eLife Assessment

This important study details changes in the brain functional connectivity in a longitudinal cohort of Gambian children assessed outside a lab setup with functional near-infrared spectroscopy (fNIRS) from age 5 to 24 months, in relation to early physical growth and cognitive flexibility capacities at preschool age. While evidence supporting conclusions on the evolution of brain connectivity are solid, the statistical power was insufficient to perform proper analyses of longitudinal data and link the connectivity trajectories with early adverse conditions such as undernutrition and later cognitive development. This study will be of significant interest to neuroscientists, psychologists and neuroimaging researchers working on infant development in relation to environmental factors.

eLife Assessment

This work defines the response dynamics in forepaw-related cortical circuits of S1 and M1 following stimulation of peripheral mechanoreceptors in the mouse. In this revised version, the authors have addressed the reviewers' prior concerns. The results are convincing and present a valuable comparison to previously published work. This study has implications for understanding the interactions between primary somatosensory and motor cortex, required for active sensing, and will be of interest to scientists seeking to better understand the functions of somatosensory and motor circuits.

eLife Assessment

The findings presented in this manuscript are fundamental, as they uncover MYL3, a member of the myosin family, as a potential entry receptor and therapeutic target for a virus that poses a major threat to aquaculture. The evidence is convincing, supported by robust in vitro and in vivo data. However, additional studies investigating the presence of MYL3 in NNV target tissues would further strengthen the authors' conclusions.

eLife Assessment

The microbiome field is constantly providing insight on various health-related properties elicited by the commensals that inhabit their mammalian hosts. Harnessing the potential of these commensals for knowledge about host-microbe interactions, as well as properties with therapeutic implications, will likely remain a fruitful field for decades to come. In this valuable study, Wang et al use various methods, encompassing classic microbiology, genomics, chemical biology, and immunology, to identify a potent probiotic strain that protects nematode and murine hosts from Salmonella enterica infection. The authors provide compelling evidence identifying gut metabolites that are correlated with protection, and show that a single metabolite can recapitulate the effects of probiotic administration.

eLife Assessment

This valuable work explores how synaptic activity encodes information during memory tasks. All reviewers agree that the work is of very high quality and that the methodological approach is praiseworthy. Although the experimental data support the possibility that phospholipase diacylglycerol signaling and synaptotagmin 7 (Syt7) dynamically regulate the vesicle pool required for presynaptic release, concerns remain that the central finding of paired-pulse depression at very short intervals may be more likely due to Ca²⁺ channel inactivation rather than vesicle pool depletion. Overall, this is a solid study although the results warrant consideration of alternative interpretations.

eLife Assessment

The open-source software Chromas tracks and analyses cephalopod chromatophore dynamics. The software features a user-friendly interface alongside detailed instructions for its application, with compelling exemplary applications to two widely divergent cephalopod species, a squid and a cuttlefish, over time periods large enough to encompass new chromatophore development among existing ones. It demonstrates accurate tracking of the position and identity of each chromatophore. The software and methods outlined therein will become an important tool for scientists tracking dynamic signaling in animals.

eLife Assessment

This important resource paper presents a library of cell-type-specific genetic driver lines that label wing-related motor and premotor neurons in the ventral nerve cord of the fruit fly, Drosophila. The toolkit is systematically validated with compelling anatomical and behavioral evidence and will provide a resource for future studies of Drosophila flight and courtship.

eLife Assessment

This useful study explores the role of RAP2A in asymmetric cell division (ACD) regulation in glioblastoma stem cells (GSCs), drawing parallels to Drosophila ACD mechanisms and proposing that an imbalance toward symmetric divisions drives tumor progression. While findings on RAP2A's role in GSC expansion are promising, the study is nevertheless incomplete. Limitations include the lack of comprehensive GBM subtype analysis, insufficient mechanistic validation, and reliance on neurosphere models without in vivo confirmation. Addressing those gaps is necessary to substantiate the study's claims.

eLife Assessment

This important and well-executed study describes how deleting the autism spectrum disorder risk gene CNTNAP2 in mice increases dorsolateral striatal projection neuron excitability and promotes repetitive behaviors and cognitive inflexibility. The evidence supporting this claim is convincing. The study provides a potential cellular explanation for the repetitive and inflexible behavior in Cntnap2 knockout mice and CNTNAP2 disorder in humans, which would interest both basic and translational neuroscientists.

eLife Assessment

This important study identified a molecular mechanism linking diabetes to AD risk and the data presented are convincing. The authors investigated the role of kallistatin in metabolic abnormalities associated with AD and identified that Kallistatin is a key player that mediates Aβ accumulation and tau hyperphosphorylation in AD. This manuscript provides novel insights into the pathogenesis of AD, indicating that the hypolipidemic drug fenofibrate attenuates AD-like pathology in Kallistatin transgenic mice.

eLife Assessment

This study presents valuable research comparing three different species of extant cartilaginous fishes and describes new data on ratfish. The methods are convincing, although there remains a concern about the claim in the title about paedomorphosis. This study will be of interest to skeletal biologists working on the evolution of chondrichthyan skeletons.

eLife Assessment

This important contribution to the field evaluated the function of the cytoskeletal protein ABBA in mediating key aspects of mitosis of neuronal precursor cells. The authors provide compelling evidence that ABBA interactions with its signaling partners is related to the development of at least some cases of microcephaly-a developmental anomaly associated with intellectual disability and other neurological findings.

eLife Assessment

This important study uses C. elegans to provide new insights into the role of the conserved protein FLWR-1/Flower in synaptic transmission. Employing a variety of techniques, including calcium imaging, ultrastructural analysis, and electrophysiology, the paper provides convincing evidence that challenges some previous thinking about FLWR-1 function. This work will be of particular interest to neuroscientists studying synaptic physiology and plasticity.

eLife Assessment

This study presents a valuable and simplified classification system for predicting clinical outcomes of RPLS patients. The data were collected and analyzed using solid and validated methodology and can be used as a starting point for personalized treatment of RPLS. The work will be of interest to scientists working in the field of RPLS.

eLife Assessment

This valuable study investigates how inter-organ communication between the tracheal stem cells and the fat body plays a key role in the directed migration of tracheal stem cells in Drosophila pupae. The evidence supporting the conclusions is convincing. The work would be of broad interest to researchers in the fields of developmental biology and cancer biology.

