Evaluated articles

eLife Assessment

This valuable study suggests that the dosage compensation complex and m6A act in a feedback loop in Drosophila melanogaster. The study provides integrated analyses of RNA sequencing and mapping data of the m6A RNA modification in the context of unbalanced genomes, which suggests that m6A modification status may influence H3K16Ac deposition through regulation of the acetyltransferase MOF. However, it is not clear whether this regulation is directly or indirectly related to m6A regulation. The evidence is considered incomplete due to technical concerns, as quantitative assessments were made using non-quantitative methods.

eLife Assessment

The paper will be of broad interest to fungal biologists and fungal immunologists seeking to understand the biosynthesis of the fungal cell wall, in particular of ß-1,6-glucan synthesis and the importance of this so far understudied constituent of the cell wall for cell wall integrity and immune response. The study is of fundamental significance and adds structural clarity to the genetic, and biochemical basis of this difficult-to-analyze carbohydrate. It opens the potential for understanding its role in immune recognition and potentially as a drug target. Overall, the data is compelling, properly controlled and analyzed.

eLife Assessment

This manuscript addresses a mechanism by which dopamine (DA) regulates synaptic plasticity. The authors build upon their previous finding that DA applied after a timing pattern that ordinarily induces long-term depression (LTD) now induces long-term potentiation (LTP). The new findings that this "DA-dependent LTP" involves de novo protein synthesis, a cyclicAMP signalling pathway, and calcium-permeable AMPA receptors (CP-AMPARs) are of valuable significance. The conclusions are convincing and largely supported by the evidence provided.

eLife assessment

This study provides a useful inventory of genes that are up- or down-regulated during the early metamorphic development of male and female larvae and proposes that the microRNA cluster miR-277/34 is involved in the development of sexual differences during early metamorphosis of Drosophila melanogaster, although its precise role remains unclear. The strength of evidence, based on a combination of diverse methods including mRNA and small RNA sequencing, in silico analyses, in vitro assays, and loss-of-function experiments, is incomplete as it lacks a general model and an examination of the potential effects of the miR-277/34 mutations on phenotypes such as morphology or developmental time. This work will be of interest to developmental biologists interested in sexual dimorphism and in the interplay between hormones and microRNAs during development.

eLife assessment

This study presents an important finding of dynamic reprogramming of global H3K4me2 during mouse oocyte-to-embryo transition. While the H3K4me2 epigenome data is convincing, the interpretation and the potential mechanistic claims of the authors are incomplete in the current shape with the primary concerns regarding the contribution of Kdm1b or Kdm1a, as well as the specificity of the inhibitor and the antibody. The work will be of interest to researchers interested in epigenetic reprogramming.

eLife Assessment

The authors have developed a robust machine learning approach to predict radio sensitivity in patients with NPC based on a defined gene signature. Some key aspects of this signature have been validated in vitro using relevant cell lines which strengthens the conclusions of this important and convincing study. The publication will be of interest to clinicians working on this indication as well as a more broader readership made up of scientists working on radiation biology and those with a bioinformatics/machine learning background.

eLife Assessment

This study presents a valuable description of the cellular and transcriptional landscape of the tumor microenvironment in 27 gastric cancer (GC) patients based on their H. pylori status (HpGC, ex-HpGC, non-HpGC). The single-cell RNA sequencing dataset and computational analysis are convincing and provide a starting point that is of value for understanding H pylori-associated GC cell type composition, cell transitions, and mechanisms of response to therapy. The section correlating immunotherapy outcomes with GC cell type compositions from bulk RNAseq would have been strengthened by further comparing H. pylori GC versus non H. pylori GC.

eLife assessment

This potentially valuable study reports new and unexpected roles of STAG3 in regulating exit from pluripotency in mouse embryonic stem cells (mESCs). However, the evidence for the proposed role of STAG3 in the post-transcriptional regulation of gene expression is viewed as yet incomplete. The work will be of interest to colleagues studying stem cells, early steps in differentiation, and gene regulation.

eLife Assessment

This important study addresses how 3' splice site choice is modulated by the conserved spliceosome-associated protein Fyv6. The authors provide compelling evidence that Fyv6 functions to enable selection of 3' splice sites distal to a branch point and in doing so antagonizes more proximal, suboptimal 3' splice sites.

