Evaluated articles

eLife Assessment

The paper presents valuable computational findings on how growth feedback affects the performance of synthetic gene circuits designed for adaptive responses. By systematically analyzing over four hundred circuit topologies, the authors provide solid evidence for their conclusions on failure mechanisms and design features that enhance robustness against growth dynamics. While the study's significance and rigor are somewhat constrained by its reliance on previously published network topologies, these results are highly relevant for advancing the engineering of gene circuits in various applications.

eLife assessment

In this valuable study, the authors use deep learning models to provide solid evidence that epithelial wounding triggers bursts of cell division at a characteristic distance away from the wound. The documentation provided by the authors should allow other scientists to readily apply these methods, which are particularly appropriate where unsupervised machine-learning algorithms have difficulties.

eLife assessment

The authors aim to develop a CRISPR system that can be activated upon sensing an RNA. As an initial step to this goal, they describe RNA-sensing guide RNAs for controlled activation of CRISPR modification. Many of the data look convincing and while several steps remain to achieve the stated goal in an in vivo setting and for robust activation by endogenous RNAs, the current work will be important for many in the field.

eLife assessment

This manuscript is an important contribution toward understanding the mechanisms of transcriptional bursting. The evidence is considered solid. Questions regarding the broader advance, details of the analysis, and the models used in the analysis were addressed by the authors.

eLife Assessment

This paper shows that it is possible to optogenetically activate single retinal ganglion cells in vivo in monkeys. This is an important step towards towards causal tests of the role of specific ganglion cell types in visual perception. The paper presents convincing evidence for the promise of the approach but further work will be needed to full explore its limitations and specificity.

eLife assessment

This valuable study focuses on the role of the Gr28 family of insect chemoreceptors. Using the Drosophila larva, the authors show that taste neurons expressing different members of this family of bitter taste receptors trigger opposite behavior – attraction and repulsion. They establish the minimal bitter taste receptor subunit composition needed in these neurons to mediate the repulsion of bitter tastants. The evidence presented is convincing, using well-validated and controlled tools and experiments.

eLife assessment

Using state-of-the-art single-nucleus RNA sequencing, Yao et al. investigate the transcriptomic features of neural stem cells (NSCs) in the human hippocampus to address how they vary across different age groups and stroke conditions. The authors report alterations in NSC subtype proportions and gene expression profiles after stroke. Although the study is valuable and the analysis is comprehensive, the significance is restricted by well-acknowledged technical limitations leading to incomplete evidence supporting some main conclusions.

eLife assessment

This important study provides a new perspective on why preparatory activity occurs before the onset of movement. The authors report that when there is a cost on the inputs, the optimal inputs should start before the desired network output for a wide variety of recurrent networks. The authors present compelling evidence by combining mathematically tractable analyses in linear networks and numerical simulation in nonlinear networks.

eLife assessment

In this technically advanced and important piece of work, the authors study the coordination of microtubule growth in kinetochore fibers using force spectroscopy and numerical simulations. With compelling evidence the authors address the question of how microtubules, which naturally exhibit variable growth rates, can coordinate their behavior by mechanical coupling so as to function as a single unit in generating forces during chromosome segregation.

eLife assessment

The authors used an appropriate micro-engineered experimental model of angiogenesis coupled to mathematical model to study the early steps of the angiogenic sprouting. To this end, the authors developed a convincing model to predict how VEGF activates Delta-Notch signaling. The work affords important new insight into the complex processes involved in the onset of angiogenesis.

eLife Assessment

In their valuable study, Bracey et al. investigate how microtubule organization within pancreatic islet beta cells supports optimal insulin secretion. Using a combination of live imaging and photo-kinetic assays in an in vitro culture system, they provide compelling evidence that kinesin-1-mediated microtubule sliding, which plays critical roles in neurons and embryos, also plays a critical role in forming the sub-membranous microtubule band in response to glucose in beta cells. This work will be of interest to cell biologists studying cytoskeletal dynamics and organelle trafficking, as well as to translational biologists focused on diabetes.

eLife assessment

The authors establish a Drosophila model to assess the severity of disease-linked alleles of Uba5. Using both in vivo and in vitro experiments, this valuable study demonstrates the alleles fall into mild, intermediate, and severe classes, with convincing evidence to support their conclusion. This well-executed study establishes a model for further characterization of Uba5-related phenotypes in a powerful model system.

eLife assessment

This study provides a useful catalog of the cardiac proteome and transcriptome in response to intermittent fasting. Although mechanistic integration is limited, the technical aspects have been executed in a solid way, and sufficient evidence is provided to support the main conclusions. Future work can build on this study to expand our understanding of the relationship between dietary perturbations and cardiac function.

eLife Assessment

Yamamoto and Matano provide convincing evidence that a G63E/R CD8+ T-cell escape mutation in the accessory viral protein Nef promote the induction of neutralizing antibody (nAb) responses in rhesus macaques infected with SIVmac239, which is usually largely resistant to neutralization. Functional analyses support that this mutation specifically impairs Nef`s ability to stimulate PI3K/Akt/mTORC2 signalling. This important study suggests that the accessory viral protein Nef impairs B cell function and effective humoral immune responses and is of interest for researchers and physicians interested in HIV/AIDS and vaccine development.

eLife assessment

This study used ChatGPT to assess certain linguistic characteristics (sentiment and politeness) of 500 peer reviews for 200 neuroscience papers published in Nature Communications. The vast majority of reviews were polite, but papers with female first authors received less polite reviews than papers with male first authors, whereas papers with a female senior author received more favourable reviews than papers with a male senior author. Overall, the study is an important contribution to work on gender bias, and the evidence for the potential utility of generative AI programs like ChatGPT in meta-research is solid.

eLife assessment

This study of extrachromosomal DNA (ecDNA) identifies genes that distinguish ecDNA+ and ecDNA- tumors. The findings in the manuscript are important and the genomic analyses convincing. However, some of the data remain observational and the inferences would therefore be more robust with experimental validation. This manuscript could well be of relevance to biologists interested in cancer biology and gene regulation.

eLife assessment

This study provides an important, original framework to study locomotion on the ground with physics-based simulations. Through numerical simulations, the authors propose that intermediate numbers of body modules and high body symmetry enhance speed. The current way discussions and conclusions are written is overly broad: evidence that evolution may favour bilateral symmetry and modularity for efficient directed locomotion is still incomplete as further performance metrics and a more accurate description of the dynamics in water are needed.

eLife assessment

In this important study, the authors integrated genetic and genomic datasets from humans and mice to unveil shared networks and pathways associated with coronary artery disease. Their compelling analysis led to the identification of new regulatory genes and pathways in vascular tissues and in the liver, allowing for a more in-depth understanding of the pathogenesis of coronary artery disease.

eLife assessment

This important study explores the interplay between Legionella Dot/Icm effectors that modulate ubiquitination of the host GTPase Rab10, which undergoes phosphoribosyl-ubiquitination by the SidE family of effectors, which in turn are required for Rab10 recruitment to the Legionella containing vacuole (LCV). The evidence supporting the claims of the authors is convincing. The study is not only relevant for the microbiology community, but will also be of interest to colleagues in the broader fields of membrane trafficking and general cell biology.

eLife assessment

This important study outlines a new role for caspases during cellular differentiation. The methodology used is convincing and state-of-the-art. The newly discovered cellular cascade described here uncovers that caspases can achieve high substrate specificity during differentiation. As such, the work will be of broad interest to cell biologists.