eLife Assessment

The study by Li et al. provides fundamental findings supported by convincing evidence that they defined cellular reprogramming of androgen receptor in neuroendocrine prostate cancer (NEPC). The findings enhance the understanding of the treatment of androgen receptor functions in NEPC.

eLife Assessment

This is an important study utilizing innovative CRISPR based approaches demonstrating the role of the KLF family of transcription factors in the post natal maturation of cortical projection neurons. The strength of evidence overall is compelling, and the study is well executed. The screen data presented provides a number of interesting candidates for future analyses into the mechanism of action of KLF family members in neuronal maturation.

eLife Assessment

This valuable study shows that mutations in specific cassava genes can reduce infection by cassava brown streak viruses. The authors also identify a key amino acid change that may be significant in how the virus interacts with the plant, but its role is not yet confirmed. While the findings are promising for developing resistant cassava varieties, in the absence of testing a quadruple mutant and without more data on the critical importance of amino acid L5 in VPg-eIF4E interactions, the evidence for several of the major claims remains incomplete.

eLife Assessment

The authors test the hypothesis that gonadal steroid signaling influences the transcriptional development of specific neurons in the mPOA during adolescence, and that such adolescent development of the mPOA is necessary for mating behaviors. The findings are valuable and supported by convincing data. This work contributes new insight into hormone-sensitive transcriptional profiles within genetically defined neuron clusters in the mPOA during adolescence and will be of interest to systems and molecular neuroscientists and those interested in development, sex differences, and/or hormonal regulation.

eLife Assessment

Following retinal injury, zebrafish Müller glia reenter the cell cycle and generate replacement cells; this potentially valuable study proposes that injury induces a cxcl18b+ transitional state in Müller cells, which then express nitric oxide, inhibiting notch signaling and allowing Müller glial to reenter the cell cycle. However, the evidence supporting the claims is incomplete; technical limitations and inconsistencies within the data raise concerns. Using larval animals complicates the analysis since the retina is still forming, and distinguishing between injury-induced regeneration and ongoing development is complex. With more rigorous testing of the signaling pathways proposed and a clear demonstration of their interdependence, the link between nitric oxide signaling and Notch activity, particularly, would interest those investigating retinal regeneration.

eLife Assessment

The authors employ an unbiased, affinity-guided reagent to label P2X7 receptor and use super-resolution imaging to monitor P2X7 redistribution in response to inflammatory signaling. The evidence is generally solid but could be further strengthened through revisions. The study will be valuable to those studying the dynamics of receptor distribution and clustering.

eLife Assessment

This important study investigates the propensity of the intravacuolar pathogen, Leishmania, to scavenge lipids which it utilizes for its accelerated growth within macrophages. The authors present compelling evidence that supports this hypothesis, although the genetic basis for the parasite's requirement for lipids remains unresolved. The study adds to other work that has implicated pathogen-derived processes in the selective recruitment of vesicles to the pathogen-containing vacuole, based on the content of the cargo.

eLife Assessment

Genetic variants have been strongly implicated in idiopathic scoliosis (IS), however, the list of variants that are causative of IS is not complete and the cellular and molecular mechanisms that underlie IS are poorly understood. These authors combined human genetic analysis with zebrafish experiments to produce valuable evidence that alleles that impair function of EPHA4 cause IS, thereby extending our understanding of the basis of IS. The human genetic data are quite convincing but the zebrafish work lacks some validations and details.

eLife Assessment

This valuable study uses C. elegans to provide new insights into the role of the conserved protein FLWR-1/Flower in synaptic transmission. Employing a variety of techniques, including calcium imaging, ultrastructural analysis, and electrophysiology, the paper provides evidence that challenges some previous thinking about FLWR-1 function. While most of the findings are convincing, some of the authors' conclusions about the mechanisms of FLWR-1 function remain somewhat speculative.

Editors Assessment:

With the recent official launch of BGI’s new CycloneSEQ sequencing platform that delivers long-reads using novel nanpores, this paper presents benchmarking data and validation studies comparing short, long-rea data from other platforms and hybrid assemblies. This study tests the performance of the new platform in sequencing diverse microbial genomes, presenting raw and processed data to enable others to scrutinise and verify the work. Being openly peer-reviewed, and having scripts and protocols also shared for the first time helps provide transparency in this benchmarking process to increase trust in this new technology. On top of benchmarking typed strains, the technology also was tested with complex microbial communities. Yielding complete metagenome-assembled genomes (MAGs) which were not achieved by short- or long-read assemblies alone. By directly reading DNA molecules without fragmentation, the study demonstrating CycloneSEQ delivers long-read data with impressive length and accuracy, unlocking gaps that short-read technologies alone cannot bridge. Future work is expanding to real samples, with and fine-tuning the balance between short-read and long-read data for even faster, higher-quality assemblies.

This evaluation refers to version 1 of the preprint

eLife Assessment

This study offers valuable insights into the conformational dynamics of the nucleic acid recognition lobe of GeoCas9, a thermophilic Cas9 from Geobacillus stearothermophilus. The authors investigate the influence of local dynamics and allosteric regulation on guide RNA binding affinity and DNA cleavage specificity through molecular dynamics simulations, advanced NMR techniques, RNA binding studies, and mutagenesis. While the mutations studied do not lead to significant changes in GeoCas9 cleavage activity, the study provides convincing evidence for the role of allosteric mechanisms and interdomain communication in Cas9 enzymes, and will be of great interest to biochemists and biophysicists exploring these complex systems.

eLife Assessment

This valuable study investigates neural circuits mediating motor responses to cold in Drosophila larvae. Using a combination of behavioral analysis, genetic manipulations, EM connectomics, and reporters of calcium activity, the authors provide solid evidence that specific sensory and central neurons are required for cold-induced body contraction. This paper may be of interest to neuroscientists interested in how nervous systems sense and respond to cold.

eLife Assessment

This study identifies a role for YAP in regulating tumor cell growth and drug response with differential effects noted based upon growth conditions in monolayer vs spheroid culture. This work has the potential to define more biologically relevant cell culture model systems for drug resistance and define targetable pathways to overcome drug resistance. The findings described are important to the cancer biology field and the evidence supporting the key findings is convincing.

