Evaluated articles

eLife Assessment

This valuable study investigates how biologically plausible learning mechanisms can support assembly formation that encodes statistics of the environment, by enabling neural sampling that is based on within-assembly connectivity strength. It convincingly shows that assembly formation can emerge from predictive plasticity in excitatory synapses, while two types of plasticity in inhibitory synapses are required: inhibitory homeostatic (predictive) plasticity and inhibitory competitive (anti-predictive) plasticity.

eLife Assessment

This valuable study reports machine learning models derived from large-scale data to predict the risk of post-stroke epilepsy. The evidence supporting the conclusions is convincing, although there are some validation issues (lack of cross-validation, possible bias in external validation results). The study may be of interest in the field of clinical neurology

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

This manuscript presents valuable findings which reveal an intricate pattern of memory expression following retrieval extinction at different intervals from retrieval-extinction to test. The novel advance is in the demonstration that, relative to a standard extinction procedure, the retrieval-extinction procedure more effectively suppresses responses to a conditioned threat stimulus when testing occurs just minutes after extinction. While the data provide solid evidence that the "short-term" suppression of responding involves engagement of the dorsolateral prefrontal cortex, there are inconsistencies in the analyses reported which obscure the interpretation and leave some of the claims with limited evidence.

eLife Assessment

Yonk and colleagues provide a valuable, timely, and in-depth study showcasing the role of thalamostriatal inputs in learning and action selection. After characterizing the synaptic properties of these inputs onto different striatal cell types in vitro, they provide solid evidence that posterior medial thalamic nucleus (POm) terminals in striatum are activated during reward expectation and arousal. The overall function of this pathway and the degree to which results are confounded by viral contamination of surrounding nuclei and movements remain open questions.

eLife Assessment

There is a growing interest in understanding the individuality of animal behaviours. In this important 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. The results show that certain behaviours are individualistic and persist robustly across external stimuli while others are less robust to these changing parameters. The data supporting their findings is extensive and convincing.

eLife assessment

This important study reports the discovery of a novel nucleotide ubiquitylation activity by the DTX3L E3 ligase. Solid evidence is presented for ubiquitin attachment to single-stranded oligonucleotides. This very interesting biochemical finding can be used as a starting point for studies to establish relevance in a physiological setting.

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

This work aimed at deconstructing how sebaceous gland differentiation is controlled in adult skin. Using monoclonal antibodies designed to inhibit specific Notch ligands or receptors, the authors present convincing evidence that the Jag2/Notch1 signaling axis is a crucial regulator of sebocyte progenitor proliferation and sebocyte differentiation. The valuable findings presented here contribute to the growing evidence that Notch signaling is not only key during the development of the skin and its appendages but also regulates cell fate in adult homeostatic tissues. From a translational perspective, it is intriguing that the effect of Jag2 or Notch1 inhibition, which leads to the accumulation of proliferative stem/progenitor cells in the sebaceous gland and prevents sebocyte differentiation, is reversible.

eLife Assessment

This valuable work presents an interesting strategy to interfere with the HBV infectious cycle as it identifies two previously unexplored HBc-Ag binding pockets. The experimental data is compelling and opens the door to generating and testing novel anti-HBV therapies.

eLife assessment

This valuable study presents the development of a single turnover stopped-flow fluorescence experiment to study the kinetics of substrate unfolding and translocation by the bacterial ClpB disaggregase. Using non-physiological nucleotides to bypass the physiological regulation mechanism of ClpB, the authors convincingly show that the ClpB disaggregase is a processive motor with a slow unfolding step preceding rapid translocation. The results of this analysis are of value for future mechanistic studies on energy-dependent unfolding, degradation, and disaggregation molecular machines.

eLife assessment

This study explores simple machine learning frameworks to distinguish between interacting and non-interacting protein pairs, offering solid computational results despite some concerns about dataset generation. The authors demonstrate a modest improvement in AlphaFold-multimers' ability to differentiate these pairs. Using a simple yet sound approach, this work is a valuable contribution to the challenging problem of reconstructing protein-protein interaction networks.

eLife Assessment

This study provides important insights into how the EBH domain of microtubule end-binding protein 1 (EB1) interacts with SxIP peptides derived from the MACF plus-end tracking protein. The revised manuscript includes convincing ITC and NMR experiments that clarify the role of flanking residues and address the influence of dimerization and cooperativity on binding. While some mechanistic aspects remain difficult to resolve experimentally, the data and analysis now more clearly justify the proposed "dock-and-lock" model and its interpretive value. This work will be of interest to structural biologists and biophysicists studying microtubule-associated protein interactions.

eLife assessment

Notario Manzano et al. offer a valuable first analysis of proteins within tunneling nanotubes (TNTs), membranous bridges connecting cells. This work distinguishes TNTs from extracellular vesicles, but further experimental and analytical tools are needed to refine the TNT proteome. Solid data supports a role for tetraspanins CD9 and CD81 in TNT function. The proposed model for CD9 and CD81 is over-interpreted and requires additional evidence for stronger support.

eLife Assessment

This important study reveals that the nucleolar protein Treacle undergoes liquid-liquid phase separation in vitro and in vivo. It provides convincing evidence that the ability of Treacle to form phase-separated condensates is necessary for the proper formation of the fibrillar center of the nucleolus, rRNA transcription, and rDNA repair. These findings will be of interest to the communities studying biomolecular condensates, nucleolar organization, and ribosome biogenesis.

eLife assessment

This paper presents useful findings on the dysmyelination phenotype of nervous system-specific Spns1 (a lysosomal lipid transporter) knockout mice. While the analysis of the phenotype is solid, the evidence for the underlying mechanisms, especially the molecular function for SPNS1, is incomplete. With more careful interpretation and/or additional experimental data, this work could have implications for understanding lipid transport and lysosomal storage diseases.

eLife Assessment

This fundamental work provides novel insights into the blood flow-dependent mechanisms of neuronal migration and the role of Gherlin signaling in the adult brain. The authors present convincing evidence that newborn rostral migratory stream (RMS) neurons are closely situated alongside blood vessels, preferentially along arterioles, and that migratory speed is correlated with blood flow. They also provide evidence (in vitro and some in vivo) that Ghrelin from blood is involved in augmenting RMS neuron migration speed.

eLife Assessment

Floeder and colleagues provide an important investigation that describes the experimental conditions that systematically produce "ramps" in dopamine signaling in the striatum. This somewhat nebulous feature of dopamine has been a significant part of recent theoretical and computational debates attempting to formally describe the different timescales on which dopamine functions. The current results are convincing and add context to that ongoing work.

eLife Assessment

This short manuscript uses mutation counts in phylogenies of millions of SARS-CoV-2 genomes to show that mutation rates systematically differ between regions that are paired or unpaired in the predicted RNA secondary structure of the viral genome. Such an effect of pairing state is not unexpected, but its systematic demonstration using millions of viral genomes is valuable and convincing.

eLife Assessment

This provocative manuscript presents important comparisons of the morphologies of Archaean bacterial microfossils to those of microbes transformed under environmental conditions that mimic those present on Earth during the same Eon. The evidence in support of the conclusions is solid. The authors' environmental condition selection for their experiment is justified.