Using DNA Subway in the Classroom Red Line Lesson Sketch

DNA Subway is a suite of bioinformatics tools which have been placed in simplified workflows. These tools allow students to work with the same data (DNA or Protein sequence data) used by biologists. The DNA Subway can be used in the classroom to illustrate the basic principles of molecular biology. Once students have mastered the biological concepts and become familiar with the bioinformatic tools, they can continue to use DNA subway to examine new data, which can result in novel findings.

For each concept you can create 3-4 step lesson plan 1.Choose a 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 be an example of the concept. 3.Use DNA subway to confirm your hypothesis 4.If possible do a “real world” in vivo experiment to demonstrate the concept. DNA Subway teaching model

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

Genomic Annotation with the Red Line Using the Red Line, you can create a lesson plan that will address the following objectives Students can gain understanding on: What a gene is and how it relates 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”) to predict genes How biological evidence (cDNAs, EST, etc.) can confirm predictions

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 ?

Where is the music? Where is the gene?

You could use a visual aid to draw students attention to the ideas like Genes are on chromosomes Genes are written as sequences of ACTGs There is a lot of DNA data and computing tools help us grasp and organize this What is a gene is and how does it relate to DNA ?

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 DNA sequence. What is a gene is and how does it relate to DNA ?

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 ?

Through your use of explanations and analogies, your students should hopefully have 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 ?

What are the components of Genes? Reasoning by analogy we can get students to understand that genes as information bearing structures have a grammar (codons). Paper exercises or analogies can help draw the student to the idea of just how a gene contains information, and just why we use computers to find that information. You can have students look for stop and start codons on paper, and then take them to subway to see how computational power enhances our efforts.

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?

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?

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?

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?

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