junction formation by identifying Rho-ROCK activity-dependent activation of the serine protease Matriptase, making Claudins available for tight junction formation. The reviewers were satisfied with the revisions and found the work important and the approach convincing.

eLife Assessment

This valuable study by Wu et al presents data on bacterial cell organization, demonstrating that the two structures that account for bacterial motility - the chemotaxis complex and the flagella - colocalize to the same pole in Pseudomonas aeruginosa cells. The work provides convincing results for the regulation underlying this spatial organization and its functioning.

eLife Assessment

This important study demonstrates that slow fluctuations in serotonin release during wakefulness and non-REM sleep correspond to periods of heightened arousal or enhanced offline information processing. The evidence supporting this claim is convincing, and the methodology is robust and broadly applicable, likely to benefit many researchers in the field. This work will be of significant interest to neuroscientists studying sleep, memory, and neuromodulation.

eLife Assessment

This important study by Lee et al. explores the heterogeneous response of non-growing bacteria to the antimicrobial peptide (AMP) tachyplesin. The authors identify a subpopulation of cells that evade lethal damage by limiting the intracellular accumulation of a fluorescently labeled tachyplesin analog. The study provides compelling evidence that reduced drug accumulation underlies the decreased susceptibility of this subpopulation to the AMP. The molecular basis of this phenotype is well supported by the data.

eLife Assessment

This valuable study reports the development of a novel organoid system for studying the emergence of autorhythmic gut peristaltic contractions through the interaction between interstitial cells of Cajal and smooth muscle cells. The authors further utilized the system to provide convincing evidence for a previously unappreciated potential role for smooth muscle cells in regulating the firing rate of interstitial cells of Cajal. The work will be of interest to those studying development and physiology of the gut.

eLife Assessment

The study presents a comprehensive multi-approach and functional investigation of RBMX2 as a host factor involved in Mycobacterium bovis pathogenesis and its potential role in promoting epithelial-mesenchymal transition and lung cancer progression. The findings are valuable since the possible connection between M. bovis and lung cancer and the underlying mechanisms provides a promising direction for future research. The evidence is solid with methods, data, and analyses broadly supporting the claims, albeit with minor weaknesses that, if addressed, will make the evidence stronger. The study remains of great interest to microbiology, oncology, and drug discovery scientists.

eLife Assessment

This work describes an inference technique for extracting information about relative contributions of excitatory and inhibitory synaptic drive onto single neurons in neural networks. The electrophysiological techniques and results are of high quality, and the analytical work is novel and potentially powerful, yet with several untested assumptions underlying the approach. This is nevertheless solid work that will be valuable to neuroscience labs interested in exploring alternative approaches to studies of integrated synaptic connectivity.

eLife Assessment

This important paper describes a comprehensive quantitative phospho-proteomic analysis of the meiotic progression of Xenopus oocytes. Using time-resolved proteomic analyses, the authors provide insights into changes in protein levels and phosphorylation states to an unprecedented depth, quality, and quantitative detail. The key findings are compelling and offer a helpful resource for the scientific community.

eLife Assessment

The authors quantified intentions and knowledge gaps in scientists' use of sex as a biological variable in their work, and used a workshop intervention to show that while willingness was high, pressure points centered on statistical knowledge and perceived additional monetary costs to research. These important findings demonstrate the difficulty in changing understanding - while interventions can improve knowledge and decrease perceived barriers, the impact was small. The evidence was solid, although the sample size was small for the intervention.

eLife Assessment

This manuscript presents important findings on how structural color can be manipulated through a specific single-gene mutation in a motile bacterium. Compelling data provide a promising model to identify genes and molecular mechanisms supporting this widespread optical phenomenon. This work will be of interest to biophysicists and microbiologists working on structural colors and Flavobacterium.

eLife Assessment

This manuscript offers important insights into how polyphosphate (polyP) influences protein phase separation differently from DNA. The authors present compelling evidence that polyP distinguishes among protein conformational ensembles, leading to divergent condensate maturation behaviors that include unfolding and polyproline II formation. In response to reviewer feedback, the authors addressed key concerns by incorporating charge-equivalent DNA controls and extending structural analysis to FruR variants, further reinforcing the polymer-specific effects of polyP. While some discrepancies between protein systems remain unresolved, the study enhances our understanding of how biopolymers influence protein assembly and conformational transitions.

eLife Assessment

This important study analyzes the effect of heat treatment on phage-bacterial interactions and convincingly shows that prior heat exposure alters the bacterial cell envelope, enhancing persistence and bacterial survival when exposed to lytic phages. The study will interest researchers working on antibiotic resistance, tolerance, and phage therapy.

