DNA Biology and Bioinformatics summer camp for high school students at Oregon State University

“Did you know that there are millions of DNA building blocks encoded in the genome of a plant? How can scientists possibly study this vast amount of data? With computers! Come and explore the tools of modern biology used to examine the complexities of DNA. This camp will involve hands-on activities where you will extract genetic material from a plant, assemble DNA sequences, identify genes using computers, examine your plant’s genome with visualization software, and test and look at your results in the laboratory. No programming skills required!”

The STEM Academy and Jaiswal laboratory at Oregon State University co-organized a week long (July 15-19, 2013) DNA Biology and Bioinformatics summer camp for high school students. The course was heavily subscribed and 12 students (4 boys and 8 girls) were enrolled on a first-come basis. These highly talented and enthusiastic 9th and 10th grade students came from Crescent Valley High School, (Corvallis, OR) and Philomath High School (near Corvallis, OR) and from as far as Newport High School, (Newport, OR) and Hood River Valley High School, (Hood River, OR). Of these, six students qualified under one or more categories of minority, female, low income and/or first generation pioneer students and received fellowships waiving their course registration fee.

The course involved a mix of lectures and hands-on exercises to learn about plant DNA and bioinformatics. In the lectures they learned about the basics of the genome, DNA, RNA, protein, genetic mutations, genetic markers (SNPs and SSRs), molecular structures, and the genetics and scoring of agronomic traits. The students worked with DNA modeling kits to learn about its structure, components, assembly of the molecule and how mutations occur in the DNA chain. This was followed by an exercise on isolating DNA from two varieties of diploid Einkorn wheat Triticum monococcum a close relative of the modern day bread wheat. A wheat genetic marker, recently-discovered in the Jaiswal laboratory, was PCR amplified from the isolated wheat DNA to illustrate differences between the varieties and learned about the applications of genetic markers in genetic and forensic studies including plant breeding and variety development. Student loading DNA sample in the gel

Using the rice chloroplast genome sequence available from the EMBL data archive as a starting point, students explored bioinformatics software, tools, and databases (including Artemis, Pfam, Cn3D, etc.) scientists use to import and annotate genome sequences to find genes, gene products (proteins), assign function to proteins, compare to other well-known homologous proteins, and model protein 3D structures.

The course ended with a lecture and hands-on exercise focusing on genetics, plant breeding and scoring differences in important agronomic traits (characters/phenotypes) such as the spike structures (seed-bearing parts/fruits) of plants from the Oregon Wolfe Barley population (http://barleyworld.org/oregonwolfe/images/owb-ac-phenotypes).

The course instructors were members of the Jaiswal Lab; Samuel Fox (former postdoc and current biology and bioinformatics faculty in Linfield College), Matthew Geniza (MCB graduate student), Justin Preece (bioinformatician), Laurel Cooper (curator and project coordinator of the Plant Ontology project), Sushma Naithani (faculty member Department of Botany and Plant Pathology and outreach coordinator for Plant Reactome project), and Kari van Zee (Biochemistry and Biophysics Department and program coordinator of the Scientists and Teachers in Education Partnerships-STEPs). The group was led by Pankaj Jaiswal, a faculty in the Department of Botany and Plant Pathology. The successful coordination of the course was led by Cathy Law and her colleagues from the STEM academy.

The funds supporting the course were provided by the National Science Foundation (NSF) funded projects, The Plant Ontology (IOS:0822201) and Gramene: A Comparative Genomics Database (IOS: 1127112).