1. Using DNA Subway in the Classroom Red Line Lesson Sketch

2. Bioinformatics tools in simplified workflows. Students work with same data and computational tools used by biologists. Can be used to illustrate basic principles of molecular biology. Can be used to examine new data and generate novel findings.

3. For each concept you can create 3-4 step lesson plan 1.Choose concept that can be illustrated in terms of genomic biology (e.g. “genes are spliced”). 2.Select (or have students research) a real example of a gene that may/may not illustrate the concept. 3.Use DNA subway to confirm/falsify your hypothesis. 4.Do a “real world,” in vivo experiment to demonstrate the concept. DNA Subway teaching model

4. DNA Subway teaching model, example What is alternative splicing? Concept: Many genes are spliced Example: Jasmonate signaling In silico discovery 1: discover splicing In silico discovery 2: discover alternative splicing In vitro: sequence spliceforms In vivo: Analyze plants

5. Genomic Annotation with the Red Line Use Red Line to create a lesson plan that addresses these objectives: 1) Students can gain understanding on: What is a gene and how does it relate to DNA What are the components of genes Dogma of molecular biology; DNA – RNA – Protein How genes can “code for” proteins How statistical models (“mathematical evidence”) help predict genes How biological evidence (cDNAs, ESTs, etc.) can confirm predictions 2) Students learn to handle a bioinformatics workflow: Set up a bioinformatics project Select appropriate analysis steps Conduct an analysis Verify results

6. It is not surprising that many students have difficulty expressing a tractable definition of what a gene is given that the science of genomics recently outpaces the adoption of new textbooks. Nice bits of trivia, but maybe not immediately useful for students! What is a gene is and how does it relate to DNA ?

7. Where is the music? Where is the gene?

8. You could use a visual aid to draw students attention to the ideas like Genes are located on chromosomes Genes are written as sequences of ACGTs Data and computing tools help us grasp and organize the information http://www.ncbi.nlm.nih.gov/genome/guide/human/ What is a gene is and how does it relate to DNA ?

9. This map can allow student to appreciate some of the complexity of the genome. Clicking on links to sequence confirms a relationship between something called a gene and a sequence of ACGTs. What is a gene is and how does it relate to DNA ?

10. You can also use GenBank to show how looking at specific gene sequences is not so informative … How does this information relate to anything? How does this make a plant? What is a gene is and how does it relate to DNA ?

11. Through your use of explanations and analogies, students will hopefully develop at least a vague concept of what a gene is, which we can focus along three dimensions. - It has to do with chromosomes (locus) - Its made from bases of DNA (composition) - It is a set of instructions or contains information (qualia) We should start answering more advanced questions about what composes a gene. -Codons, especially start and stop codons. What is a gene is and how does it relate to DNA ?

12. First, use DNA subway to show how we can reveal features of a sequence. Create a project using a sample sequence. Once students have mastery, they can come back and create their own projects using real data. What are the components of Genes?

13. Using the synthetic contig as our example, take students through project creation and run repeat masker and on of the gene prediction algorithms ( Augusts and FGenesH) then open Apollo. What are the components of Genes?

14. In stepwise fashion, you can use the synthetic contig in Apollo to introduce the following component concepts introns and exonsstart and stop codons What are the components of Genes?

15. As you add components of evidence, you can discuss how these predictions are made and the need for biological evidence biological evidence Codons, UTRs, reading frames, splicing What are the components of Genes?

16. How to confirm with experiment? Use PCR mutagenesis to add/delete codons