eLife Assessment

This important study offers a powerful empirical test of a highly influential hypothesis in population genetics. It incorporates a large number of animal genomes spanning a broad phylogenetic spectrum and treats them in a rigorous unified pipeline, providing the convincing negative result that effective population size scales neither with the content of transposable elements nor with overall genome size. These observations demonstrate that there is still no simple, global hypothesis that can explain the observed variation in transposable element content and genome size in animals.

eLife Assessment

This manuscript reports valuable findings on the role of the Srs2 protein in turning off the DNA damage signaling response initiated by Mec1 (human ATR) kinase. The data provide convincing evidence that Srs2 interaction with PCNA and ensuing SUMO modification is required for checkpoint downregulation. However, while the model that Srs2 acts at gaps after camptothecin-induced DNA damage is reasonable, direct experimental evidence for this is currently lacking. The work will be of interest to cell biologists studying genome integrity.

eLife Assessment

This study reports a fundamental observation concerning cell death regulation by the anti-apoptotic BCL2 family NOXA. The authors convincingly demonstrate that NOXA is destabilized through the interaction with WSB2, a substrate receptor in CRL5 ubiquitin ligase complex, sensitizing the cells to treatments. These are key findings for cell biologists and cancer researchers as they identified a new target impacting drug responsiveness in cancer therapies.

eLife Assessment

This paper reports on a correlation between diminished cardiolipin content and the severity of steatohepatitis in human subjects. This is supported further by experimental evidence from mice in which the gene encoding a key enzyme in cardiolipin synthesis has been compromised in the liver. The correlations established between lipidology, mitochondrial function, and the induction of respiration and oxidative stress are notable and will be useful to researchers in the field. However, given that the causal relationship between lipid perturbation and the progression of steatohepatitis implied in the title has not been tested experimentally, the evidence supporting the paper's key conclusion is incomplete.

eLife Assessment

This important manuscript investigates the role of olfactory cues in Pieris brassicae larvae, focusing on their interactions with the host plant Brassica oleracea and the parasitoid wasp Cotesia glomerata. The authors' demonstration that impaired olfactory perception reduces caterpillar performance and increases susceptibility to parasitism is convincing. These findings highlight the ecological significance of olfaction in mediating feeding behavior and predator avoidance in herbivorous insects.

eLife Assessment

This is an important study that characterized proteins associated with electrical synapses in zebrafish and mouse retinal neurons using proximity labeling approaches, complemented by biochemical and histological validations. The resulting protein interactome datasets are convincing and reveal novel scaffold proteins at the electrical synapse. Additional quantification and validation would strengthen the work further.

eLife Assessment

This valuable study explores changes in remote memory impairment in an amyloid pathology mouse model, demonstrating that progressive deficits coincide with inhibitory interneuron alterations. While the findings shed light on circuit remodeling in this model, the mechanistic links between heightened inhibition and memory loss are currently incomplete. Additional data and deeper analysis may be needed to fully substantiate the authors' interpretations.

eLife Assessment

This valuable study presents a novel approach to enhance the therapeutic potential of mesenchymal stromal cells (MSCs) by genetically modifying their glycogen synthesis pathway, resulting in increased glycogen accumulation and improved cell survival under starvation conditions, particularly in the context of experimental pulmonary fibrosis. The methods and findings are generally solid and could be strengthened by investigating the kinetics of persistence, the immunomodulatory effects, and the underlying improved mechanism of action of MSCs in this pulmonary fibrosis model. If confirmed, this approach could suggest potential methods to improve the therapeutic functionality of MSCs in cell therapy strategies.

eLife Assessment

Valencia et al. combine elegant in vitro biochemical experiments with functional assays in cardiomyocytes to determine which properties of the FHOD3 formin are essential for sarcomere assembly. Using separation-of-function mutants, they show that FHOD3's elongation activity, rather than its nucleation, capping, or bundling activities, is key to its sarcomeric function. This is an important finding and the data presented in the manuscript are convincing; however, the presence of FHOD3 at filament barbed ends in the TIRF elongation assays should probably be verified directly in a future study.

eLife Assessment

This useful study presents Altair-LSFM, a solid and well-documented implementation of a light-sheet fluorescence microscope (LSFM) designed for accessibility and cost reduction. While the approach offers strengths such as the use of custom-machined baseplates and detailed assembly instructions, its overall impact is limited by the lack of live-cell imaging capabilities and the absence of a clear, quantitative comparison to existing LSFM platforms. As such, although technically competent, the broader utility and uptake of this system by the community may be limited.

eLife Assessment

This important study identifies a novel Legionella effector, Lfat1, which binds F-actin via a coiled-coil domain and structurally resembles the RID toxin, with cryo-EM revealing key interactions mediated by a hydrophobic helical hairpin. While the study is mostly complete and has compelling data, a few minor changes are recommended.

