The more than 130 billion nucleotides of DNA sequence residing in Genbank and other databases now challenge biology students to come to grips with the complex genomes of higher organisms. The human genome is chock full of non-coding introns and transposons - as well as a new class of RNA genes - that interact in unexpected and still largely unknown ways to regulate gene expression. Thus, in 2006 we continued our work with CSHL researchers to develop interfaces to DNA databases, which open a window on the strange and wonderful world of genome science.
Dynamic Gene is the educational outreach component of Gramene, an online resource for analyzing and comparing genes from plants in the Gramineae, or grass, family. This group includes the cereal grains that feed most of the world's people - rice, wheat, corn, barley, sorghum, millet, oats, and rye. The site is being developed in collaboration with CSHL genomicists Doreen Ware and Lincoln Stein, as well as three faculty producers: Debra Burhans (Canisius College, Buffalo, NY), Charlie Gutierrez (John H. Reagan High School, Austin, TX), and Bob Wheeler (Pine Creek High School, Colorado Springs, CO).
Dynamic Gene is designed to let students learn about plant genomes by using bioinformatics to analyze newly sequenced genes in rice and maize. Many of these genes have only been predicted by computers and have never been closely examined by human beings! The site's name emphasizes the gene both as a dynamic structure that changes through evolutionary time, but also as a dynamic concept that changes with our increasing knowledge of genome organization. The design for Dynamic Gene recalls the "streamlining movement" that influenced design during the middle of the 20th century with ideas borrowed from aviation and automobile design.
Animated tutorials in the first three sections - Meaning, Structure, and Evidence - illustrate: 1) how DNA sequences encode biological information, 2) how bioinformatics uncovers sequence patterns that predict the structural components of genes, and 3) how computer-generated gene "models" are annotated with gene features and evidence from biological experiments. The Annotation section provides step-by-step instructions on how to analyze a gene model with Apollo, research software that was used to annotate the Drosophila genome. Once students understand the basics of gene annotation, they go to the Projects section to download large DNA sequences from cereal chromosomes. They then pit their logic against the computer that predicted the gene models you encounter and upload their new annotations to share with other researchers.