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High School Students Genotype Einkorn Wheat Varieties in DNA Biology Summer Camp at Oregon State University. Our 2nd STEM camp

Twelve students (9th-12th grade) from local schools attended DNA Biology Summer Camp organized by Jaiswal laboratory at Oregon State University in July 2014. The activities in the camp included short introductory lectures and follow up exercises using models and laboratory experiments. The learning in a collaborative environment was encouraged to further enrich their camp experience. Dr. Laurel Cooper, a research associate in the Jaiswal laboratory, introduced the students to the basics of the plant cell, and genetic material. Using a plant cell model, students identified the parts of the plant cell, including the subcellular structures such as organelles. In the following hands-on exercise using DNA model kits, they constructed a DNA sequence and its complementary strand, and then worked together as a group to form a double helix molecule. These exercises demonstrated how DNA, RNA, and proteins are all related and how they are responsible for the various functions of living cells.

Matthew Geniza, a graduate student in the Jaiswal lab, explained various types of mutations, the concept of genetic markers (SNPs and SSRs), and how the polymerase chain reaction (PCR) can be used to detect differences in the DNA sequences of two closely related individuals or plant varieties. To illustrate these principles and gain practical experience, students genotyped two varieties (G3116 and DV92) of Einkorn wheat (Triticum monococcum). OSU STEM camp students at building the DNA chain

Einkorn wheat has a diploid genome, and is a close relative of hexaploid common wheat. Thus, it is often used as a model to study wheat genetics. Einkorn wheat, Triticum monococcum, originated around the Karacadağ Mountains in Turkey, and is one of the few crops that were domesticated by early agriculturists prior to 7000 B.C. during the Neolithic period. Triticum monococcum G3116 is a wild winter wheat, while, DV92 is the domesticated spring wheat. The wild accessions normally have brittle rachis that allows plant to disperse seed over a span of a few months, which helps it to survive in nature. But in order to maximize the crop yields, humans selected for tough rachis to avoid seed loss. Other traits that were selected for were plumper seeds, and for break of dormancy.

Under the supervision of Matthew Geniza and Dr. Sam Fox (former postdoc of Jaiswal and now a Faculty at Linfield College), students isolated genomic DNA from the G3116 and DV92 seedlings and genotyped the two varieties by PCR amplifying a known SSR marker and analyzed the DNA fragments using agarose-gel electrophoresis. This marker was identified in the Jaiswal laboratory by sequencing and assembly of transcriptomes of G3116 and DV92 varieties published recently (Fox et al 2014).

DNA Biology summer camp was a collaborative effort of the Gramene project, and Plant Ontology project, with Oregon State University STEM Academy. The 9th-12th graders were from various local high schools including Crescent Valley High School, Corvallis High School, Philomath High School, and Lebanon High School. Other participants included one home-school student from halsey, OR and one international student visitor. Dr. Pankaj Jaiswal, Associate Professor at Oregon State University, led the instruction, planning and coordination of this course. Dr. Cathy Law, Director of the STEM Academy at OSU, coordinated student enrollment and logistics. Funds for this course were provided by the National Science Foundation (NSF) funded projects; The Plant Ontology (IOS:0822201) and Gramene: A Comparative Genomics Database (IOS: 1127112).

News source: Source: Gramene News (http://www.gramene.org/node/311)

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. Student loading DNA sample in the gel 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.

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).

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