eLife Assessment

The work provides important insights into how this lncRNA regulates gene expression via complex mechanisms, however, the biological relevance awaits validation in other models. This paper provides extensive and carefully analysed data that is of value in efforts to understand the role of the lncRNA EPB41L4A-AS1 in a human cell line. The data is generally convincing and supported by clever integrative analysis; however, the known extensive artefacts from individual Gapmer oligonucleotides cast some doubt over the interpretation of those experiments where only one targeting and one control Gapmer are used.

eLife Assessment

In this manuscript, the authors describe a software package for automatic differentiation of action potentials generated by excitatory and inhibitory neurons, acquired using high-density microelectrode arrays. The work is valuable as it offers a tool with the potential to automatically identify these neuron types in vitro. However, it is incomplete due to limited comparison with ground truth data from optogenetically identified interneuron subtypes and with existing spike sorting pipelines available to users.

eLife Assessment

This study provides important information on the ultrastructural organization of layer 1 of the human neocortex. The quantitative assessment of various synaptic parameters, astrocytic coverage and mitochondrial morphology is based on convincing experimental approaches. These data provide new information on the detailed morphology of human neocortical tissue that will be of interest to neuroscientists working on different network functions.

eLife Assessment

This study provides valuable insights into the organization of second-order circuits of gustatory neurons, particularly in how these circuits integrate opposing taste inputs and are modulated by metabolic state to regulate feeding behavior. Through an elegant combination of complementary techniques, the authors identify the target neurons involved in gustatory integration. The evidence supporting their conclusions is convincing.

eLife Assessment

This theoretical study makes a useful contribution to our understanding of a subtype of type 2 diabetes - ketosis-prone diabetes mellitus (KPD) - with a potential impact on our broader understanding of diabetes and glucose regulation. The article presents an ordinary differential equation-based model for KPD that incorporates a number of distinct timescales - fast, slow, as well as intermediate, incorporating a key hypothesis of reversible beta cell deactivation. The presented evidence is solid and shows that observed clinical disease trajectories may be explained by a simple mathematical model in a particular parameter regime.

eLife Assessment

The findings are important and intriguing, with theoretical or practical implications beyond a single subfield. The computational methods employed are clever and sophisticated and the strength of evidence is convincing. Both the hypotheses and the exploratory nature of additional analyses are clearly stated.

eLife Assessment

Argunşah et al. investigate the mechanisms underlying the differential response dynamics of barrel vs septa domains in shaping the responses to single vs multiple whiskers. Based on the observation of a higher density of SST+ interneurons in the septa, the authors investigate the hypothesis that Elfn1-dependent short-term plasticity shapes these responses. This important study is, however, supported by incomplete evidence; factors restricting the strength of evidence are the limited spatial resolution of the multi-unit activity, as well as the lack of a mechanistic explanation. This provocative and intellectually stimulating hypothesis provides a contribution to work on how different cell types shape cortical representation.

eLife Assessment

This important study reports that the human posterior inferotemporal cortex (hPIT) functions as an attentional priority map, integrating both top-down and bottom-up attentional signals rather than serving solely as an object-processing region. The experiments and analyses are well conducted and provide convincing evidence that hPIT bridges dorsal and ventral attention networks and is robustly modulated by attention across diverse visual tasks. The study will be relevant for researchers investigating visual attention, high-level visual cortex, and the neural mechanisms that integrate endogenous and exogenous attentional control.

eLife Assessment

This study provides important findings on the neural circuits underlying dishabituation of the olfactory avoidance response in Drosophila. The data as presented provide solid evidence that the dishabituation involves distinct pathways from habituation. They show that reward-activated dopaminergic neurons provide input for within-modal dishabituation, while punishment-activated dopaminergic neurons provide input for cross-modal dishabituation. The work will interest neuroscientists, particularly behavioral neuroscientists working on habituation, neural circuits, and the dopaminergic system.

eLife Assessment

This manuscript presents a valuable computational tool for identifying 3-5 gene regulatory network topologies capable of generating oscillatory dynamics. The application of Monte Carlo Tree Search to circuit design is novel and effectively expands the scale at which non-linear behaviours can be explored in silico. The efficiency of the proposed algorithm is convincing, and the work will be of interest to the systems and synthetic biology communities. While the evolutionary implications remain unclear, the methodological contribution represents a significant advance in the field.

eLife Assessment

This useful study reports findings that support the use of the Open Field Test in Drosophila as a model to study "emotion-like states", which are behavioral responses to several stressful or aversive treatments, and resilience upon their subsequent removal. Behavioral data, by employing established stress-causing treatments and genetic manipulations, are solid. While the results and conceptual framework of this work will be of interest to behaviorists regardless of animal models, the novelty of this work over previous studies could have been clearer.

