Clearing house for DNA gets a boost


October 21, 2011

Arizona State University’s Biodesign Institute is home to a rich trove of biological material. Known as DNASU, this growing storehouse – a sort of genetic Library of Congress – holds over 147,000 plasmids, (circular DNA samples that can be used to produce individual proteins), as well as full genome collections from numerous organisms and proteins associated with many leading human diseases. 

A new $6.5 million grant from the National Institute of Health will help expand a critical component of this genetic archive known as the Protein Structure Initiative-Materials Repository (PSI:Biology-MR).  Download Full Image

The PSI:Biology-MR effort began in 2006 in the laboratory of Joshua LaBaer, then at the Harvard Medical School Institute of Proteomics. LaBaer has directed Biodesign’s Virginia G. Piper Center for Personalized Diagnostics since 2009, where the PSI materials repository has continued its mission of collecting, annotating, storing, maintaining, and distributing plasmids – the design templates for specific proteins created by researchers within the PSI’s multi-institution structural genomics consortium. 

Plasmids are small pieces of DNA, generally of a circular structure. They provide ancillary genetic information in bacteria and prokaryotic organisms, often containing specialized genes for essential functions. Plasmids are a particularly important tool for biotechnology. Researchers use them to study the effect of individual genes in cells or within an organism. Plasmids are also commonly used by researchers as biological flash drives that can be inserted into bacteria to make multiple copies of genes or express genes as proteins. 

Proteins play an essential role in virtually all life processes. As LaBaer explains, expression-ready plasmids are vital to biomedical research, particularly for the study of human health and disease.

“Proteins provide the verbs to biology.  They energize, connect, signal, digest, activate, inactivate, move, transport, and dozens of other activities.  Researchers use plasmids to make these proteins, in order  to learn about what they do and how to regulate them.  Nearly all drugs today act by altering the activity of a protein or are proteins themselves,” LaBaer says.

The field of structural genomics has undergone rapid advance in recent years, due to the increasing availability of sequence data. Such study holds enormous promise for a more complete understanding of the role of proteins both in normal biological processes and in disease. Four large-scale and numerous specialized PSI Centers have created tens of thousands of plasmids containing genes or their fragments to be used for protein expression, purification, crystallization and structure determination. 

As of September 2011, over 50,000 PSI plasmids containing genes from over 890 organisms have been assembled, curated and shared with the research community.

Like a lending library for books, PSI-Biology-MR acts as a global distribution network, delivering plasmids to researchers worldwide, including critical information about the genes they contain, annotations concerning the full length sequence, vector information, and associated publications for cross referencing – all of which are stored in a freely available, searchable database. 

Once the detailed 3-D structure of a given protein has been worked out or ‘solved’ by PSI researchers, the task of unraveling the biological function of the protein can commence. The PSI resources can be used by researchers to study the biochemistry and biological functions of key proteins. Further, expression-ready plasmids for proteins coded by hypothetical genes or genes of unknown function assist biologists in determining the function of these proteins more quickly.

LaBaer says that besides providing these plasmids at a low cost from an easily accessible centralized location, his group has also dramatically simplified the legal process of acquiring plasmids for study; streamlining the Material Transfer Agreement – a necessary contractual document. This was accomplished through multi-institute cooperation, reducing delays for plasmid transfers and accelerating the pace of discovery. 

At the heart of DNASU and the PSI:Biology-MR is the Nexus Universal BioStore Freezer. LaBaer’s team acquired this state-of-the-art storage and robotic retrieval system through funding provided by the American Recovery and Reinvestment Act. The BioStore system is essential for maintaining the integrity of the plasmids, properly tracking the location of each sample in the repository and ensuring rapid and accurate access to these samples. 

Plasmids are stored as glycerol stocks in 2D barcoded tubes at -80 degrees Celsius. The Nexus and repository are integrated for a seamless flow between ordering and plasmid selection; saving time, safeguarding samples from cross-contamination and human error, and accelerating distribution of materials to researchers. The BioStore is capable of storing and retrieving up to 855,000 sample tubes, all managed automatically from a computer.

LaBaer stresses that the integrated PSI:Biology-MR system, including a growing repository of expression-ready plasmids, an automated pipeline, and a rapid process for receiving and distributing plasmids more effectively will be a boon to the community of researchers hoping to dissect the biological functions of proteins: 

”We have always had the philosophy that sharing tools and reagents is critical to accelerating scientific discovery.  It doesn’t make sense for one researcher to have to repeat the work that someone else has already done.  This facility makes sharing easy.”

Richard Harth

Science writer, Biodesign Institute at ASU

480-727-0378

Sun Devils hit the jackpot with Homecoming events at Polytechnic


October 21, 2011

ASU Polytechnic is placing all bets on Homecoming this year with its signature event, Casino Night, Oct. 25. Students from all campuses are welcome to attend the Las Vegas-themed festivity and try their hand at blackjack and poker.

“In addition to all of the standard casino card games and slot machines, we will host a Las Vegas costume contest,” said Alexis Acedo, PABp homecoming director. “From Elvis to Wayne Newton, or even Alan from the Hangover, we can’t wait to see how creative the students can get when it comes to tapping into their inner Vegas.” Download Full Image

Casino Night is from 8 to 11 p.m. in the Student Union ballrooms, dining area and patio. Performances for Open Mic Night also will provide entertainment in the dining area.

Other homecoming week festivities include Chalk the Walk on Oct. 23 where student organizations will show the creative-side of their school spirit. All of the chalk art will be an artistic outlet for students to promote their organizations and programs during the homecoming kick-off event on Oct. 24 in the student union.

“Locks of Love” and “Goin’ Bald for Bucks” are university-wide community service events that will take place at all ASU campuses on Oct. 26. “Locks of Love” is a non-profit organization that helps provide wigs to cancer patients who have lost their hair during chemotherapy. “Goin’ Bald for Bucks” is a symbolic fundraiser where students to shave their heads to show support to the same cause. All students are encouraged to participate in the cause by getting a haircut and donating money. All proceeds donated go directly to a local charity that focuses on cancer awareness.

On Oct. 28 ASU’s College of Technology and Innovation will host its weekly “Thing on Thursday” event as a time for students at the Polytechnic campus to work on Homecoming floats at locations all across campus.

Throughout the week, the Pre-Vet Club at Morrison School of Management and Agribusiness students will hold its annual “Kiss the Pig” contest to raise money for the club. 

“We are really looking forward to celebrating ASU Homecoming on the Polytechnic campus” said Acedo. “Hosting events that are unique to Poly and participating in events that are University-wide promotes our school spirit and gives us a reason to come together for great causes.”