Evaluated articles

eLife Assessment

This manuscript presents a valuable and insightful contribution to the understanding of how Legionella pneumophila remodels its vacuolar niche through coordinated ubiquitination mechanisms. The identification of Rab5 as a target of both canonical and phosphoribosyl ubiquitination, and the demonstration of a detergent-resistant ubiquitin "cloud" surrounding the LCV, represent significant advances in the field. The findings are supported by rigorous experimental design, robust quantitative analyses, and clear mechanistic insight, meeting a standard of evidence that is compelling and exceeds current state-of-the-art approaches.

eLife Assessment

This work, combining behavioural genetics and calcium imaging, provides evidence for a form of learning in Drosophila that derives solely from direct or (optogenetically induced) phantom experience of punishment or reward. Flies that experience foot-shock alone show a subsequent decrease in avoidance to all odorants, together with increased odor-evoked activation of reward-encoding dopaminergic neurons that innervate the mushroom body. Phantom reward, delivered via optogenetic activation of reward-encoding dopaminergic neurons, increases subsequent odour-avoidance. While the findings are valuable to the field, there are aspects of the work that are incomplete, and some of the conclusions and terminology are also not completely justified; three major issues include : (a) the use of the term "priming" to describe this form of learning seems inappropriate and inconsistent with the accepted definition of this term; (b) a key 1998 publication with an initial description of this behavioural phenomenon needs to be cited and presented as context; and (c) the work on reward induced increase in odor-aversion seems relatively preliminary.

eLife Assessment

This is a useful study, describing transcriptome-based PPGL subtypes and exploring the mutations, immune correlates, and disease progression of cases in each subtype. The cohort is a reasonable size, and a second cohort is included from TCGA. The identification of driver mutations in PPGL is incomplete, and this compromises characterisation for prognostic purposes. This is a reasonable starting point from which to further elucidate PPGL subtypes.

eLife Assessment

This valuable study explores the role of the chromatin regulator ATAD2 in mouse spermatogenesis. It convincingly demonstrates that ATAD2 is essential for proper chromatin remodeling in haploid spermatids, influencing gene accessibility, H3.3-mediated transcription, and histone eviction. Using Atad2 knockout (KO) mice, the authors link ATAD2 to the DNA-replication-independent incorporation of sperm-specific proteins like protamines and histone H3.3. Although the findings highlight chromatin abnormalities and impaired in vitro fertilization in KO mice, natural fertility remains unaffected, suggesting possible in vivo compensatory mechanisms. However, in its current form, the study lacks mechanistic insight and provides only partial evidence for ATAD2's molecular role, limiting its functional conclusions.

eLife Assessment

This study provides valuable insights with solid evidence into altered tactile perception in a mouse model of ASD (Fmr1 mice), paralleling sensory abnormalities in Fragile X and autism. Its main strength lies in the use of a novel tactile categorization task and the careful dissection of behavioral performance across training and difficulty levels, suggesting that deficits may stem from an interaction between sensory and cognitive processes. However, while the experiments are well executed, the reported effects are subtle and sometimes non-significant. The interpretation of results may be over-extended given the nature of the data (solely behavioral) and the absence of mechanistic, causal, or computational approaches limits the strength of the broader conclusions. The work will be relevant to those interested in autism, cognition, and/or sensory processing.

eLife Assessment

This work demonstrates an objective way to select parameter values for a quadratic integrate-and-fire model so that its bifurcation diagram matches a specific target diagram, generated from the Wang-Buzsaki model. The method is useful for the field and is presented with convincing evidence. The method is currently limited in its ability to be applied to data, but improves our mathematical tools to treat a rarely studied type of bifurcation.

eLife Assessment

This study presents a valuable finding on whether executive resources mediate the impact of language predictability in reading in the context of aging. The presentation of evidence is incomplete; further conceptual clarifications, methodological details, and addressing potential confounds would strengthen the study. The work will be of interest to cognitive neuroscientists working on reading, language comprehension, and executive control.

eLife Assessment

This study used a conditional knockout mouse line to remove Ptbp1 in retinal progenitors and showed that its deletion has no effect on retinal neurogenesis or cell fate specification, thereby challenging the prevailing view of Ptbp1 as a master regulator of neuronal fate. The findings are convincing, supported by transcriptome analysis, histology, and proliferation assays. This study is important, though the genetic tools employed may not fully capture Ptbp1's potential role during the earliest stages of retinal development.

eLife Assessment

This valuable study presents a mechanistic model of predictive coding by medial entorhinal cortex grid cells, implemented with biologically detailed conductance-based neurons. The evidence supporting the emergence of this coding scheme from specific membrane currents and the anatomical connectivity among inhibitory neurons is solid. However, the justification for the choice of connectivity patterns and other network parameters remains somewhat incomplete. This work will be of interest to neuroscientists working on spatial navigation, circuit dynamics, and neuronal coding.