eLife Assessment

This study provides valuable insights into the role of sensory stimulation in neurogenesis in the mammalian olfactory epithelium, where new olfactory sensory neurons are continually born throughout an animal's lifespan. The authors show that exposure to two different musk-related odors specifically increases the birth rates of those neurons that respond to these odors. This potentially results in adaptive changes in the subtype composition of the olfactory sensory neuron population. Solid evidence, well supported by control experiments, is presented to support these findings, though further work is needed to confirm that this phenomenon generalizes to olfactory sensory neurons expressing other types of odorant receptor and to explore the mechanisms underlying the stimulus specificity of neurogenesis.

eLife Assessment

This manuscript demonstrates that Oct4 overexpression synergizes with Notch inhibition (Rbpj knockout) to promote the conversion of adult murine Müller glia (MG) into bipolar cells. These findings are important as the authors used rigorous genetic lineage tracing (GLAST-CreER; Sun-GFP) to confirm that neurogenesis indeed originates from MGs, addressing a key issue in the field. The single-cell multiomic analyses are compelling, and while functional studies of MG-derived bipolar cells would strengthen the conclusions, they are beyond the scope of this study.

eLife Assessment

This study presents a valuable finding on the role of secretory leukocyte protease inhibitors (SLPI) in developing Lyme disease in mice infected with Borrelia burgdorferi. The evidence supporting the authors' claims is solid. However, several concerns raised by the reviewers remain unaddressed. This paper would be of interest to scientists in the infectious inflammatory disease field.

eLife Assessment

This important work uses an innovative approach to understand similarities between haemodynamic and electrophysiological activity of the human brain, and how the brain might carry out multiple functions concurrently across different brain regions by using multiple timescales. The study provides convincing evidence to indicate that while spatially similar functional brain networks are found in both modalities, there is a tendency for these to occur asynchronously. This work will be of interest to neurophysiological and brain imaging researchers.

eLife Assessment

This study presents an important finding on the alterations in the autophagic-lysosomal pathway in a Huntington's disease model. The evidence supporting the claims of the authors is convincing. The original reviewers have found most of the issues previously raised have been addressed although further suggestions are given for consideration. These comments are listed below. The work will be of interest to neuroscientists working on HD.

eLife Assessment

This is an important study demonstrating that cholecystokinin is a key modulator of auditory thalamocortical plasticity during development and in young adult but not aged mice, though cortical application of this neuropeptide in older animals appears to go some way to restoring this age-dependent loss in plasticity. A strength of this work is the use of multiple experimental approaches, which together provide convincing support for the proposed involvement of cholecystokinin. While there are some limitations in the electrophysiological recordings and areas where the manuscript would benefit from further clarification, this work is likely to be influential in opening up a new avenue of investigation into the roles of neuropeptides in sensory plasticity.

eLife Assessment

This manuscript presents an important machine-learning-based approach to the automated detection of urine and fecal deposits by rodents, key ethological behaviors that have traditionally been very poorly studied. The strength of evidence for the claim is solid, showing accuracy near 90% across several contexts. Training and testing for the specific contexts used by other experimenters, however, is probably warranted to make the model most relevant to the data that may be analyzed.

eLife Assessment

This valuable study combines a computational language model, i.e., HM-LSTM, and temporal response function (TRF) modeling to quantify the neural encoding of hierarchical linguistic information in speech, and addresses how hearing impairment affects neural encoding of speech. The analysis has been significantly improved during the revision but remain somewhat incomplete - The TRF analysis should be more clearly described and controlled. The study is of potential interest to audiologists and researchers who are interested in the neural encoding of speech.

eLife Assessment

The study presents valuable findings on Mendelian randomization-phenome-wide association, with BMI associated with health outcomes, and there is a focus on sex differences. The phenotype and genotype data are convincing. The work will be of interest to researchers and clinicians in epidemiology, public health and medicine.

eLife Assessment

This valuable study investigates both online responses to, and offline replay of, visual motion sequences. Sophisticated MEG analyses provide convincing evidence for both feature-specific and non-specific sequence representations. These intriguing findings will be of interest to perception and learning researchers alike.

eLife Assessment

This valuable study introduces a self-supervised machine learning method to classify C. elegans postures and behaviors directly from video data, offering an alternative to the skeleton-based approaches that rely on often error-prone tracking. This novel approach holds promise for advancing ethology research. That said, the strength of evidence is currently incomplete, as key aspects - including measuring head-tail orientation, increased behavioral interpretability, and quantitative comparisons to established methods - are underdeveloped and would benefit from further validation.

eLife Assessment

This paper presents important findings regarding the rhythmicity of overlapping target and distractor processing and how this affects behaviour. The methods are, in general, clearly laid out and defensible; however, the evidence supporting the central claims is incomplete due to potential biases in the analysis methods. Further control analyses would be beneficial and could greatly strengthen the conclusions that can be drawn from these data.

eLife Assessment

This study proposes an updated analysis technique that allows researchers to identify rhythms in behavior. If the proposed analyses control the rate of false positives, this will be an important contribution for all neuroscientists interested in rhythmic cognition. At present, the strength of evidence is incomplete, as the simulations ignore one crucial aspect of temporal structure in behavior.

eLife Assessment

This carefully conducted study aims to understand how the early visual experience of premature infants induces lasting deficits, including compromised motion processing. This important question is addressed in a ferret animal model, in which the developing visual system was exposed prematurely to patterned visual input by opening one or both eyes early, at a time when both retinal waves and light traveling through closed lids drive sensory responses. Convincing evidence is presented, suggesting that eye opening at this time impacts temporal frequency tuning and elevates spontaneous firing rates. These findings will have great relevance for neuroscientists studying visual system development, particularly in the context of premature birth.

eLife Assessment

This computational modeling study builds on multiple previous lines of experimental and theoretical research to investigate how a single neuron can solve a nonlinear pattern classification task. The study presents solid evidence that the location of synapses on dendritic branches, as well as synaptic plasticity of excitatory and inhibitory synapses, influences the ability of a neuron to discriminate combinations of sensory stimuli. The ideas in this work are very interesting, presenting an important direction in the computational neuroscience field about how to harness the computational power of "active dendrites" for solving learning tasks.