eLife Assessment

This important study demonstrates the significance of incorporating biological constraints in training neural networks to develop models that make accurate predictions under novel conditions. By comparing standard sigmoid recurrent neural networks (RNNs) with biologically constrained RNNs, the manuscript offers compelling evidence that biologically grounded inductive biases enhance generalization to perturbed conditions. This manuscript will appeal to a wide audience in systems and computational neuroscience.

eLife Assessment

This useful study attempts to place an ancient maize sample from Bolivia, dated to the end of the Incan empire, in genetic and geographical context. The analyses show that this sample is most closely related to ancient Peruvian maize, but the data are inadequate to determine the direction of dispersal. There are additional deficiencies in the statistical analyses and selection inferences. The topic of the study would appeal to researchers studying maize dispersal and adaptation.

eLife Assessment

This important study provides a novel approach for delineating subcortical-cortical white matter bundles. The authors provide convincing evidence by harnessing state-of-the-art methods and cross-species data. Together, this effort will be of interest to scientists across multiple subfields.

eLife Assessment

This valuable work presents how PRDM16 plays a critical role during colloid plexus development, through regulating BMP signaling. Solid evidence supports the context-dependent gene regulatory mechanisms both in vivo and in vitro. The work will be of broad interest to researchers working on growth factor signaling mechanisms and vertebrate development.

eLife Assessment

In this valuable study, Roiuk et al combined ribosome profiling and reporter assays to provide compelling evidence that eIF2A does not have a major impact on mRNA translation in HeLa cells. These findings are consistent with several recent publications that disaffirm the previously proposed role of eIF2A in directing protein synthesis under stress. Considering that stress-dependent perturbations in translation play a major role in homeostasis and several pathological states (e.g., cancer and neurological disorders), this work should be of broad interest to researchers studying regulation of gene expression, stress-adaptation, cancer and neurobiology.

eLife Assessment

This important manuscript by Genzoni et al. reports the striking discovery of a regulatory role for trophic eggs in ant caste determination. Prior to this study, trophic eggs were widely assumed to play only a nutritional role in the colony, but this compelling study shows that trophic eggs can suppress queen development, and therefore regulate caste determination in specific social contexts.

eLife Assessment

This study reports useful information on the mechanisms by which a high-fat diet induces arrhythmias in the model organism Drosophila. Specifically, the authors propose that adipokinetic hormone (Akh) secretion is increased with this diet, and through binding of Akh to its receptor on cardiac neurons, arrhythmia is induced. The authors have revised their manuscript but the evidence remains incomplete. Nonetheless, the data presented will be helpful to those who wish to extend the research to a more complex model system, such as the mouse.

eLife Assessment

This study provides fundamental information on how Arg-II participates in cardiac aging. The phenotypic data provide convincing evidence of non-cell-autonomous contributions to aging-related pathologies. Overall, the study highlights the importance of intercellular signaling in maintaining cardiac health during aging.

eLife Assessment

The findings represent an important contribution to understanding whether BMI influences head and neck cancer (HNC) risk after accounting for tobacco use. Within the context of the Mendelian Randomization (MR) field, the strength of evidence appears convincing, supported by rigorous methods and a thorough exploration of multiple genetic models of adiposity using diverse MR approaches. Limitations include the absence of associations in sensitivity models designed to better account for pleiotropy, which prevents evaluation of whether incorporating an instrumental variable for tobacco use would alter the findings. Additionally, the lack of a formal power assessment for detecting associations with the instrumental variables employed limits the interpretability and reach of the results.

eLife Assessment

This study identifies novel approaches to improving transgene expression in the injured mammalian myocardium through a combination of a tissue regeneration enhancer element and engineered AAVs - specifically, a liver-detargeting capsid, AAV.cc84, and an in vivo library screen-selected AAV-IR41. The evidence is convincing, and the AAV vectors are of fundamental value to the field of cardiac gene therapy. Future research exploring how to combine the features of AAV.cc84 and AAV-IR41 could yield an even more promising vector for therapeutic use.

eLife Assessment

This valuable study concerns a model for transgenerational epigenetic inheritance, the learned avoidance by C. elegans of the PA14 pathogenic strain of Pseudomonas aeruginosa. A recent study questioned whether transgenerational inheritance in this paradigm lacks robustness. The authors of this study have worked independently of the group that reported the original phenomenon and also independently of the group that challenged the original report. With solid data, this study independently validates findings previously reported by the Murphy group, confirming that the paradigm is reproducible elsewhere. The present study is therefore of broad interest to anyone studying genetics, epigenetics, or learned behavior.