eLife Assessment

Complementing previous work (Namiki et al, 2018), this study provides an important resource for the Drosophila community as it reports 500 lines targeting descending neurons (DN), in addition to compiling 306 existing DN lines from the literature. The compelling work characterizes 146 DNs and makes a critical link with the DNs identified in Electron microscopy (EM). The lines in this paper will be of interest to Drosophila neuroscientists who will be able to use the reported genetic drivers for further functional characterization of DNs and circuit mapping in conjunction with existing EM datasets.

eLife Assessment

Using single-cell transcriptomic data from adult mouse inner ear hair cells, the authors identify the differences and similarities of the four hair cell types. They make an important finding: that vestibular hair cells can express many ciliary motility-related genes. Some hair cell kinocilia display motility, suggesting that the kinocilium of vestibular hair cells may function as an active force generator to increase sensitivity. The evidence is incomplete as to whether all kinocilia beat and what the function of kinocilia movement is.

eLife Assessment

This useful study provides new insights into the liver stage antigen LSA3, its export to erythrocytes, and its role in liver stage development. While the functional importance of LSA3 is well-demonstrated, the data underlying conclusions about antibody specificity, liver stage localization, and phenotype remain incomplete. A key gain is the use of mosquito and humanized mouse models to access life cycle stages rarely studied in most laboratories.

eLife Assessment

This valuable study characterizes the emergence of the membrane-associated periodic cytoskeleton (MPS) in the axons of human motor neurons derived from induced pluripotent stem cells. Super-resolution imaging of beta-II spectrin provides convincing evidence for the patterned assembly of spectrin-poor gaps and spectrin-rich MPS in the medial region of the axons and its enhancement by the kinase inhibitor staurosporine. The data advocates against gap formation by cytoskeleton disassembly in a continuous MPS. Instead, a continuous MPS may result from nascent MPS patches and their maturation, a model that would benefit from live imaging for validation.

eLife Assessment

To evaluate phenotypic correlations between complex traits, this study aimed to measure the genetic overlap of traits by evaluating GWAS signals assisted by eQTL signals. They suggested an improved version of the previous Sherlock to integrate SNP-level signals into gene-level signals. Then they compared 59 human traits to identify known and novel genetic distance relationships. This work is valuable to the field, but still needs substantial improvement because many parts of the paper are incomplete.

eLife Assessment

This valuable study introduces a data augmentation approach based on generative unsupervised models to address data imbalance in immune receptor modeling. Support for the findings is solid, showing that the use of generated data increases the performance of downstream supervised prediction tasks, e.g., TCR-peptide interaction prediction. However, the validation, mainly relying on synthetic data, could be completed, especially regarding unseen epitopes, and given the exclusive focus on CDR3β. The results should be of interest to the communities working on immunology and biological sequence data analysis.

eLife Assessment

This valuable study combines microscopy and CRISPR screening in two different cell lines to identify factors involved in global chromatin organization, using centromere clustering as a proxy. Follow-up cell cycle synchronisation studies confirm roles in centromere clustering in mitosis. However, incomplete characterisation of the cell lines used limits the interpretation of the findings. The study will interest researchers studying genome organisation in mitosis.

eLife Assessment

The analysis of neural morphology across Heliconiini butterfly species revealed brain area-specific changes associated with new foraging behaviours. While the volume of the centre for learning and memory, the mushroom bodies, was known to vary widely across species, new, valuable results show conservation of the volume of a center for navigation, the central complex. The presented evidence is convincing for both volumetric conservation in the central complex and fine neuroanatomical differences associated with pollen feeding, delivered by experimental approaches that are applicable to other insect species. This work will be of interest to evolutionary biologists, entomologists, and neuroscientists.

eLife Assessment

This study offers a valuable theoretical framework for quantifying molecular transport across interfaces between coexisting liquid phases, emphasizing interfacial resistance as a central factor governing transport kinetics. The mathematical derivations are solid. To enhance the paper's relevance and broaden its appeal, it would be helpful to clarify how the key equations connect to existing literature and to elucidate the physical mechanisms underlying scenarios that give rise to substantial interfacial resistance.

eLife Assessment

This valuable work advances our understanding of the relation between multimodal MRI, cognition, and mental health. Convincing use of statistical learning techniques in UK Biobank data shows that 48% of the variance between an 11-task derived g-factor and imaging data can be explained. Overall, this paper contributes to the study of brain-behaviour relations and will be of interest for both its methods and its findings on how much variance in g can be explained.

[Editorial note: a previous version was reviewed by Biological Psychiatry]

eLife Assessment

This valuable study investigates the self-assembly activity of death-fold domains. The data collected using advanced microscopy and distributed amphifluoric FRET-based flow cytometry methods provide solid evidence for the conclusions, although the interpretations based on these conclusions remain speculative in some cases. This paper is broad interest to those studying a variety of biological pathways involved in inflammatory responses and various forms of cell death.