eLife Assessment

This important study by Jeong and Choi studied neural activity in the medial prefrontal cortex (mPFC) while rats performed a foraging paradigm in which they forage for rewards in the absence or presence of a threatening object (Lobsterbot). The authors present interesting observations suggesting that the mPFC population activity switches between distinct functional modes conveying distinct task variables- such as the distance to the reward location and types of threat-avoidance behaviors-depending on the location of the animal. Although the specific information represented by individual neurons remains to be clarified through further investigation, the reviewers thought that this study is solid, appreciated the value of studying neural coding in naturalistic settings, and felt that this work offers significant insights into how the mPFC operates during foraging behavior involving reward-threat conflict.

eLife Assessment

This study examines how self-citations in selected neurology, neuroscience, and psychiatry journals differ according to seniority, geography, gender and subfield. The evidence supporting the claims is convincing, and the article is a valuable addition to the literature on self-citations.

eLife Assessment

This important contribution to the field demonstrates the role of a single transcription factor with cell-autonomous functions in the differentiation of two distinct neuronal populations in regulating the interactions between those cells in a non-autonomous manner to generate their final organized projection pattern. There are additional quantifications and controls that would enhance the study and would improve the strength of the evidence from incomplete if they were performed.

eLife Assessment

This important study investigates how neural representations in the postrhinal and medial entorhinal cortices evolve with the learning of a visual associative memory task in mice. The findings provide new insights into how non-spatial information is differentially encoded across interconnected brain areas, with strong evidence that stimulus encoding is robust in the postrhinal cortex and emerges more weakly in the medial entorhinal cortex with learning. The evidence is solid overall, particularly in the use of sophisticated population-level analyses and two-photon imaging across learning phases, although the interpretation of regression models and clustering would benefit from additional clarity and control. The work will be of broad interest to systems neuroscientists studying learning, memory, and cortical circuit function.

eLife Assessment

In this important study, Baniulyte and Wade provide convincing evidence that translation of a short ORF denoted toiL positioned upstream of the topAI-yjhQP operon is responsive to different ribosome-targeting antibiotics, consequently controlling translation of the TopAI toxin as well as Rho-dependent transcription termination. Strengths of the study include combining a genetic screen to identify 23S rRNA mutations that affect topA1 expression and a creative approach to map the different locations of ribosome stalling within toiL induced by different antibiotics, with ribosome profiling and RNA structure probing by SHAPE to examine consequences of different antibiotics on toiL-mediated regulation. The work leaves unanswered how bacteria benefit by activating expression of the genes using the proposed strategy and the mechanism underlying ToiL's sensing of structurally distinct antibiotics.

eLife Assessment

This study provides the most comprehensive analysis of Salmonella Dublin to date, uncovering distinct genotypic adaptations, antimicrobial resistance patterns, and virulence strategies that influence epidemiological success. The revised manuscript is very valuable, rigorous and compelling.

eLife Assessment

In this interesting and important work, the authors use detailed behavioral analysis and rigorous quantitative modeling to support the idea that C. elegans uses an "accept-reject" strategy to make behavioral decisions upon encountering food patches based on learned features of its environment. The work convincingly expands our understanding of the behavioral repertoire of this species and provides a strong foundation for future mechanistic studies.

eLife Assessment

This valuable study employed a multi-omics approach to elucidate the regulatory mechanism underlying parturition and myometrial quiescence. The data presented to support the main conclusion are solid. This work will be of interest to both basic researchers who work on reproductive biology and clinicians who practice reproductive medicine.

eLife Assessment

This important study confirms the molecular function of putative components of the N-glycan-dependent endoplasmic reticulum protein quality control (ERQC) system in the pathogen Cryptococcus neoformans. The study demonstrates an involvement in fitness, virulence, and the secretion and composition of extracellular vesicles, albeit in ways that are not yet fully understood. The evidence provided is convincing, with rigorous, well-controlled assays and the use of complemented strains.

eLife Assessment

This valuable study presents a theoretical framework in which spatial periodicity in grid cell firing emerges as the optimal solution for encoding two-dimensional spatial trajectories via sequential neural activation. The idea is supported by solid evidence, though it rests on several key assumptions that merit careful consideration. This work will be of interest to neuroscientists investigating the neural mechanisms underlying spatial navigation.

eLife Assessment

This valuable investigation provides new and solid evidence for a specific cognitive deficit in cerebellar degeneration patients. The authors use three tasks that modulate complexity and error presence to show specific slowing of reaction times in the presence of errors but not with task complexity. While the authors interpret these findings as indicating that the cerebellum is required for the processing of violations of expectations, the exact patterns of results may suggest alternative interpretations. Nonetheless, the work provides a new, invaluable data point in describing the cognitive contribution of cerebellar processing.

eLife Assessment

This important study uses an innovative task design combined with eye tracking and fMRI to distinguish brain regions that encode the value of individual items from those that accumulate those values for value-based choices. It shows that distinct brain regions carry signals for currently evaluated and previously accumulated evidence. The study provides solid evidence in support of most of its claims, albeit with current minor weaknesses concerning the evidence in favour of gaze-modulation of the fMRI signal. The work will be of interest to neuroscientists working on attention and decision-making.

eLife Assessment

This study provides important insights into the CO₂-dependent activation of Cx43 hemichannels through a well-defined carbamylation motif, supported by multiple independent assays and validation in hippocampal tissue. The evidence convincingly demonstrates that increased pCO₂ enhances Cx43 hemichannel activity, which has potential implications for cellular signaling in cardiomyocytes and astrocytes. While further investigation is needed to fully elucidate the structural mechanisms, the findings offer a foundation for future research in gap junction biology and CO₂ regulation of proteins.

eLife Assessment

This study presents a valuable finding that KDM5 inhibition activates the interferon response and antigen presentation genes in breast cancer cells through R-loops. The evidence supporting the claims of the authors is solid, although the inclusion of further in vivo studies displaying the effects of KDM5 inhibitors on the immunotherapy responses of breast tumors would have strengthened the study. The work will be of interest to scientists working in the field of breast cancer immunotherapy.

eLife Assessment

This important study shows that nutrient stress emanating from the microenvironment induces metabolic vulnerabilities in pancreatic ductal adenocarcinoma (PDAC). Using a combination of cell-based and mouse models, the authors provide compelling evidence showing that arginine restriction in the microenvironment disrupts lipid homeostasis in PDAC, resulting in the induction of ferroptosis upon exposure of tumors to polyunsaturated fatty acids. This report is likely to be of broad interest to researchers interested in studying cancer biology, tumor microenvironment, metabolism, and stress adaptation mechanisms.