eLife Assessment

This study presents a useful finding showing that the high susceptibility to sepsis of Kit-mutant mice is due to dysbiosis. However, the data provided is incomplete and would benefit from more rigorous approaches. With the mechanism part strengthened, this paper would be of interest to researchers on mast cell biology and mucosal immunology.

eLife Assessment

This study provides important insights into the role of polyUbiquitination in neurodegenerative diseases, elucidating how pUb promotes neurodegeneration by affecting proteasomal function. The findings not only offer a new perspective on the pathophysiology of neurodegenerative diseases but also provide potential targets for developing new therapeutic strategies. The results provide solid evidence to support the conclusions.

eLife Assessment

This important study, which has been improved further upon revision, reveals a critical role of the transcription factor NR2F2 in mouse fetal Leydig cell (FLC) differentiation. With elegantly carried out experiments, the authors provide compelling evidence that NR2F2 helps to initiate the differentiation of certain interstitial cells into FLC until these cells mature into functional secretory cells that produce androgen and insulin-like peptide 3 (INSL3). The particular importance of the work comes from the fact that NR2F2 affects FLCs without altering paracrine signals known to be involved in FLC differentiation. The work will be of interest to colleagues studying reproductive development in mammals including humans or the biological functions of the nuclear receptor family.

eLife Assessment

This important work describes results from a set of simulation and empirical studies of a set-up assessing exploratory behavior in a potentially rewarding environment that contains danger. The core idea is that an instrumental agent can be helped to be both effective and safe, thus avoiding excessive danger, during exploratory behavior, if the influence of an independent Pavlovian fear is flexibly gated based on uncertainty. This work is grounded in previous foundational work on Pavlovian control of instrumental choice, and significantly extends prior work showing that the impact of Pavlovian reward biases can be flexibly gated. The conclusion that safe but effective exploration can be achieved based on a flexibly weighted combination of a Pavlovian and an instrumental agent is convincing.

eLife Assessment

This valuable study reports the first characterization of the CG14545 gene in Drosophila melanogaster, which the authors name "Sakura." Acting during germline stem cell fate and differentiation, Sakura is required for both oogenesis and female fertility, although some mechanistic details require further investigation. This solid study presents a wide-ranging and well-controlled characterization of Sakura, and accordingly the findings and associated reagents described will be of use to scientists interested in oogenesis and early development.

eLife Assessment

This study provides important insights into how cryptic pockets play a role in shaping binding preferences of protein-nucleic acid interactions. By combining biochemical assays and state-of-the-art molecular dynamics simulations, mechanism underlying viral protein 35 (VP35) homologs to bind the backbone of double stranded RNA is presented. The evidence is compelling for molecular determinants that suggest two different dsRNA binding modes for VP35 and also underscores the evolutionary importance of these pockets.

eLife Assessment

This important study offers convincing evidence that intra-Golgi transport slows from cis to trans and varies between cargos even within the same cisternae, supporting a more stable compartment model. Using nocodazole-induced ministacks, the authors show cargo-specific transport kinetics with distinct velocities and residence times. These findings refine the cisternal progression model and prompt further investigation into alternative mechanisms, such as rapid partitioning or rim progression. This study will be of interest to cell biologists studying membrane trafficking, Golgi organization, and protein secretion, as well as researchers investigating the mechanisms of organelle dynamics and the molecular basis of intracellular transport.

eLife Assessment

In this important study, the authors conducted atomistic molecular dynamics simulations to probe the interactions between IRE and unfolded peptides. The results help reconcile contradicting experimental findings in the literature and offer mechanistic insights into the activation of the unfolded protein response. The level of evidence is considered solid, although the use of enhanced sampling and more quantitative analysis would further strengthen the conclusions.

eLife Assessment

This work provides one of the first important attempts to look at Drosophila immune responses against bacterial, viral, and fungal pathogens in a way that combines the roles of four major arms in immunity (Imd signaling, Toll signaling, phagocytosis, and melanization) rather than studying them separately. The findings are convincing, and the tools provided can be used as they are, or built upon, in various contexts.

eLife Assessment

This important study reports an advancement in the diagnosis of Animal African Trypanosomosis (AAT), which adapts a CRISPR-based diagnostic tool (SHERLOCK4AAT) to detect different trypanosome species responsible for AAT. The evidence supporting the conclusions is convincing and in line with the current state-of-the-art diagnostics. This study will be of interest to the fields of Epidemiology, Public Health, and Veterinary Medicine.

eLife Assessment

This important study investigates frequency-dependent effects of transcutaneous tibial nerve stimulation (TTNS) on bladder function in healthy humans and, through a computational model, shows that low-frequency stimulation accelerates, and high-frequency delays, the urge to void. The integration of experimental and modeling approaches provides a solid foundation for clinical trials targeting urinary retention. However, concerns were raised about over-interpretation of modest effects and the limited physiological validity of the computational model, especially its mismatch with typical bladder behaviour and lack of quantitative validation.

