Open data partnership leads to release of data from Nobel Prize-winning laboratory for public use
24 Oct 2012
Over the last decade an ENU mutagenesis program was operated by the Beutler laboratory at The Scripps Research Institute in La Jolla, CA. The laboratory has recently moved to UT Southwestern Medical Center in Dallas, TX, where this work has continued. The aim of this program was to create random, inheritable, mutations and link these mutations to phenotypes, physical characteristics and identifiable disruptions in cellular function. The main focus has centered on the immune system, extending studies of innate and adaptive immunity that won Bruce Beutler, Jules Hoffmann, and Ralph Steinman The Nobel Prize in Physiology or Medicine 2011. However this data set has many more applications throughout biology and medicine.
Through its innovative partnership with LabArchives, a provider of online lab notebook software, BioMed Central’s open access journal BMC Research Notes has published Mutagenetix, an online open access repository of ENU-generated data. The data, which underpin the Beutler Lab’s discoveries, match gene mutation via location, structure, and function of the mutated protein, to physical and cellular changes in mice. The dataset is published through the LabArchives platform and is linked permanently to a ‘Data Note’ article published in BMC Research Notes. The Mutagenix database, is available for reuse by other scientists freely, under a Creative Commons waiver. Together these resources can be used to suggest potential mechanisms behind human diseases.
Prof Beutler, explained, “Over a period of eleven years we accumulated hundreds of mutations, induced in the mouse genome using the germ line mutagen ENU. Some of these mutations caused striking phenotypes, and broke new ground in immunology, metabolism, neuroscience, and basic cell biology. In effect, we created many new genetic disease in mice, most of which are also represented in humans. Other mutations were not known to cause phenotypes, and were identified ‘incidentally.’
He continued, “The dataset we have acquired allows us to make strong inferences about how mutagenesis works. For example, how likely it is that an amino acid change induced by ENU will cause phenotype? Does ENU attack DNA randomly, or is it somewhat biased? Our data also provide the basic information needed to model mutagenesis in vitro, to predict just how many genes will be damaged or destroyed in a given population of mice.”
Iain Hrynaszkiewicz, from BioMed Central commented, “This is an excellent example of how valuable publishing datasets with accompanying journal publications can be. As a result of our partnership with LabArchives, data which extend the Beutler lab’s Nobel Prize-winning discoveries are available for public use, and the data are put into context with an associated peer-reviewed journal publication in BMC Research Notes. Also, the authors exemplify best practice in linking data to publications and in data citation, which we hope will help motivate more scientists and funders of research to publish their data in an open access environment.”
All of the phenotypes and their accompanying mutations are described in detail at
http://mutagenetix.utsouthwestern.edu, and in the LabArchives notebook http://dx.doi.org/10.6070/H4VD6WC9.
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Notes to Editors
1. ENU-induced phenovariance in mice: inferences from 587 mutations
Carrie N Arnold, Michael J Barnes, Michael Berger, Amanda L Blasius, Katharina Brandl, Ben Croker, Karine Crozat, Xin Du, Celine Eidenschenk, Philippe Georgel, Kasper Hoebe, Hua Huang, Zhengfan Jiang, Philippe Krebs, Diantha La Vine, Xiaohong Li, Stephen Lyon, Eva Marie Y Moresco, Anne R Murray, Daniel L Popkin, Sophie Rutschmann, Owen M Siggs, Nora G Smart, Lei Sun, Koichi Tabeta, Wataru Tomisato, Victoria Webster, Sungyong Won, Yu Xia, Nengming Xiao and Bruce Beutler
BMC Research Notes 2012, 5:577 doi:10.1186/1756-0500-5-577
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