Evaluated articles

eLife assessment

This useful study reports that a water-soluble analog of heliomycin, 4-dmH, induces protein degradation of not only SirT1 but also tNOX, unlike heliomycin, which induces degradation of SirT1 but not tNOX, a difference that could in principle explain why 4-dmH induces apoptosis while heliomycin induces autophagy. The presented data provide solid support for the authors' conclusions.

eLife assessment

This compelling and novel mathematical method assesses drug pro-arrhythmic cardiotoxicity by examining the electrophysiology of untreated cardiac cells. It will be valuable for future drug safety design.

eLife assessment

This valuable study advances our understanding of the forces that shape the genomic landscape of transposable elements. By exploiting both long-read sequencing of mutation accumulation lines and in vivo transposition assays, the authors offer compelling evidence that structural variation rather than transposition largely shapes transposable element copy number evolution in budding yeast. The work will be of interest to the transposable element and genome evolution communities.

eLife assessment

Using a variety of methods including mutant analyses, the authors study chromatin structure during spermatogenesis in Drosophila and transcriptional profiling in single cells/nuclei. This description of the dramatic changes in chromatin structure during spermatogenesis leads to some new observations, with convincing evidence, and it is useful for the field.

eLife assessment

This valuable study advances our understanding of the evolution of protein complexes and their functions. Through convincing experimental and computational methodologies, the authors show that the specialization of protein function following gene duplication can be reversible. The work will be of interest to investigators working in biochemical evolution and those working on heat shock proteins.

eLife assessment

The authors have developed a compelling coarse-grained simulation approach for nucleosome-nucleosome interactions within a chromatin array. The data presented are solid and provide new insights that allow for predictions of how chromatin interactions might occur in vivo. The tools presented herein will be valuable for the chromosome biology field.

eLife assessment

The study has added value to what we have already known in the potential pharmacological immunomodulatory therapies in LPS-induced sepsis, and especially the use of oral leucine might be of great interest to the readers engaged in this field. We believe this study is important and provides solid evidence on the potential use of leucine in sepsis.

eLife assessment

This paper provides potentially useful insight into why memory consolidation may differ between children (5-7 years of age) and adults. The work hints at developmental differences in neural engagement during the retrieval of recent and remote memories. However, there are several major issues with the experimental design and analyses that render the evidence supporting the authors' main claims incomplete.

eLife assessment

This manuscript provides valuable insights to the underlying mechanism for Spinocerebellar ataxia 6 (SCA6) due to defective endolysosomal trafficking of BDNF and its receptor TrkB. The findings are compelling and significant in understanding the underlying pathology of SCA6. The authors have acknowledged the experimental weaknesses and recognize there may be multiple mechanisms to explain the findings.

eLife assessment

This important work provides convincing data on neuronal heterogeneity in the dorsal raphe nucleus (DRN), focusing on their electrophysiological properties, morphology, and susceptibility to the neurodegeneration of noradrenaline and dopamine systems in the Parkinsonian state. These findings suggest a significant interplay between catecholaminergic systems in healthy and parkinsonian conditions, as well as neuronal structure and function. Such findings provide a strong foundation for basic scientists as well as pre-clinical researchers interested in the role of dorsal raphe neurons in Parkinson's disease.

eLife assessment

The authors identify a new role for C1ql2 at mossy fiber synapses in the hippocampus and convincingly find that C1ql2, whose expression is controlled by Bcl11b, controls the recruitment of synaptic vesicles to active zones and is necessary for synaptic plasticity. These important results build upon prior discoveries of how Bcl11b, a disease-relevant molecule, contributes to our understanding of mossy-fiber synaptic development.

eLife Assessment

This paper, on the role of calcium and integrin-binding protein 2 and 3 in the hair-cell in the mechano-electrical transduction (MET) apparatus, is a mix of confirmatory studies with new and potentially important data. Some parts, such as zebrafish studies, the modelling and simulations, are regarded as necessary and convincing. Other parts of the paper do not have the same novelty. Both Liang et al. (2021) and Wang et al. (2023) had previously demonstrated a role for CIB2/CIB3 in auditory and vestibular cells in mice. Moreover, there are also data in Riazuddin et al. (2012) paper that demonstrates the importance of CIB2 in zebrafish and Drosophila. Breaking the manuscript up to focus on specific aspects of the problem might alleviate the limitations of this multi-faceted study.

eLife Assessment

This valuable study combines experiments and modelling to advance our understanding of the nonlinear nature of homeostatic structural plasticity and its interaction with synaptic scaling. The methodology and findings are solid, although additional work is needed to better link models with experiments and support some of the conclusions drawn. This study will be of interest to theoretical and experimental neuroscientists working in homeostatic plasticity.

eLife assessment

This study presents a useful description of transcriptional responses in adult zebrafish olfactory bulb microglia and neurons following exposure to infectious hematopoietic necrosis virus. This solid work advances our understanding of central nervous system responses to viral infection and provides an inventory of gene expression changes in particular cell types that can be used as hypothesis generators for future studies. Experiments to assess behavioral and neural responses to the virus in adults and larvae are inadequate and would benefit from a clearer conceptual framework that connects these avenues of investigation both to published literature and to the authors' single cell RNA sequencing results.

eLife Assessment

This is an important technical method paper that details the development and quality assessment of a 3D MERFISH method to enable spatial transcriptomics of thick tissues, representing a major step forward in the technical capacity of the MERFISH. The evidence presented is convincing.

eLife Assessment

This important study enhances our understanding of ephaptic interactions by utilizing earthworm recordings to refine a general model and use it to predict ephaptic influences across various synaptic configurations. The integration of experimental evidence, a robust mathematical framework and computer simulations convincingly demonstrate the effects of action potential propagation and collision properties on nearby membranes. The study will interest both computational neuroscientists and physiologists.

eLife Assessment

This study provides an important computational tool for analyzing and deconvoluting a pool of plasmids sequenced without barcoding using nanopore long-read sequencing. The tool, which has been convincingly validated, is readily available to scientists interested in rapid and cost-effective verification of plasmid sequences as well as in scaling up analysis by pooling samples within barcodes.

eLife assessment

This is an important study that leverages a human-chimpanzee tetraploid iPSC model to test whether cis-regulatory divergence between species tends to be cell type-specific. The evidence supporting the study's primary conclusions together provide convincing evidence for enrichment of species differences in gene regulation in cell type-specific genes and regulatory elements, motivating future work with larger sample sizes of cell lines. This work will be of broad interest in evolutionary and functional genomics.

eLife assessment

With a carefully collected dataset and compelling analyses, this fundamental manuscript demonstrates detailed links between societal and academic interest and natural species across the globe. In doing so, the authors reveal biases that may be diminishing our abilities to care for the species on our planet that may need our care the most. While some parts of this manuscript reflect previously published work, the authors are commended for putting all the puzzle pieces together for the first time. Their work highlights our uneven knowledge of biodiversity and its potential causes.

eLife assessment

This study presents important findings about synaptic connectivity among subsets of unipolar brush cells (UBCs), a specialized interneuron primarily located in the vestibular lobules of the cerebellar cortex. The evidence supporting the claims are interesting and solid. The work will be of interest to cerebellar neuroscientists as well as those focussed on synaptic properties and mechanisms. Although several compelling pieces of data were presented, some in vivo work remains to be conducted in order to test if the hypothesis and predictions translate into the behaving animal and how it would impact the processing of feedback or feedforward activity that would be required to promote behavior.