eLife assessment

This fundamental work advances our understanding of the regulation of corneal stem cell fate and differentiation, identifying Sox9 as a player in this process. The evidence supporting the conclusions is compelling, with rigorous genomic experiments and genetic mouse models that are state-of-the-art in the field. The work will be of broad interest to developmental, stem cell, and transcriptional biologists.

eLife assessment

This study provides a useful analysis of the changes in chromatin organization and gene expression that occur during the differentiation of two cell types (anterior endoderm and prechordal plate) from a common progenitor in zebrafish. Although the findings are consistent with previous work, the evidence presented in the study appears to be incomplete and would benefit from more rigorous interpretation of single-cell data, more in-depth lineage tracing, overexpression experiments with physiological levels of Ripply, and a clearer justification for using an explant system. With these modifications, this paper will be of interest to zebrafish developmental biologists investigating mechanisms underlying differentiation.

eLife Assessment

This valuable study a computational language model, i.e., HM-LSTM, to quantify the neural encoding of hierarchical linguistic information in speech, and addresses how hearing impairment affects neural encoding of speech. Overall the evidence for the findings is solid, although the evidence for different speech processing stages could be strengthened by a more rigorous temporal response function (TRF) analysis. The study is of potential interest to audiologists and researchers who are interested in the neural encoding of speech.

eLife Assessment

This important study shows that Type 3 secretion translocons in Edwardsiella tarda and other bacteria activate the NAIP-NLRC4 inflammasome. The data from cellular and biochemical experiments showing that EseB is required for activation of the NLRC4 inflammasome are convincing. This paper is broadly relevant to those investigating host-pathogen interactions in diverse organisms.

eLife Assessment

This important study presents interesting results aimed at explaining the effects of a human mutation on the mitochondrial import protein TIMM50 on mitochondrial function and neuronal excitability. While the evidence supporting the conclusions is convincing, the mechanisms driving changes in the levels of certain proteins within and outside the mitochondria (such as certain ion channels) remain unexplained. This paper will be of interest to scientists in the mitochondria field.

eLife Assessment

This valuable study revealed numerous distinct lineages that evolved within a local human population in Alberta, Canada, leading to persistent cases of E. coli O157:H7 infections for over a decade and highlighting the ongoing involvement of local cattle in disease transmission, as well as the possibility of intermediate hosts and environmental reservoirs. This study also showed a shift towards more virulent stx2a-only strains becoming predominant in the local lineages. The evidence supporting the role played by cattle in the transmission system of human cases of E. coli O157:H7 in Alberta is solid.

eLife Assessment

Periods in which experience regulates early plasticity in sensory circuits are well established, but the mechanisms that control these critical periods are poorly understood. In this important study, the authors examine early-life critical periods that regulate the Drosophila antennal lobe and show that constant odor exposure markedly reduces the volume, synapse number, and function of a specific glomerulus. The authors offer compelling evidence that these changes are mediated by the invasion of ensheathing glia into the glomerulus where they phagocytose connections via a mechanism involving the engulfment receptor Draper.

eLife assessment

This important study integrates microfluidic experiments and mathematical modeling to investigate how flow dynamics and biofilm growth and detachment influence each other. Using Pseudomonas aeruginosa as a model organism, the study identifies several key effects and stages in biofilm development, albeit with some weaknesses in clearly defining the setup and some of their interpretations. The comparison between experimental results and theoretical models is convincing, providing a robust analysis of the biofilm's behavior under varying flow conditions. The findings will be helpful for researchers working on biofilms and their applications.

eLife Assessment

This study presents valuable experimental and numerical results on the motility of a magnetotactic bacterium living in sedimentary environments, particularly in environments of varying magnetic field strengths. The evidence supporting the claims of the authors is compelling and the study will be of specific relevance to biophysicists interested in bacterial motility.

eLife Assessment

This manuscript presents a potentially important strategy for stimulating mammalian Müller glia to proliferate in vivo by manipulating cell cycle components. The results are convincing that a large number of Müller glia can be induced to re-enter the cell cycle without a damage stimulus. These findings are likely to appeal to retinal biologists and neuroscientists in general.

eLife Assessment

Goswami and colleagues used rod-specific Gls1 (the gene encoding glutaminase 1) knockout mice to investigate the role of GLS1 in photoreceptor health when GLS1 was deleted from developing or adult photoreceptor cells. This study is fundamental as it shows the critical role of glutamine catabolism in photoreceptor cell health using in vivo model systems. The evidence supporting the authors' claims is compelling. The studies add new insight into how specific metabolites support vision.