PSI:Biology Profile Archive



PSI:Biology-Materials Repository: Keeping the Wheels of Structure Determination in Motion


PSI:Biology-MR Logo Since the beginning of the Protein Structure Initiative (PSI) over 100,000 protein expression plasmids have been created by PSI researchers, and almost 100 new cloning vectors have been designed and tested. The PSI:Biology-Materials Repository (PSI:Biology-MR), Joshua LaBaer located at the Biodesign Institute at Arizona State University in Phoenix, provides a centralized resource for the worldwide distribution of these resources. Dr. Joshua LaBaer, Director of the Virginia G. Piper Center for Personalized Diagnostics at ASU’s Biodesign Institute, oversees this facility that currently holds 178,000 plasmids, of which 63,000 were developed by PSI Centers. In addition, 97 empty vectors created by PSI researchers are distributed to be used for cloning, bacterial, mammalian, yeast, mycobacterial, or cell-free expression, co-expression, and increased solubility. In addition to Dr. LaBaer, eleven people, nine of whom are full-time, work to keep the facility running and providing the highest quality plasmids and services. Each plasmid is verified using DNA sequencing and annotated by a bioinformaticist, Dr. Jin Park, and Dr. Catherine Seiler, Scientific Liaison, before it is added to the library and released for distribution via the DNASU website.

The PSI:Biology-Materials Repository was established as part of the PSI at the Harvard Institute of Proteomics in 2006 and moved to Arizona in June 2009. Since the move to ASU, technicians have filled 2593 orders for over 111,000 plasmids that were shipped to 47 states and 38 countries (see map below). This works out to an average of ~140 orders every month. To date in 2012, nearly 82,000 plasmids have been distributed.

PSI:Biology-MR distribution map

Database programmers and website designers work together to ensure that the entire collection can be searched by almost any aspect of the vector or plasmid, DyNA vector map such as gene name, vector name, depositing PSI center, PDB ID, or BLAST search using accession numbers or protein or nucleotide sequence. Each of the plasmids in the database are linked to many external databases, including NCBI, species specific websites, the PDB, and the PSI Structural Biology Knowledgebase (PSI SBKB), which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data through TargetTrack. All of this information can be found by clicking on the CloneID in the search output. Recently, a new vector mapping feature was developed by Lab Geni.us and has been added to every page (see picture). The different features of the vector are displayed in this graphic, such as operators, promoters, and restriction sites; all restriction enzymes available through New England Biolabs are hyperlinked to the appropriate product page. Also, when users mouse over other vector features, such as antibiotic resistance genes or protease cleavage sites, boxes pop up to provide more detailed information.

A comprehensive overview of the search capabilities, procedures, and services provided by the PSI:Biology-MR can be found in an online presentation at http://psimr.asu.edu/overview.html. For more information on deposition and distribution of materials, please contact Dr. Catherine Seiler.

Posted November 2012.

Access the PSI:Biology-MR and other PSI resources through the Methods and Technologies Hub of the SBKB.



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