eLife Assessment

Using highly sophisticated switching linear dynamical systems (SLDS) analyses applied to functional MRI data, this study provides important insights into network dynamics underlying threat processing. After identifying distinct neural network states associated with varying levels of threat proximity, the paper provides compelling evidence of intrinsically and extrinsically driven contributions to these within-state dynamics and between-state transitions. Although the findings could be made more biologically meaningful, this work will be of interest to a wider functional neuroimaging and systems neuroscience community.

eLife Assessment

This important study reports human single-neuron recordings in subcortical structures while participants performed a tactile detection task around the perceptual threshold. The study and the analyses are well conducted and provide convincing evidence that the thalamus and the subthalamic nucleus contain neurons whose activity correlates with the task, with stimulus presentation, and even with whether the stimulation is consciously detected or not. The study will be relevant for researchers interested in the role of subcortical structures in tactile perception and the neural correlates of consciousness.

eLife Assessment

This useful study provides the first assessment of potentially interactive effects of seasonality and blood source on mosquito fitness, together in one study. During revision, the manuscript has been substantively improved, providing additional solid data to support the robustness of observations. Overall, this interesting study will advance our current understanding of mosquito biology.

eLife Assessment

This important work advances our understanding of how the SARS-CoV-2 Nsp16 protein is regulated by host E3 ligases to promote viral mRNA capping. Support for the overall claims in the revised manuscript is convincing . This work will be of interest to those working in host-viral interactions and the role of the ubiquitin-proteasome system in viral replication.

eLife Assessment

This manuscript shows that chronic chemogenetic excitation of dopaminergic neurons in the mouse midbrain results in differential degeneration of axons and somas across distinct regions (SNc vs VTA). These findings are important for two reasons. This approach can be used as a mouse model for Parkinson's Disease without the need for the infusion of toxins (e.g. 6-OHDA or MPTP) — this mouse model also has the advantage of showing axon-first degeneration over a time course (2–4 weeks) that is suitable for experimental investigation. Also, the findings that direct excitation of dopaminergic neurons causes differential degeneration sheds light on the mechanisms of dopaminergic neuron selective vulnerability. The evidence that activation of dopaminergic neurons causes degeneration, alters motor behavior, and alters mRNA expression is convincing. This is an exciting paper that will have an impact on the Parkinson's Disease field.

eLife Assessment

This valuable study reveals that the structural protein vimentin promotes the epithelial-mesenchymal transition in breast cancer cells. Utilizing robust and validated methodologies, the data collected provide a solid foundation for further investigation into metastasis models. This work will be of significant interest to researchers in the field of breast cancer.

eLife Assessment

This study provides compelling evidence that SLC7A11 may serve as a potential therapeutic target for trastuzumab-resistant HER2-positive breast cancer. While the findings are well-supported by robust data, the study could have been further strengthened by incorporating additional cell line experiments and providing more detailed clarification on patient sample selection. Nevertheless, this valuable work represents a significant contribution and will be of considerable interest to researchers in the field of breast cancer.

eLife Assessment

This 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. Simulated effects of voltage on the movement of charged amino acids appear solid as they are generally consistent qualitatively and quantitatively with previous experimental and structural results, providing a potentially valuable way to calculate the contribution of individual charges to voltage-sensitivity. Simulations of conformational changes and interactions associated with channel opening and K+ conduction are likely incomplete owing to the timescale of the simulation and theoretical limitations in simulating K+ and water movement, but nonetheless provide helpful initial predictions and a framework for future improvement. This paper will likely be of interest to ion channel biologists and biophysicists focused on voltage-dependent channel gating mechanisms.

eLife Assessment

This study presents a valuable investigation into cell-specific microstructural development in the neonatal rat brain using diffusion-weighted magnetic resonance spectroscopy. The evidence supporting the core claims is solid, with innovative in vivo data acquisition and modeling, although some conclusions would benefit from stronger validation and methodological justification. The work will be of interest to researchers studying brain development and biophysical imaging methods.

eLife Assessment

This valuable study demonstrates that silencing of inhibitory interneurons in zebra finch HVC, a premotor nucleus critical for song production, disrupts song. However, song naturally recovers in a way that is surprisingly independent of LMAN, a distinct premotor nucleus required for normal song plasticity. The authors provide solid evidence that disruption is associated with microglial activation, activation of MHCI, synaptic changes, and altered neural dynamics in HVC. However, the manuscript would benefit from a clearer narrative structure, contextualization of the microglial results, and quantitative analyses to fully characterize song syntax and recovery after LMAN lesions.

eLife Assessment

The manuscript represents a fundamental advance in designing peptide inhibitors targeting Cdc20, a key activator and substrate-recognition subunit of the APC/C ubiquitin ligase. Supported by compelling biophysical and cellular evidence, the study lays a strong foundation for future developments in degron-based therapeutics. The revised manuscript has been strengthened by additional clarifications and data that address prior reviewer concerns. The work provides a robust framework for developing tools to manipulate protein degradation and will be of broad interest to researchers in protein engineering, cell cycle regulation, and targeted protein degradation.

eLife Assessment

This is an interesting study that adds useful new data addressing how different DAG pools influence cellular signaling. The study dissects how the enzyme Dip2 modulates the minor lipid signaling DAG pool, which is distinct from the lipid metabolism DAG pool utilized in membrane production. Overall the analysis is solid and broadly supports the claims.

eLife Assessment

The authors show that an automated approach using artificial neural networks, which focuses on behaviourally relevant dimensions, can predict human similarity data up to a certain level of granularity. This study has the potential to be a valuable contribution to the broader field of cognitive computational neuroscience, as it provides a tool for the automated collection of similarity judgments under certain conditions. However, as of now, the significance of this method is somewhat limited because of its inability to generalise beyond between-category distinctions and the limited model evaluation. In terms of broader implications, the degree to which this work provides insights into DNN-brain alignment and a better understanding of the functional organisation of the visual system is supported by incomplete evidence.

eLife Assessment

This study presents a valuable finding on the direct cytotoxic effects of DuoHexaBody-CD37 in diffuse large B-cell lymphoma, mediated via SHP-1 activation and antibody clustering, independent of complement. The evidence supporting this mechanism is incomplete, with additional work needed to clarify SHP-1's role, the contribution of Fc receptor crosslinking, and the biological relevance across normal and malignant B cells. As the findings are based primarily on in vitro models, further validation would be required to support broader translational conclusions.

