Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

Abstract

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery.

Inactivation of the HIF-1α/PDK3 Signaling Axis Drives Melanoma toward Mitochondrial Oxidative Metabolism and Potentiates the Therapeutic Activity of Pro-Oxidants

“…PDK3 overexpression in melanoma cell lines was obtained by transfection with pJP1520-PDK3 vector [provided through central repository DNASU (http://dnasu.asu.edu; ref. 23)] DCA, and/or elesclomol were added 48 hours after transfection. HBL cells lacking mitochondrial DNA (HBL r 0 ) were generated as published (24).…”

Annotation of proteins of unknown function: initial enzyme results

“…Plasmids that can express these proteins must be obtained from sources such as DNASU [17–19]. Substrates are then ordered from commercial suppliers such as Sigma-Aldrich.…”

Sustainability in a Hospital-Based Biobank and University-Based DNA Biorepository: Strategic Roadmaps

“…Originally established at the Harvard Institute of Proteomics in 2006 as the PlasmID Repository, the repository moved and re-established itself at ASU in 2009 as DNASU. [7][8][9] The overall goal and mission of DNASU (https://dnasu.org) is to facilitate research by providing high quality, annotated plasmids and resources to the research community and to support research scientists by functioning as a centralized facility to distribute plasmids that they create as part of their research. 9 Plasmids are circular pieces of DNA, each of which contains one or multiple genes, and serve as a useful experimental resource to have stored in and distributed by a centralized repository.…”

“…For example, the National Institute of General Medical Sciences (NIGMS) funded DNASU for 10 years to function at the PSI-MR. [7][8][9] Within this collaboration, DNASU evaluated the full-length DNA sequence of the gene inserts for over 90,000 plasmids from PSI researchers and significantly improved the DNASU website and database to support the distribution of these plasmids. In addition, DNASU was awarded an American Recovery and Reinvestment Act (ARRA) grant to enable the purchase of a Brooks automated freezer storage system.…”

“…A key operational improvement for DNASU was the development of an expedited material transfer agreement (MTA), in which institutions are invited to sign a simplified universal agreement that covers all contents of the repository in advance. 7 Once the institution is a signatory, any member of that institution can obtain a plasmid from DNASU by simply clicking agreement on the webpage, as there is already a signed document from the institution on file. This shortens the turnaround time from ordering to shipping from several weeks or months to only a few days by eliminating the time required to review and sign an MTA.…”