eLife Assessment

This valuable study provides insights into the structure and function of bacterial contractile injection systems that are present in the cytoplasm of many Streptomyces strains. A convincing high-resolution model of the structure of extended forms of the cytoplasmic contractile injection system assembly from Streptomyces coelicolor is presented, with some investigation of the membrane protein CisA in attachment of the extended assembly to the inner face of the cytoplasmic membrane and the firing of the system. The work expands the current understanding of these diverse bacterial nanomachines.

eLife Assessment

This important study provides information on the TMEM16 family of membrane proteins, which play roles in lipid scrambling and ion transport. By simulating 27 structures representing five distinct family members, the authors captured hundreds of lipid scrambling events, offering insights into the mechanisms of lipid translocation and the specific protein regions involved in these processes. While the data on comparison of scrambling competence is compelling, the evidence for outside-the-groove scramblase activity without experimental validation is missing and is based on a limited set of observed events.

eLife Assessment

This study presents important insights into the regulation of left-right organ formation. By combining genetic perturbation of all three Meteorin genes in zebrafish and timelapse imaging, the authors identify an essential role for this protein family in the establishment of left-right patterning. They provide convincing evidence that Meteorins are required for the morphogenesis of dorsal forerunner cells, the precursors of the left-right organizer (also named Kupffer's vesicle) in zebrafish. In line with this, Meteorins were shown to genetically interact with integrins ItgaV and Itgb1b to regulate dorsal forerunner cell clustering.

eLife Assessment

The study provides a valuable analysis of escape from X-inactivation based on three rare female GTEX-donors with non-mosaic X-inactivation. The methods and analyses are solid and broadly support the authors' claims. Their data are more comprehensive than those presented previously and add significant weight to evidence for which genes are inactivated or escape from X inactivation in humans.

eLife Assessment

This important study uncovers the mechanism of inhibition of a membrane pyrophosphatase by non-hydrolyzable phosphonate substrate analogs. Convincing crystallography, EPR spectroscopy, and functional measurements support the presence of a distinct conformational equilibrium of TmPPase in solution, and further supports the notion of asymmetric inhibitor binding at the active site, while maintaining a symmetric conformation at the periplasmic interface.

eLife Assessment

This study presented valuable findings regarding the basic molecular pathways leading to the cystogenesis of Autosomal Dominant Polycystic Kidney Disease, suggesting BICC1 functions as both a minor causative gene for PKD and a modifier of PKD severity. Although some solid data were supplied to show the functional and structural interactions between BICC-1 and PKD2 and their relevance to the pathogenesis of ADPKD, the characterization of such interactions appear to be incomplete, which renders the specific relevance of these findings for disease etiology unclear.

eLife Assessment

The ratio of nuclei to cell volume is a well-controlled parameter in eukaryotic cells. This important study now substantially advances our understanding of the regulatory relationship between cell size and the number of nuclei by identifying novel players in this process. The evidence supporting the conclusions is compelling, with biochemical assays and state-of-the-art microscopy. The paper will be of broad interest for cell biologists and fungal biotechnologists seeking to understand mechanisms determining cell size and number of nuclei, and why this knowledge is also of significant importance for the production of enzymes, and thus production strains not only of Aspergillus oryzae, but also other industrially used fungi.

eLife Assessment

The manuscript presents a valuable finding that CCDC32, beyond its reported role in AP2 assembly, follows AP2 to the plasma membrane and regulates clathrin-coated pit assembly and dynamics. The authors further suggest that the alpha-helical region of CCDC32 interacts with AP2 via the alpha appendage domain to mediate this function. While live-cell and ultrastructural imaging data are solid, future biochemical studies will be needed to confirm the proposed CCDC32-AP2 interaction.

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

eLife Assessment

This study provides an in-depth exploration of the impact of X-linked ZDHHC9 gene mutations on cognitive deficits and epilepsy, with a particular focus on the expression and function of ZDHHC9 in myelin-forming oligodendrocytes (OLs). These valuable findings offer insights into ZDHHC9-related X-linked intellectual disability (XLID) and shed light on the regulatory mechanisms of palmitoylation in myelination. The experimental design and analysis of results are solid, providing a reference for further research in this field.

eLife Assessment

This manuscript determines how PA28g, a proteasome regulator that is overexpressed in tumors, and C1QBP, a mitochondrial protein for maintaining oxidative phosphorylation that plays a role in tumor progression, interact in tumor cells to promote their growth, migration and invasion. Additional experiments and analyses that supported the theoretical models for the interaction have been performed in response to the reviews. The overall findings and conceptual framework are important and the evidence is solid. A logical extrapolation of this work is to test the C1QBP mutants using functional assays to determine whether the mutations can decrease the protein stability mediated by the interaction with PA28g.

