iPlant Workshop/DNA Subway Day 1

My goals for this workshop:
1.  Look for new curriculum ideas for biology class and biotech class. 
2.  Look for biotechnology independent research idea.
3.  Network with scientists and teachers at high school and college.

The workshop was led by lecturers from Cold Spring Harbor:  Jason Williams and Sheldon McKay(Bioinformatics Experts).

Except for the two coffee breaks and lunch, we worked really hard to learn the DNA subway system in the 9am-5pm session on the first day.  We ran slightly over time but everyone worked very hard. Learning the program took some time.  There were a lot of materials to be covered.  According to Jason, we are to take the parts needed and leave the parts not needed for our classroom.  Some parts can be for all students and some parts can be for the very few that are able to do independent research. 

I learned so much both in content and skill.  I relearned the definition for epigenetics (i.e. histone folding and DNA methylation) from one of the participants' question.  When I go to these sessions, I have to brace myself for more unfamiliar terms because we do not use these terms in regular basis when teaching high school biology.

I also learned that 80% of the human genome actually has some kind of function and they are not considered "junk region."  I already knew that the very small portion coded for protein -  genes, ~ 1.5%.  Now we learned that the other portions are needed for regulation especially for transcription.  There is a good website that I need to read up on http://www.nature.com/encode .  It is a consortium of research papers with information on the non-protein code DNA and how it is used in the cell.  I definitely need to read up on the topic. 

We learned how to use the red line (DNA subway) today - building a gene model.  It was interesting to use the BLASTn and BLASTx to come up with a model.  I can definitely see AP biology class using this program.  Not sure how to incorporate it to my biology x class.  It will take really long time to bulid the gene model.  This can be used  for science fair as well.  Maybe students can figure out the gene model and annotate it and.... maybe publish.  According to the lecturer, corn/maize has not been annotated yet.

The fun part, of course, is the lab work.  I picked up two leaves, one from red hibiscus and one from white with pink trim hibiscus.  I was curious since red one has serrated edge and the white one had smooth edge.  Scientific name for red hibiscus is hibiscus rosa-sinensis.  I should look this one up on Blast to see if they have any data.  We grinded it up then collected DNA using some buffers.  Tomorrow, we will PCR it then it will be sent for sequencing.  How exciting! We will have the data automatically uploaded to our account.  I need to pay close attention to what kind of primer we are using today.  This is something my students can do. 

I have to really start thinking how I can incorporate this into my biology curriculum.  If I don't use it, I lose it.  That was the case with SMART board training.  I just did not have the time to set it up after the presentation.  I really wanted to use it since it has been sitting in our computer lab for a while.