Workshop on Stabilization of Biological Materials
When: March 26, 2010
Where: Center for Molecular Genetics (CMG), UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0634.
Time: 10:00am - 12:00noon
Meeting Agenda
10:00-10:10am Welcome by Judy Muller-Cohn, Ph. D., CEO, Biomatrica Inc.
10:10-10:30am Adopting Dry Storage Technology in a Plant Genetics Lab.
Virginia Walbot, Ph. D. andDarren Morrow, Department of Biology, Stanford University, Stanford, CA.
From 1998 through 2003, we generated hundreds of thousands of sequencing templates for EST discovery and for sequencing next to Mu transposable element insertion sites in maize. Many of these resources remain valuable, because the plasmid templates are derived from different inbred lines than the sequenced genome, a B73 inbred line. Our sequencing project provided about 400 - 500 high quality bases for cDNAs and about 800 bases for the right and left flanking sequence of Mu insertion sites. The template plasmids are up to 16 kb in length, therefore, additional sequencing can be used to discover and confirm polymorphisms (SNPs and indels). On the other hand, the Unigene EST collections (best sequence or longest sequence EST unique to a gene) and Mu insertion site library plates in 96-well and 384-well format occupied most of a -80 C freezer. Converting portions of the collection to dry storage and the rest of the collection to -20 C (walk-in freezer room) allowed us to retire one freezer. The dry storage materials occupy a small cube on a desk, are more easily accessed than frozen samples, and should last longer. In addition, they can provide a secondary backup to critical materials (such as RNA) stored at -80C, thereby avoiding the loss of priceless samples due to power loss. We also are participating in the Stanford sustainability freezer project -- unplugging two freezers in return for a newer, more energy-efficient freezer. This extra incentive makes the switch to dry storage even easier. For future high throughput projects, converting finished materials to dry storage will be the logical choice.
10:30 – 10:50 Real-World Testing of Room Temperature Nucleic Acid Storage in a Genomics Laboratory
Wilson Liao, MD, Department of Dermatology, UCSF School of Medicine, San Francisco, CA.
Maintaining the long-term integrity of nucleic acids in the laboratory has traditionally required the use of freezers. However, novel nucleic acid stabilization technologies may allow for the storage of DNA and RNA at room temperature in a cost-effective, environmentally friendly manner. We evaluated the integrity and quality of DNA stored using Biomatrica's DNA SampleMatrix technology against DNA stored in a -20C freezer by performing downstream testing with short-range PCR, long range PCR, DNA sequencing, and genome-wide SNP microarrays. In addition, we tested Biomatrica's RNAstable product for its ability to preserve RNA at room temperature for use in a quantitative reverse transcription PCR assay. Evaluation was performed in the context of a genomics laboratory, with attention paid towards ease of workflow.
10:50–11:10 Challenges and opportunities in shipping patient specimen from participating sites.
Martin Latterich, Ph. D.,,Proteogenomics Research Institute for Systems Medicine (PRISM), 11107 Roselle St, San DIego, CA.
Sampling blood and its derived plasma or serum from a patient is among the least invasive techniques in medical practice. It can be readily obtained in large quantities, and many diagnostic assays have been devised to quantify biomarkers in plasma or serum. While there are standardized phlebotomy isolation and plasma generation protocols used in every clinic, they are generally ill suited for biomarker discovery projects. Slight variations in phlebotomy protocol and timing from blood draw to plasma aliquoting and storage can result into significant changes due to proteolysis of plasma proteins by plasma borne proteases as well as other programmed changes in composition. It is therefore critical, especially in cases when multi-center studies are performed, to adhere to rigorous sampling protocols, and to conduct sample collection with phlebotomy tubes that incorporate a protease inhibitor cocktail to minimize protelolytic changes of plasma during blood draw, processing and subsequent storage . We will provide evidence that outlines the many challenges and opportunities associated with biomarker preservation in clinical specimen, especially blood, and outline a strategy to better preserve clinical specimen for biomarker discovery initiatives.
11:10–11:30 Extremophile Biology leads the path to sustainable bio-specimen stability
Rolf Muller, Ph.D., President & Chief Scientific Officer, Biomatrica, Inc., San Diego, CA.
Biostability is of concern to every biological scientist. Biological samples and reagent quality determines the quality of our research results. New technologies have evolved to study systems biology and high through-put discovery, while our ability to manage bio-specimens has not evolved as much over the past hundred years. Scientists are required to protect their biological samples and reagents from degradation in a cold chain that can be unreliable, often impairs sample quality over time through multiple freeze/thaw cycles, as well as potential freezer break-downs. Extremophile biology can have a tremendous impact on bio-sample stabilization and storage. The use of Taq polymerase is a classic example for the development of the PCR process – extremophile protein stability in thermal vents at 100ºC. How is it possible that Tardigrades can survive in a dry state for 120 years while protecting their DNA, RNA, proteins and cells against degradation and be revived by a drop of water? The study of extremophile biology is a valuable example and a useful biomimicry tool that can help scientists solve issues related to maintaining biological sample integrity. This talk will examine nature’s creativity and how humans can harness such natural occurrences to create new technologies that assist biological research in facilitating efficient assays and pristine samples.
11:30-11:40 Transition to room temperature storage and retirement of -80C freezer
Steven Wasserman, Ph.D., Professor, Department of Biology, UC San Diego, La Jolla, CA.
We will describe how our lab transitioned about 3,000 DNA samples from one of our cold freezers (-80C) to ambient room temperature storage.
11:40-12:00 Q & A
12:00 Meeting Closes
This event will be webcasted. To obtain dial-in instructions, you will need to register for the event by completing the form below:
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