Evaluated articles

eLife Assessment

The work presented is important for our understanding of the development of the cardiac conduction system and its regulation by T-box transcription factors. The conclusions are supported by convincing data. Overall this is an excellent study that advances our understanding of cardiac biology and has implications beyond the immediate field of study.

eLife Assessment

This valuable study by Ganesh and colleagues examined how both the value and salience of sensory information can affect economic decision-making. The results provide insights into how different sources of uncertainty found in the real world, including those related to the perception of objects and those related to values associated with objects, can together influence decision-making behavior in systematic ways. The evidence is solid but overlaps with previous studies and could be improved by clarifying novelty and experimental details and considering additional models.

eLife Assessment

This important manuscript provides insights into the competition between Splicing Factor 1 (SF1) and Quaking (QKI) for binding at the ACUAA branch point sequence in a model intron, regulating exon inclusion. The study employs rigorous transcriptomic, proteomic, and reporter assays, with both mammalian cell culture and yeast models. Nevertheless, while the data are convincing, broadening the analysis to additional exons and narrowing the manuscript's title to better align with the experimental scope would strengthen the work.

eLife Assessment

The authors report that a secreted ubiquitin ligase of Shigella, called IpaH1.4, mediates the degradation of a host defense factor, RNF213. The data are solid and represent an important contribution to our understanding of cell-autonomous immunity and bacterial pathogenesis, as they provide new mechanistic insight into how the cytosolic bacterial pathogen Shigella flexneri evades IFN-induced host immunity.

eLife Assessment

This valuable study provides solid support for the participation of the BMP-binding domain of MuSK, a tyrosine kinase mostly known for its role at the neuromuscular junction, in the maintenance and activation of muscle stem cells (SCs). These mononucleated cells, located between the muscle fiber basal lamina and its plasma membrane, are normally quiescent, but following muscle damage, become activated, proliferate, and mediate muscle regeneration. These cells are known to respond to a variety of signaling pathways, but this study makes the case for BMP acting via binding to MuSK in maintaining the quiescent state.

eLife Assessment

The authors use single molecule imaging and in vivo loop-capture genomic approaches to investigate estrogen mediated enhancer-target gene activation in human cancer cells. These potentially important results suggest that ER-alpha can, in a temporal delay, activate a non-target gene TFF3, which is in proximity to the main target gene TFF1, even though the estrogen responsive enhancer does not loop with the TFF3 promoter. To explain these results, the authors invoke a transcriptional condensate model. The reviewers were split on the strength and interpretation of the evidence presented, which is considered incomplete at this stage. We encourage a revision which buttresses the findings with additional control experiments and careful consideration of alternative explanations and mathematical models. Further, the depth of the discussion on existing literature could be improved. This work will be of interest to those studying transcriptional gene regulation and hormone-aggravated cancers.

eLife Assessment

This study provides convincing evidence for functional subpopulations of β-cells responsible for Ca2+ signal initiation and maintenance using novel three-dimensional light sheet microscopy imaging and analysis of pancreatic islets. The findings are important as they help decode the mechanistic underpinnings of islet calcium oscillations and the resulting pulsatile insulin secretion. The work will be of general interest to cell biologists and of particular interest to islet biologists.

eLife Assessment

This paper presents valuable findings on how autophagosomes are positioned along microtubules for their efficient fusion with lysosomes, providing significant insights into the mechanism. The evidence supporting the conclusions is solid, with high-quality fluorescence microscopy combined with Drosophila genetics. This work will be of broad interest to cell biologists interested in autophagy and related cell biology fields.

eLife Assessment

This valuable study reveals extensive binding of eukaryotic translation initiation factor 3 (eIF3) to the 3' untranslated regions (UTRs) of efficiently translated mRNAs in human pluripotent stem cell-derived neuronal progenitor cells. The authors provide solid evidence to support their conclusions, although this study may be enhanced by addressing potential biases of techniques employed to study eIF3:mRNA binding and providing additional mechanistic detail. This work will be of significant interest to researchers exploring post-transcriptional regulation of gene expression, including cellular, molecular, and developmental biologists, as well as biochemists.

