Download Red line lesson sketch

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.
DNA Subway teaching model
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, 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 vivo: Analyze plants
In vitro: sequence spliceforms
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
What is a gene is and how does it relate to DNA ?
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!
Where is the music?
Where is the gene?
What is a gene is and how does it relate to DNA ?
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
http://www.ncbi.nlm.nih.gov/genome/guide/human/
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 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.
What are the components of Genes?
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
start and stop codons
introns and exons
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
How to confirm with experiment?
Use PCR mutagenesis to add/delete codons