eLife Assessment

This important study reports solid evidence for the significant role of mother-child neural synchronization and relationship quality in the development of Theory of Mind (ToM) and social cognition. The findings effectively bridge brain development with children's behavior and parenting practices, and will be of interest to researchers studying brain development and social cognition, as well as the general public.

eLife Assessment

This important study presents a compelling theoretical framework for understanding phase separation of membrane-bound proteins, with a focus on the organization of tight junction components. By incorporating non-dilute binding effects into thermodynamic models and validating the model's predictions with in vitro experiments on the tight junction protein ZO-1, the authors provide a quantitative tool that will be of interest for biologists interested in membrane-associated condensates. While further clarification of model assumptions and broader mechanistic context would strengthen the work even further, the combination of theory and experiment here is robust and a key advancement in the field.

eLife Assessment

This fundamental study examines whether synaptic cell adhesion molecules neuroligin 1-3 resident on astrocytes, rather than neurons, exert effects on synaptic structure and function. With compelling evidence, including rigorous validation of neuroligin deletion efficiency in astrocytes and independent confirmation using human neuron-mouse glia co-cultures, the authors report that deletion of neuroligins 1-3 specifically in astrocytes does not alter synapse formation or astrocyte morphology in the hippocampus or visual cortex. This study provides definitive evidence highlighting the specific role of neuronal neuroligins rather than their astrocytic counterparts in synaptogenesis.

eLife Assessment

This fundamental work extends our understanding of the role of TGFβ2 as a modulator of mechanosensing in the eye and identifies the TRPV4 ion channel as a common regulator of Trabecular Meshwork (TM) contractility and pathological OHT and the data and evidence provided are convincing. This work will clearly be of interest to researchers investigating the role of mechanosensors in the TM and may underpin future research into treatments that aim to lower intra ocular pressure. This work will additionally be of interest to the growing field of researchers investigating the regulation of force sensing via ion channels and their roles in health and disease, in particular the ion channel TRPV4.

eLife Assessment

This important study presents a pipeline for discovering cooperative transcription factor (TF) interactions that regulate development, and applies this pipeline in a systematic investigation of TF co-regulation in 11 human embryonic tissues. The authors provide overall solid bioinformatics and experimental support for their findings: although they make a convincing argument for the role of TEAD factors as co-repressors of regulatory activity with tissue-specific TFs, other aspects of the study would benefit from additional validation. This work would be of interest to cell biologists focused on development or on discovery of TF relationships.

eLife Assessment

There is a growing interest in understanding the individuality of animal behaviours. In this article, the authors build and use an impressive array of high throughput phenotyping paradigms to examine the 'stability' (consistency) of behavioural characteristics in a range of contexts and over time. They find that certain behaviours are individualistic and persist robustly across external stimuli while others are less robust to these changing parameters. The data, while extensive are incompletely analysed/explained. With more appropriate statistical methods adopted, the findings would have important implications for the study of individual variability.

eLife Assessment

This important study tests the development of motor reinforcement learning from toddlerhood to adulthood, using a large online sample. They show that learning improves with age in a task that, like real-life movement, involves a continuous range of response options and probabilistic rewards, and link this shift to reduced movement variability and more efficient feedback-based learning through behavioural modeling. Simplifying the task with discrete actions and deterministic outcomes boosted younger children's performance, suggesting early learning is limited by spatial and probabilistic processing. The evidence is convincing, although future work may investigate more naturalistic movement.

eLife Assessment

This study provides an important set of analyses and theoretical derivations to understand the mechanisms used by recurrent neural networks (RNNs) to perform context-dependent accumulation of evidence. The results regarding the dimensionality and neural dynamical signatures of RNNs are convincing and provide new avenues to study the mechanisms underlying context-dependent computations. This manuscript will be of interest to a broad audience in systems and computational neuroscience.

eLife Assessment

The manuscript contains important findings regarding inflammatory macrophage subsets that have theoretical and/or practical applications beyond the field of rheumatology. The authors demonstrate with compelling evidence the effects of PGE2 on TNF signaling. This work will be of broad interest to immunologists and cell biologists.

