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Cold Spring Harbor Laboratory
Outcomes, Challenges, and Resources
Outcomes
- We have developed an integrated labortory and computer system that allows students to examine their own DNA polymophisms, share data via the Internet, and reconstruct human evolution. This learning program is supported by biochemical kits distributed by Carolina Biological Supply Company and bioinformatics tools at the DNALC WWW site.
- We have implemented a large-scale program to bring hands-on genetics into middle school classrooms. The Geneics as a Model for Whole Learning Program involves more than 10,000 students per year from 22 school districts and five private schools in metropolitan New York.
Challenges
- Delivering genetics education to middle schools has required a large commitment of staff time. Four DNALC staff members provide instruction both on-site and in the particpating schools.
- Our effort to popularize the analysis of human DNA polymoprhisms has taken perserverance over more than a decade. We have developed and redeveloped the biochemical system to make it virtually foolproof. This required that we give up thousands of dollars of free reagents and move into a system that cost more but gave far better results. We also abandonned more than five years' of work in one polymorphism system, when a single study suggested a relationship to a human phenotype.
Resources
- Our work to simplify lab techniques for amplifying human DNA polymorphisms in educational settings culminated with the release in 1998 of three Advanced Technology (AT) PCR kits by Carolina Biological Supply Company, the nation's oldest educational science supplier. The kits use a simple 30-minute method to isolate template DNA from hair sheaths or buccal cells and streamlined PCR chemistry based on Pharmacia Ready-To-Go Beads, which incorporate Taq polymerase, deoxynucleotide triphosphates, and buffer in a freeze-dried pellet:
z Human Alu Insertion Polymorphism Kit AT assays for the presence (+) or absence (-) of the Alu transposable element at the PV92 locus on chromosome 16 (Catalog # 21-1232).
z Human VNTR Polymorphism Kit AT assays for a VNTR (variable number of tandem repeats) polymorphism at the pMCT118 locus on chromosome 1 (Catalog # 21-1235).
z Human Mitochondrial DNA Kit AT amplifies a 460-nucleotide sequence within the control region of the mitochondrial genome, which can then be sequenced to show single nucleotide polymorphisms, or SNPs (Catalog # 21-1238).
- In parallel with the lab experiments, we developed a suite of database/statistical applications and easy-to-use interfaces that allow students to use their own DNA data to explore human population genetics and to test theories of human evolution. Database searches and statistical analyses are launched from a centralized workspace. Workshop participants were introduced to these and other resources available at the DNALC WWW site (http://vector.cshl.org/resources/bioservers.html):
z Allele Server tests Hardy-Weinberg equilibrium and statistically compares PV92 data from world populations.
z Sequence Server uses DNA sequence data to search Genbank using BLASTN, compare sequences using CLUSTALW, and create phylogenetic trees using PHYLIP.
z Simulation Server uses a Monte Carlo generator to model the long-term effects of drift, selection, and population bottlenecks.
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