Evaluated articles

eLife Assessment

This study presents a new toolbox for Representational Similarity Analysis, representing a valuable contribution to the neuroscience community. The authors offer a well-integrated platform that brings together a range of state-of-the-art methodological advances within a convincing framework, with strong potential to enable more rigorous and insightful analyses of neural data across multiple subfields.

eLife Assessment

The authors describe the important finding that the Legionella-containing vacuole is surrounded by a dense ubiquitin "cloud" that is highly resistant to detergent extraction. The study provides compelling evidence that this structure is generated through a combination of canonical ubiquitination mediated by the SidC Legionella ligase and phosphoribosyl-ubiquitination mediated by the SidE family of Legionella ligases. These findings provide insight into how Legionella remodels the host vacuolar environment through complex ubiquitin modifications.

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 valuable study describing transcriptome-based pheochromocytoma and paraganglioma (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 the Cancer Genome Atlas (TCGA). One of the key premises of the study is that identification of driver mutations in PPGL is not complete and that compromises characterisation for prognostic purposes. This is a solid starting point on which to base characterisation using different methods.

eLife Assessment

This valuable study explores the role of the chromatin regulator ATAD2 in mouse spermatogenesis. The data convincingly demonstrate 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. Future experiments will be needed to tease out the precise molecular role of ATAD2 in spermatogenesis. This work will be of interest to the epigenetics and developmental fields.

eLife Assessment

This study provides valuable insights with convincing evidence detailing 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 and quantitative 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. The behavioral experiments are well executed and set the stage for subsequent mechanistic, causal, and computational approaches. The work is 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 evidence is solid in the investigation of prediction in reading, with one caveat that the text materials used could be biased against the aging population. 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 demonstrated 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 data are convincing, supported by transcriptomic analysis, histology, and proliferation assays. This study is important, and the broader implications for other CNS regions warrant further investigation.

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 mouse inner ear hair cells, the authors compare for the first time gene expression across the four recognized hair cell types in adults, generating information fundamental to understanding hair cell relationships between the ancient vestibular compartment and the more recent cochlea. Among observed differences, compelling evidence is provided for the expression in vestibular hair cells but not cochlear hair cells of certain ciliary motility-related genes, suggesting that the kinocilium of vestibular hair cells may function as an active force generator to increase sensitivity.

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 the conclusions regarding antibody specificity, liver-stage localization, and phenotype remain incomplete. A key strength of the study is the use of mosquito and humanized mouse models to access life-cycle stages that are 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 axonal degeneration or 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 important study combines microscopy and CRISPR screening to identify factors involved in global chromatin organisation, using centromere clustering as a proxy. The authors present solid evidence demonstrating that acute depletion of a range of mitotic regulators alters centromere distribution in interphase. The work will be of interest to researchers studying genome organisation, nuclear architecture, chromosome biology, and the mechanisms linking mitosis to interphase nuclear organisation.

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, these new, valuable results show conservation of the volume of a center for navigation, the central complex, but with specific changes in neuropeptide expression in the noduli and in the numbers of ellipsoid body ring neurons. 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 relationship between multimodal magnetic resonance imaging (MRI) measures, cognition, and mental health. Compelling 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.