eLife Assessment

This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to assess heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila. A cell cycle based clustering approach allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their convincing analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

eLife Assessment

The article presents important findings describing the role of IL27 in maintaining HSCs at steady state, and in emergency haematopoiesis in response to T. goodii by limiting the inflammatory monocyte outcomes. However, the evidence is still incomplete, as not enough evidence is provided to support that IL27 only acts at the level of HSCs and not downstream. This study will be of interest to immunologists and hematologists, as well as infectious disease researchers.

eLife Assessment

The granularity with which neural activity in the sensorimotor cortex of mice corresponds to voluntary forelimb motion is a key open question. This paper provides convincing evidence for the encoding of low-level features like joint angles and represents an important step forward toward understanding the cortical origins of limb control signals.

eLife Assessment

This useful study reports a method to detect and analyze a novel post-translational modification, lysine acetoacetylation (Kacac), finding it regulates protein metabolism pathways. The study unveils epigenetic modifiers involved in placing this mark, including key histone acetyltransferases such as p300, and concomitant HDACs, which remove the mark. Proteomic and bioinformatics analysis identified many human proteins with Kacac sites, potentially suggesting broad effects on cellular processes and disease mechanisms. While the data presented are solid, the functional validation of the sites would add significantly to the manuscript's description of this modification; the study will be of interest to those studying protein and metabolic regulation.

eLife Assessment

This paper investigates how isoform II of transcription factor RUNX2 promotes cell survival and proliferation in oral squamous cell carcinoma cell lines. The authors used gain and loss of function techniques to provide convincing evidence showing that RUNX2 isoform silencing led to cell death via several mechanisms including apoptosis and ferroptosis that was partially suppressed through RUNX2 regulation of PRDX2 expression. The study provides valuable insight into the underlying mechanism by which RUNX2 acts in oral squamous cell carcinoma.

eLife Assessment

This important study offers a molecular characterization of neurons and glia in the adult nervous system of the fruit fly Drosophila melanogaster. The study focuses on the progeny of a specific set of neural stem cells that contribute to the central complex, a conserved brain region that plays key roles in sensorimotor integration. The data are convincing and collected using validated methodology, generating an invaluable resource for future studies. The study will be of interest to developmental neurobiologists.

eLife Assessment

This manuscript presents an important contribution to the field of single-cell transcriptomic analysis in cancer by introducing a novel computational framework-SCellBOW-which applies embedding techniques from natural language processing to model phenotypic heterogeneity in tumors. The revised version includes new validation experiments and significant clarifications that provide convincing evidence for the method's utility. The authors have benchmarked SCellBOW across diverse datasets, including glioblastoma, breast, and metastatic prostate cancer, and have demonstrated its superior performance compared to existing state-of-the-art methods.

eLife Assessment

The submission by Praveen and colleagues reports important findings describing the structure of genetic and colour variation in its native range for the globally invasive weed Lantana camara. Whilst the importance of the research question and the scale of the sampling is appreciated, the analysis, which is currently incomplete, requires further tests to support the claims made by the authors.

eLife Assessment

The authors present an algorithm and workflow for the inference of developmental trajectories from single-cell data, including a mathematical approach to increase computational efficiency. In this latest version, the authors addressed the benchmarking of the novel method, but the absence of quantitative comparisons to state-of-the-art methods still make this study incomplete. Based on the shown validation approaches, one can neither ultimately judge if the shown method will be an advance over previous work nor whether the approach will be of general useful applicability.

eLife Assessment

This study provides a valuable and comprehensive dataset on transcription factor binding in Pseudomonas aeruginosa, along with analyses of its regulatory network, key virulence and metabolic regulators, and a pangenomic examination of transcription factors. Utilizing large-scale ChIP-seq and multi-omics integration, the research convincingly supports the hierarchical regulatory structures and offers insights into virulence mechanisms. While further experimental validation is needed, this publicly accessible PATF_Net database enhances its utility for researchers investigating this significant pathogen associated with hospital infections and antibiotic resistance.

eLife Assessment

In contrast with mammals, measures of cochlear tuning in budgerigars do not match the frequency dependence of behavioral tuning. Earlier behavioral data in the budgerigar had shown good selectivity at around 3-4 kHz, but it was unknown whether this unusual selectivity arose in the inner ear or was a more central adaptation. The authors measured both auditory-nerve tuning curves and stimulus-frequency otoacoustic emissions and found fairly normal-looking cochlear tuning in the budgerigar. These important findings imply that any behavioral/perceptual differences in frequency selectivity are likely more central in original. These solid new data also provide significant support for the utility of otoacoustic estimates of cochlear tuning.

eLife Assessment

This important study provides compelling evidence for the evolutionary diversification and conserved NFκB-inducing function of RHIM-containing RIP kinase proteins across animal lineages, combining thorough bioinformatic analysis with functional assays in human cells. The findings are of broad interest to immunologists and evolutionary biologists, though some novel observations would benefit from deeper conceptual integration.

eLife Assessment

This important study investigates the molecular mechanisms by which the p53 isoforms Δ133p53α and Δ160p53α exert dominant-negative effects on full-length p53 (FLp53). Through a combination of chromatin immunoprecipitation, transcriptional reporter assays, subcellular localization analyses, and protein aggregation experiments, the authors provide solid evidence that these N-terminally truncated isoforms promote co-aggregation with FLp53, disrupting its transcriptional activity and cellular distribution. The revised manuscript successfully addresses prior reviewer concerns, and the findings are well supported by the experimental data.