eLife Assessment

This study represents a potentially useful tool for extracting quantitative data from intravital microscopy directed at in vivo cancer models. In general, this is an area of interest as accessible non-proprietary tools are needed and some evidence of the tool's utility is provided. However, the work in its current form is incomplete as it is heavily reliant on proprietary software to segment, track, and correct the data. In addition, there are significant reservations regarding the methods used to produce statistics in the software, limiting its applicability and the potential advance over other approaches.

eLife Assessment

This manuscript reports important findings that the methyltransferase METTL3 is involved in the repair of abasic sites and uracil in DNA, mediating resistance to floxuridine-driven cytotoxicity. Convincing evidence shows the involvement of m6A in DNA based on single cell imaging and mass spec data. The authors present evidence that the m6A signal does not result from bacterial contamination or RNA, but the text does not make this overly clear.

eLife Assessment

In this manuscript, Kaplan et al. study mesenchymal Meis2 in whisker formation and the links between whisker formation and sensory innervation. These useful findings analyze the impact of the conditional deletion of Meis2 using the Wnt1 driver on whisker development and their interaction with trigeminal nerves. The evidence supporting the conclusions is incomplete lacking mechanistic links to the phenotype described and detailed information on the methods used to analyze single-cell RNA sequencing data. The work will be of interest to developmental and skin biologists.

eLife Assessment

This study provides valuable insights into the evolutionary histories and cellular infection responses of two Salmonella Dublin genotypes. While the evidence is compelling, a more phylogenetically diverse bacterial collection would enhance the findings. This research is relevant to scientists studying Salmonella and gastroenteritis-related pathogens.

eLife Assessment

This important study suggests that the composition of the extracellular matrix in a mouse model of liver fibrosis changes depending on the cause of liver fibrosis. The data could be used as a foundation for future antifibrotic therapies. The strength of evidence is solid with respect to the use of animal models and proteomic analysis. The study provides a helpful inventory of proteins up or down-regulated, but functional analyses are limited and translational data are lacking.

eLife Assessment

Following up on their previous work, the authors investigated whether cell-to-cell transmission of HIV-1 activates the CARD8 inflammasome in macrophages. This is important given that inflammasome activation in myeloid cells triggers proinflammatory cytokine release. The data are solid and support the idea that CARD8 is activated by the viral protease and promotes inflammation. However, time-course analyses in primary T cells and macrophages and further information on the specific inflammasome involved would further increase the significance of the study.

eLife Assessment

This study provides evidence that cerebellar projections to the thalamus are required for learning and execution of motor skills in the accelerating rotarod task. This important study adds to a growing body of literature on the interactions between the cerebellum, motor cortex, and basal ganglia during motor learning. The data presentation is generally sound, especially the main observations, with some limitations in describing the statistical methods and a lack of support for two segregated cerebello-thalamic pathways, which is incomplete in supporting the overall claim.

eLife Assessment

This valuable study investigates prey capture by archer fish, showing that even though the visuomotor behavior unfolds very rapidly (within 40-70 ms), it is not hardwired; it can adapt to different simulated physics and different prey shapes. Although there was agreement that the model system, experimental design, and main hypothesis are certainly interesting, opinions were divided on whether the evidence supporting the central claims is incomplete. A more rigorous definition and assessment of "reflex speed", more detailed evidence of stimulus control, and a more detailed analysis of individual subjects could potentially increase confidence in the main conclusions.

eLife Assessment

This important study advances our understanding of the way neurons in the auditory cortex of mice respond to unpredictable sounds. Through the use of state-of-the-art recording methods, compelling evidence is provided that responses to local and global violations in sound sequences are prediction errors and not simply the consequence of stimulus-specific adaptation. Although the cell-type-specific results are intriguing, further work is needed to establish their reliability.

eLife Assessment

This important study partially fills the gap in the knowledge of olfaction at the level of the Anterior Olfactory Nucleus (AON) and Piriform Cortex with functional magnetic resonance imaging, electrophysiology, and modeling. The methods used are convincing. Some of the findings confirm ongoing hypotheses, such as the behavioral importance of AON for odor source discrimination. Other results shed light on the dynamics of the connection between the olfactory system and the rest of the brain.

eLife Assessment

This study describes a new analysis strategy to compare active neurons during behavioral tasks across the brain. This is significant because analysing how different brain areas are active during behavior requires better methods. The evidence provided in support of the method is solid. Although useful now, the work may increase its significance following appropriate revisions.