eLife Assessment

The authors study the context of the skeletal remains of three individuals and associated sediment samples to conclude that the hominin species Homo naledi intentionally buried their dead. Demonstration of the earliest known instance of intentional funerary practice – with a relatively small-brained hominin engaging in a highly complex behavior that has otherwise been observed from Homo sapiens and Homo neanderthalensis – would represent a landmark finding. The authors have revised their manuscript extensively in light of the reviews of their initial submission, with improved illustration, context, discussion, and theoretical frameworks, leading to an improved case supporting their conclusion that Homo naledi intentionally buried their dead. One of the reviewers concludes that the findings convincingly demonstrate intentional burial practices, while another considers evidence for such an unambiguous conclusion to be incomplete given a lack of definitive knowledge around how the hominins got into the chamber. We look forward to seeing the continued development and assessment of this hypothesis. It is worth noting that the detailed reviews (both rounds) and comprehensive author response are commendable and consequential parts of the scientific record of this study. The editors note that the authors' response repeatedly invokes precedent from previous publications to help justify the conclusions in this paper. While doing so is helpful, the editors also note that scientific norms and knowledge are constantly evolving, and that any study has to rest on its own scientific merit.

eLife Assessment

The songbird vocal motor nucleus HVC contains cells that project to the basal ganglia, the auditory system, or to downstream vocal motor structures. In this fundamental study, the authors conduct optogenetic circuit mapping to clarify how four distinct inputs to HVC act on these distinct HVC cell types. They provide compelling evidence that all long range projections engage inhibitory circuits in HVC and can also exhibit cell-type specific preferences in monosynaptic input strength. Understanding HVC at this microcircuit level is critical for constraining models of song learning and production.

eLife Assessment

The study reports valuable findings from a very rich EEG-fMRI dataset, including 107 participants, which was collected during nocturnal naps. Using overall solid methods, the authors link activity in memory-related brain regions (e.g., hippocampus, thalamus, and medial prefrontal cortex), and their functional connectivity to the occurrence of canonical sleep rhythms (spindles and slow oscillations) in non-rapid eye movement sleep. This work will be of broad interest to sleep and memory researchers and beyond.

eLife Assessment

The findings of this study are valuable, offering insights into the neural representation of reversal probability in decision-making tasks, with potential implications for understanding flexible behavior in changing environments. The study contains interesting comparisons between neural data and models, including evidence for partial consistency with line attractor models in this probabilistic reversal learning task. However, it remains incomplete due to issues related to how the RNN training and the analysis of its dynamics, which renders the evidence as not complete.

eLife Assessment

This valuable paper uses a quantitative modeling approach to explore a well-studied transition in motor behavior in the nematode C. elegans. The authors provide solid evidence that this transition, which has been considered by many in the field to be a two-state behavior, can instead be described as a process whose parameters are smoothly modulated within a single state. This finding provides insight into the relationships between latent internal states and observable behavioral states, and suggests that relatively simple neuronal mechanisms can drive behavioral sequences that appear more complex.

eLife Assessment

This study provides valuable insights into the evolutionary conservation of sex determination mechanisms in ants by identifying a candidate sex-determining region in a parthenogenetic species. The strength of evidence is solid, using genomic analyses to identify differences in heterozygosity between females and diploid males, though the conclusions are limited by the lack of functional analysis.

eLife Assessment

This manuscript presents an interesting new framework (VARX) for simultaneously quantifying effective connectivity in brain activity during sensory stimulation and how that brain activity is being driven by that sensory stimulation. The reviewers thought the model was original and its conclusion that intrinsic connectivity is reduced (rather than increased) during sensory stimulation is very interesting, but that for ideal performance, one must specify all sensory features in the model, which is not possible. Overall, however, this work is important with convincing evidence for its conclusions - it will be of interest to neuroscientists working on brain connectivity and dynamics.

eLife Assessment

This valuable work presents an interpretable protein-DNA Energy Associative (IDEA) model for predicting binding sites and affinities of DNA-binding proteins. While the method is convincing, it requires some adaptation for application to different proteins. The IDEA method is available and can be potentially used for predicting genome-wide protein-DNA binding sites.

eLife Assessment

In this important paper, the authors use single-cell RNA sequencing to understand post-mitotic cone and rod developmental states and identify cone-specific features that contribute to retinoblastoma genesis. The authors report findings that have practical implications for retinal development, gene expression, and cell fate specification. The evidence is compelling as the experimental design and analysis are exceptionally rigorous.

eLife Assessment

This useful manuscript addresses a stability issue for long-term chronically implanted array recordings and electrolytic lesioning, which is relevant to both basic science and translational research. The authors provide a systematic scanning electron microscopy (SEM) of explanted arrays, evaluating electrode damage and sharing extensive datasets accessible through interactive plots. The strength of the evidence is solid, but it can be improved by performing additional analyses on complementary neurophysiology, functional, or histological data.

eLife Assessment

This fundamental study demonstrates how a left-right bias in the relationship between numerical magnitude and space depends on brain lateralization. The evidence is compelling, and the manuscript could be strengthened by improving its contextualization, presentation, and discussion. The results will be of interest to researchers studying numerical cognition, brain lateralization, and cognitive brain development more broadly.