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

eLife Assessment

This important study advances our understanding of maladaptive innate immune training. The experimental evidence supporting the conclusions is convincing and the expert reviewers strongly endorse the manuscript. The work will be of high interest to both researchers in the trained immunity field and clinician scientists.

eLife Assessment

In this preregistered study, Kunkel and colleagues set out to compare the magnitude and duration of placebo versus nocebo effects in healthy volunteers, and also to examine the different factors contributing to these effects. The authors follow a rigorous methodology in a within-subjects design, taking into consideration standard conventions for manipulation of expectations, and using an appropriate sham condition. They present compelling evidence of long-lasting placebo and nocebo effects, with nocebo responses demonstrating consistently greater strength. These valuable results have the potential for a great impact in the field of experimental and clinical pain.

eLife Assessment

This paper describes the study of the evolution of the N-terminal domain of the MSH6 mismatch repair protein in regard to the presence or absence of histone reader domains. While the presence of the histone reader domains was previously known, the phylogenetic analysis of these domains performed here establishing their insertion through convergent evolution is important, definitively done, and establishes an interesting feature of the MSH6 family of proteins. The work is convincing but the presentation of the structural features of MSH6 could be improved.

eLife Assessment

This study provides valuable insights into how auditory stimuli influence the temporal dynamics of visual perception by modulating brain rhythms (oscillations) in the alpha band. The authors present convincing evidence that auditory input induces a drop in visual alpha frequency, increasing the time window for audio-visual integration, and subsequently shifting the predictive role from prestimulus alpha frequency to alpha phase. The conclusions are well-supported by the combination of psychophysics, electrophysiological recordings (EEG), non-invasive brain stimulation (tACS), and computational modelling.

eLife assessment

In this useful study, the authors tested the ability of bumblebees to use bird-view and ground-view for homing in cluttered landscapes using modeling and behavioral experiments, claiming that bumblebees rely most on ground-views for homing. However, due to a lack of analysis of the bees' behavior during training and a lack of information as to how the homing behavior of bees develops over time, the evidence supporting their claims is currently incomplete. Moreover, there was concern that the experimental environment was not representative of natural scenes, thus limiting the findings of the study.

eLife Assessment

This important study investigates whether neural prediction of words can be measured through pre-activation of neural network word representations in the brain; solid evidence is provided that neural network representations of neighboring words are correlated in natural language. Therefore, it is crucial to differentiate between neural activity that predicts the upcoming word and neural activity that encodes the current words - information that can be used to predict the upcoming word. The study is of potential interest to researchers investigating language encoding in the brain or in large language models. Additional discussions are needed regarding the distinction between prediction and stimulus dependency and potential methods to distinguish them.

eLife Assessment

This study offers valuable insights into brain responses to words in the visual cortex of blind and sighted individuals. However, the evidence supporting the authors' claims remains incomplete, and the conclusions would benefit from a more comprehensive characterization of the conceptual properties of the word stimuli. This work will be of broad interest to cognitive neuroscientists, psycholinguists, and neurologists investigating meaning representation in the brain.

eLife Assessment

In this important study, the authors advance our understanding of copper uptake by chalkophores and their targeted metalloproteins in Mycobacterium tuberculosis. These convincing data demonstrate that chalkophore-acquired copper is solely incorporated into the Mtb bcc:aa3 copper-iron respiratory oxidase under low copper conditions, and that chalkophore-mediated protection of the respiratory chain is critical to Mtb virulence. These findings may be leveraged for drug discovery and will be of broad interest to those studying bacterial pathogenesis.

eLife Assessment

This is a valuable study that tests the functional role of food-washing behavior in removing tooth-damaging sand and grit in long-tailed macaques and whether dominance rank predicts level of investment in the behavior. The evidence that food-washing is deliberate is compelling and the evidence that individual investment in the behavior varies is solid. Overall, the paper should be of interest to researchers interested in foraging behavior, cognition, and primate evolution.

eLife Assessment

This important study identifies a mechanism by which caspases are activated in a non-lethal context to induce functional modulation in Drosophila olfactory receptor neurons. To deliver, the authors generated a new reporter of caspases, used TurboID to identify proteins proximal of the Drosophila executioner caspases Drice, and then focused on Fasciclin 3 as a mediator. The experimental results and the main conclusions are convincing. This substantial body of work will be of interest to researchers across fields, from neuroscience of olfaction to development and cell biology.

eLife Assessment

In this useful study, the authors tested the ability of bumblebees to use bird-view and ground-view for homing in cluttered landscapes using modeling and behavioral experiments, claiming that bumblebees rely most on ground-views for homing. However, due to a lack of analysis of the bees' behavior during training and a lack of information as to how the homing behavior of bees develops over time, the evidence supporting their claims is currently incomplete. Moreover, there was concern that the experimental environment was not representative of natural scenes, thus limiting the findings of the study.

eLife Assessment

These important findings detail the role of Pim1 and Pim2 in controlling the behaviour and activity of 'killer' T cells; a vital cell within of our immune system. The authors capitalized on high resolution quantitative analysis of the proteomes and transcriptomes of Pim1/Pim2-deficient CD8 T cells to provide compelling evidence for how the PIM1/2 kinases control TCR-driven activation and IL-2/IL-15-driven proliferation and differentiation into effector T cells. It's also noteworthy that Pim1/Pim2 impact is better revealed through quantitative proteomics than transcriptomics.

eLife Assessment

This article presents a valuable genetic spatio-temporal analysis of malaria-infected individuals from four villages in a highly seasonal transmission setting in The Gambia, covering the period between December 2014 and May 2017. Evidence generated by the study's laboratory and data processing approaches is solid and helps to advance the understanding of malaria in The Gambia, particularly due to its longitudinal design and the inclusion of asymptomatic cases.

eLife Assessment

The authors show MRI relaxation time changes that are claimed to originate from cell membrane potential changes. This would be a substantial contribution if true because it may provide a mechanism whereby membrane potential changes could be inferred noninvasively. However, the membrane potential manipulations applied here are performed on a slow time scale and are known to induce cell swelling. Cell swelling has been previously shown to affect relaxation time. Experiments could be performed to rule out this hypothesis, but the authors have chosen not to perform these experiments. The study is therefore useful, but the evidence is incomplete.

eLife Assessment

A regression discontinuity analysis finds essentially no effect of 1 additional year of secondary education on brain structure in adulthood. This is a valuable finding that adds to the literature on the impact of education on brain health. While the finding is convincing on its own, as the analysis was pre-registered and very carefully conducted, the impact is limited as the manipulated variable only relates to a single additional year of education (remaining in education to 15 vs 16 years of age).

eLife Assessment

The work presented is important for our understanding of the development of the cardiac conduction system and its regulation by T-box transcription factors. The conclusions are supported by convincing data. Overall this is an excellent study that advances our understanding of cardiac biology and has implications beyond the immediate field of study.

