eLife

Latest preprint reviews

1. FAK loss reduces BRAFV600E-induced ERK phosphorylation to promote intestinal stemness and cecal tumor formation

   This article has 10 authors:

   1. Chenxi Gao
   2. Huaibin Ge
   3. Shih-Fan Kuan
   4. Chunhui Cai
   5. Xinghua Lu
   6. Farzad Esni
   7. Robert E Schoen
   8. Jing H Wang
   9. Edward Chu
   10. Jing Hu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     In this important study, the authors use a genetically engineered mouse model to reveal a tumor suppressive role for focal adhesion kinase in right-sided colon cancer. The evidence in support of the authors' claims is generally solid, although the data supporting the mechanism through which FAK deletion promotes tumorigenesis are incomplete. This work will be of interest to cancer researchers and others studying the biological consequences of tuning signal transduction pathways.

   Reviewed by eLife

2. The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability

   This article has 10 authors:

   1. Huishan Wang
   2. Xingyan Liu
   3. Yamin Liu
   4. Chencheng Yang
   5. Yaxin Ye
   6. Xiaomei Yu
   7. Nengyin Sheng
   8. Shihua Zhang
   9. Bingyu Mao
   10. Pengcheng Ma

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study focuses on gene regulatory mechanisms essential for hindbrain development. Through molecular genetics and biochemistry, the authors propose a new mechanism for the control of Hox genes, which encode highly conserved transcription factors essential for hindbrain development. The strength of evidence is solid, as most claims are supported by the data. This work will be of interest to developmental biologists.

   Reviewed by eLife

3. Detection of TurboID fusion proteins by fluorescent streptavidin outcompetes antibody signals and visualises targets not accessible to antibodies

   This article has 6 authors:

   1. Johanna Odenwald
   2. Bernardo Gabiatti
   3. Silke Braune
   4. Siqi Shen
   5. Martin Zoltner
   6. Susanne Kramer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study demonstrates how proximity labeling with streptavidin can be used to boost fluorescence signals in otherwise hard-to-label regions of cells. The experimental verification of amplification of fluorescence near epitope tags in phase-separated compartments is solid, demonstrating enhanced signal-to-noise compared to immunofluorescence. This study will be of particular interest to those using correlative light and electron microscopy or expansion microscopy when the signal is limiting or inaccessible.

   Reviewed by eLife

4. Artificially inserted strong promoter containing multiple G-quadruplexes induces long-range chromatin modification

   This article has 8 authors:

   1. Shuvra Shekhar Roy
   2. Sulochana Bagri
   3. Soujanya Vinayagamurthy
   4. Avik Sengupta
   5. Claudia Regina Then
   6. Rahul Kumar
   7. Sriram Sridharan
   8. Shantanu Chowdhury

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study demonstrates that genomic insertion of a G4-containing sequence can be sufficient to induce chromosome loops and alter gene expression. The evidence supporting the conclusions is convincing. Effects were shown by Hi-C as well as qPCR for chromatin modifications and expression, and the specificity of the effects was controlled by mutating the G4-containing sequence or treating with LNA probes to abolish G4 structure formation. The work will be of interest to researchers working on chromatin organization and gene regulation.

   Reviewed by eLife

5. Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense

   This article has 4 authors:

   1. Dario Galanti
   2. Jun Hee Jung
   3. Caroline Müller
   4. Oliver Bossdorf

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study presents a significant methodological advance by leveraging previously discarded, unmapped DNA sequence reads to estimate pest infestation loads across plant accessions, and map variation in these apparent pest loads to defense genes. The bioinformatics approach is compelling, and the results should bear broad implications for phenotype-genotype prediction, especially regarding the use of unmapped reads for GWAS.

   Reviewed by eLife

6. Structure, function and assembly of soybean primary cell wall cellulose synthases

   This article has 5 authors:

   1. Ruoya Ho
   2. Pallinti Purushotham
   3. Louis FL Wilson
   4. Yueping Wan
   5. Jochen Zimmer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     It is well established that cellulose synthesis in higher plants requires three different but related catalytic subunits known as CESA proteins. Here the authors provide cryo electron microscopy structural information on soybean CESA1, CESA3, and CESA6 and find substantial differences between the structure of these CESA homotrimers and the previously-resolved secondary cell wall CESAs. They present an important model with convincing evidence in which the multi-subunit cellulose synthase complexes are made of multiple homotrimers.

   Reviewed by eLife

7. Noncaloric monosaccharides induce excessive sprouting angiogenesis in zebrafish via foxo1a-marcksl1a signal

   This article has 8 authors:

   1. Xiaoning Wang
   2. Jinxiang Zhao
   3. Jiehuan Xu
   4. Bowen Li
   5. Xia Liu
   6. Gangcai Xie
   7. Xuchu Duan
   8. Dong Liu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study investigates the effect of noncaloric monosaccharides, sugar substitutes that are commonly used by diabetic patients, on angiogenesis in the zebrafish embryo. The authors show that noncaloric monosaccharides and glucose similarly induce excessive blood vessel formation due to the increased formation of tip cells by endothelial cells through the foxo1a-marcksl1a pathway. This solid study is of interest for the medical community in charge of the prevention and of the treatment of diabetes and other metabolic diseases.

   Reviewed by eLife

8. Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

   This article has 5 authors:

   1. Aurélie Anne-Gaëlle Gabriel
   2. Julien Racle
   3. Maryline Falquet
   4. Camilla Jandus
   5. David Gfeller

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents an important computational tool for the quantification of the cellular composition of human tissues profiled with ATAC-seq. The methodology and its application results on breast cancer tumor tissues are convincing. It advances existing methods by utilizing a comprehensive reference profile for major cancer-relevant cell types, compatible with a widely-used cell type deconvolution tool.

   Reviewed by eLife

9. A Deep Learning Pipeline for Mapping in situ Network-level Neurovascular Coupling in Multi-photon Fluorescence Microscopy

   This article has 10 authors:

   1. Matthew Rozak
   2. James Mester
   3. Ahmadreza Attarpour
   4. Adrienne Dorr
   5. Shruti Patel
   6. Margaret Koletar
   7. Mary Hill
   8. JoAnne McLaurin
   9. Maged Goubran
   10. Bojana Stefanovic

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work describes a highly complex automated algorithm for analyzing vascular imaging data from two-photon microscopy. This tool has the potential to be extremely valuable to the field and to fill gaps in knowledge of hemodynamic activity across a regional network. The solid biological application provides a demonstration of their pipeline's capabilities and suggests intriguing hypotheses around prolonged vascular tone changes, but will need to be followed up by further experiments to be conclusively demonstrated.

   Reviewed by eLife

10. Single-cell RNA sequencing of iPSC-derived brain organoids reveals Treponema pallidum infection inhibiting neurodevelopment

    This article has 7 authors:

    1. Qiu-Yan Xu
    2. Yong-Jing Wang
    3. Yun He
    4. Xin-Qi Zheng
    5. Man-Li Tong
    6. Yu Lin
    7. Tian-Ci Yang

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This is a valuable study that describes the effects of T. pallidum on neural development by applying single-cell RNA sequencing to an iPSC-derived brain organoid model. The evidence supporting the claims of the authors is solid, although further evidence to understand the differences in infection rates would strengthen the conclusions of the study. In particular, the conclusions would be strengthened by validating infection efficiency as this can impact the interpretation of single-cell sequencing results, and how these metrics affect organoid size as well as comparison with additional infectious agents. Furthermore, additional functional validations of downstream effectors could be insightful.

    Reviewed by eLife