1. Biochemistry and Chemical Biology
  2. Cell Biology
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Science Forum: The Brazilian Reproducibility Initiative

  1. Olavo B Amaral  Is a corresponding author
  2. Kleber Neves
  3. Ana P Wasilewska-Sampaio
  4. Clarissa FD Carneiro
  1. Federal University of Rio de Janeiro, Brazil
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Cite this article as: eLife 2019;8:e41602 doi: 10.7554/eLife.41602

Abstract

Most efforts to estimate the reproducibility of published findings have focused on specific areas of research, even though science is usually assessed and funded on a regional or national basis. Here we describe a project to assess the reproducibility of findings in biomedical science published by researchers based in Brazil. The Brazilian Reproducibility Initiative is a systematic, multi-center effort to repeat between 60 and 100 experiments: the project will focus on a set of common laboratory methods, repeating each experiment in three different laboratories. The results, due in 2021, will allow us to estimate the level of reproducibility of biomedical science in Brazil, and to investigate what the published literature can tell us about the reproducibility of research in a given area.

Data availability

All data cited in the article is available at the project's site at the Open Science Framework (https://osf.io/6av7k/).

The following data sets were generated

Article and author information

Author details

  1. Olavo B Amaral

    Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    For correspondence
    olavo@bioqmed.ufrj.br
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4299-8978
  2. Kleber Neves

    Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    Competing interests
    The authors declare that no competing interests exist.
  3. Ana P Wasilewska-Sampaio

    Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    Competing interests
    The authors declare that no competing interests exist.
  4. Clarissa FD Carneiro

    Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8127-0034

Funding

Instituto Serrapilheira

  • Olavo B Amaral

CNPq

  • Clarissa FD Carneiro

The project's funder (Instituto Serrapilheira) made suggestions on the study design, but had no role in data collection and interpretation, or in the decision to submit the work for publication. K. N. and A.P.W.S. are supported by post-doctoral scholarships within this project. C.F.D.C. is supported by a PhD scholarship from CNPq.

Reviewing Editor

  1. Peter A Rodgers, eLife, United Kingdom

Publication history

  1. Received: September 3, 2018
  2. Accepted: January 25, 2019
  3. Accepted Manuscript published: February 5, 2019 (version 1)
  4. Version of Record published: February 13, 2019 (version 2)

Copyright

© 2019, Amaral et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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Further reading

    1. Biochemistry and Chemical Biology
    Neha Puri et al.
    Research Article Updated

    In many bacteria and eukaryotes, replication fork establishment requires the controlled loading of hexameric, ring-shaped helicases around DNA by AAA+(ATPases Associated with various cellular Activities) ATPases. How loading factors use ATP to control helicase deposition is poorly understood. Here, we dissect how specific ATPase elements of Escherichia coli DnaC, an archetypal loader for the bacterial DnaB helicase, play distinct roles in helicase loading and the activation of DNA unwinding. We have identified a new element, the arginine-coupler, which regulates the switch-like behavior of DnaC to prevent futile ATPase cycling and maintains loader responsiveness to replication restart systems. Our data help explain how the ATPase cycle of a AAA+-family helicase loader is channeled into productive action on its target; comparative studies indicate that elements analogous to the Arg-coupler are present in related, switch-like AAA+ proteins that control replicative helicase loading in eukaryotes, as well as in polymerase clamp loading and certain classes of DNA transposases.

    1. Biochemistry and Chemical Biology
    Alan Rodriguez Carvajal et al.
    Research Article

    The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase for linear/Met1-linked ubiquitin chain formation. One of the LUBAC components, HOIL-1L, was recently shown to catalyse oxyester bond formation between ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. Here, we present the first 3D reconstruction of human LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that this event depends on HOIL-1L catalytic activity. By cross-linking mass spectrometry showing proximity between the catalytic RBR domains, a coordinated ubiquitin relay mechanism between the HOIP and HOIL-1L ligases is suggested. In mouse embryonic fibroblasts, these heterotypic chains were induced by TNF, which is reduced in cells expressing an HOIL-1L catalytic inactive mutant. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains by the concerted action of HOIP and HOIL-1L.