eLife Assessment

This manuscript makes important contributions to our understanding of cell polarization dynamics by demonstrating how compensatory regulatory and spatial mechanisms enhance the robustness of polarization patterns. By integrating a computational pipeline with comparisons to experimental data, the authors provide convincing evidence that stability and asymmetry in reaction-diffusion networks are crucial for polarization in C. elegans zygotes. Their findings offer novel insights into essential biological processes such as cell migration, division, and symmetry breaking. Future theoretical and experimental work could refine the model by addressing its acknowledged limitations.

eLife Assessment

This important study uses the delay line axon model in the chick brainstem auditory circuit to examine the interactions between oligodendrocytes and axons in the formation of internodal distances. This is a significant and actively studied topic, and the authors have used this preparation to support the hypothesis that regional heterogeneity in oligodendrocytes underlies the observed variation in internodal length. In a solid series of experiments, the authors have used enhanced tetanus neurotoxin light chains, a genetically encoded silencing tool, to inhibit vesicular release from axons and support the hypothesis that regional heterogeneity among oligodendrocytes may underlie the biased nodal spacing pattern in the sound localization circuit.

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

eLife Assessment

The authors use a multidisciplinary approach to provide a valuable link between Beta-alanine and S. Typhimurium (STM) infection and virulence. The work shows how Beta-alanine synthesis mediates zinc homeostasis regulation, possibly contributing to virulence. The work is convincing as it adds to the existing knowledge of metabolic flexibility displayed by STM during infection. However, the authors need to address some lingering concerns.

eLife Assessment

By taking advantage of noise in gene expression, this important study introduces a new approach for detecting directed causal interactions between two genes without perturbing either. The main theoretical result is supported by a proof. Preliminary simulations and experiments on small circuits are solid, but further investigations are needed to demonstrate the broad applicability and scalability of the method.

eLife Assessment

This important study provides compelling data from in vitro models and patient-derived samples to demonstrate how modulation of GSK3 activity can reprogram macrophages, revealing potential therapeutic applications in inflammatory diseases such as severe COVID-19. The study stands out for its clear and systematic presentation, convincing experimental approach, and the relevance of its findings to the field of immunology.

eLife Assessment

This important work presents a stochastic branching process model of tumour-immune coevolution, incorporating stochastic antigenic mutation accumulation and escape within the cancer cell population. They then used this model to investigate how tumour-immune interactions influence tumour outcome and the summary statistics of sequencing data of bulk and single-cell sequencing of a tumour. The evidence is currently incomplete: statistical comparisons between the observed mutational burden distribution and theoretical predictions in the absence of immune selection should be carried out. Conclusions should be tested extensively for robustness/sensitivity to parameters.

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. Many of the methodological concerns raised after the first round of review were addressed in the revised version, although all three reviewers also highlighted that the exploratory nature of the paper and the lack of clarity regarding the hypotheses make it hard to assess the impact of the results on existing theories.

eLife Assessment

This work provides important insights into mucosal antibody responses against SARS-CoV-2 following intranasal immunization by characterizing a large number of monoclonal antibodies at both mucosal and non-mucosal sites. The evidence supporting the claims is solid. The demonstrated in vitro antiviral activity of antibodies characterized provides a rationale for developing mucosal vaccines, especially if confirmed in vivo and benchmarked against antibodies generated following intramuscular vaccination.

eLife Assessment

This study uses C. elegans to investigate how the Calcium/Calmodulin-dependent kinase CMK-1 regulates adaptation to thermo-nociceptive stimuli. The authors use compelling approaches to identify Calcineurin as a phosphorylation target of CMK-1 and to investigate the relationship between CMK-1 and Calcineurin using gain and loss of function genetic and pharmacological methods. The findings of this study are valuable as they show that CMK-1 and Calcineurin act in separate neurons in an antagonistic and complex manner to regulate thermo-nociceptive adaptation, and these results may be relevant for understanding some chronic human pain conditions.

eLife Assessment

The authors developed a methodology to graph antigenic surface loops on influenza virus neuraminidases. The hybrid proteins retained the structure of the neuraminidase scaffold and the antigenicity of the grafted loops. This fundamental work should help in developing novel neuraminidase constructs for use in influenza virus vaccines. The paper presents compelling evidence supporting the conclusions arrived at by the authors.

eLife Assessment

This is an important study that examines the role of TFAM, a protein that helps maintain mtDNA, in mtDNA mutator mice. With convincing evidence, the authors have demonstrated that TFAM's counteractive role in mtDNA mutator mice is tissue-specific. The study does a thorough job of assessing the impact of modulating TFAM levels in a polg mutator mouse model of aging. The authors have thoroughly addressed all the points raised during the first round of review.

eLife Assessment

This important paper describes the regulatory pathway of rRNA synthesis by Meioc-Piwil1 in germ cell differentiation in zebrafish. Using the molecular genetic and cytological approaches, the authors provide convincing evidence that Meioc antagonizes Piwil1, which downregulates the 45S pre-rRNA synthesis by heterochromatin formation for spermatocyte differentiation. The results will be of use to researchers in the field of germ cell/meiosis as well as RNA biosynthesis and chromatin.

eLife Assessment

This study provides new insights into the expression profile of ILCs that demonstrate a history of RAG expression. It examines in part the potential intrinsic regulation of RAG expression and seeks to understand how the epigenetic state of ILCs is established, although a full understanding of intrinsic factors is only partially supported. The work provides a convincing and important molecular dataset, and strengthens our understanding of intrinsic regulation, and would be of interest more broadly to cell biologists seeking to understand immune cell development.

eLife Assessment

This important revised manuscript presents compelling findings by delineating two molecularly distinct liver cancer subtypes through comprehensive multi-omics integration and constructing a rigorously validated prognostic model. The authors have strengthened the analytical framework and validation across multiple datasets, including single-cell RNA sequencing. The evidence remains robust, with enhanced methodological clarity and expanded validation in both internal and independent cohorts. The revisions have improved the study's rigor and translational relevance.

eLife Assessment

In this important work, a quantitative analysis method for three-dimensional morphogenetic processes during embryonic development is introduced. The proposed method is a pipeline combining several methods, allowing quantitative analysis of developmental processes without cell segmentation and tracking. Upon application of their method, the authors obtain convincing evidence that ascidian gastrulation is a two-step process. This work should be of interest to a broad range of developmental biologists who aim to obtain a quantitative understanding of morphogenesis.