2012 September 10

==Matters arising==
#Good news-- People are signing in to edit
#Bad news-- Progress on our ENCODE page seems limited. What issues are students encountering?
#Reading online vs using hard copies
#Other challenges or issues?
==ENCODE discussion and content generation==
(continued from last class)
==Review of student contributions==
#Randomizer of Doom: Show us something you've done since last class
==Assignments for Wed 12 September==
#Continue to add and edit content, including class notes for today, chapter 2 exercises, problems, and weblems, concepts and jargon you encounter in chapter 2, and the ENCODE article. We will come back to the encode article later in the semester.
#YFG (your favorite gene): Start a wiki page and write a one-paragraph introduction.
#Identify any issues within Chapter 2 that require clarification or amplification, and bring them to class
==Class Notes==
A General Note:
*J.Burke suggested that we plan to have 3-4 wiki editing session a week for at least 1+ hours at a time.
*Remember to add any and all jargon we come across.
*We discussed free programs for organizing references: Mendeley & Sente.
*Also discussed programs enabling you to highlight and make notes on online journal articles: Adobe, Acrobat.
Summary of recent page contributions:
*Current Phylogenetic Programs: Can be used to compare gene sequences between species. E.g. Geneious, used for clade diagrams, organize sequences. 
*Genetic Counseling: Counseling to assess probability of unborn child having a genetic disease. With more genetic sequences there will be more tools to give exact diagnosis. More genetic testing = more genome sequences!
*ENCODE, the future of: No end in site, expansion to other species.
*Alternative Splicing: generating multiple protein isoforms from the same pre-mRNA sequence
*Landscape Genomics: Fairly new field. Looking at genomes of a certain species with in a certain landscape. Can be used to study migration and disease susceptibility.
*Exercise 2.2: Calico Cats vs. Kangaroos, random x-chromosome silencing vs. paternal x-chromosome silencing.
*Metagenome: Can be used to predict protein function and folding patterns of DNA sequences.
*GATTACA (film): Summary of movie added to wiki.
*Haploid cells were brought up so J.Burke added a page.
*Haplotypes were discussed briefly as we will learn about them more later in the semester.
The ENCODE Project was discussed:
A useful article in understanding the ENCODE project is article #3 on the ENCODE page - A user's guide to the encyclopedia of DNA elements (ENCODE).
What's the purpose of ENCODE? to find genes with function. It is described as a HUGE annotation project indicating where various basepairs are more than just As,Ts,Cs,and Gs by encoding for something.
Phase I was a pilot study to evaluate the feasibility of the methods mentioned below:
chromatin immunoprecipitation: (ChIP) immunoprecipitation of chromatin to discover interactions between proteins and DNA. It is usually used to determine binding sequences of transcription factors, to find origins of DNA replication or histon binding sites. The protein of interest is allowed to bind to the DNA sequence. By using specific antibodies, this protein with the DNA is than extracted. The DNA is purified and its sequence is determined.
Quantitative PCR (RT-PCR): this method allows to follow nucleic acid amplification in real time. RT PCR is commonly used for quantifying gene expression (f.e. gene upregulation).
ENCODE Phase II: What is the full range of methods used in phase II?
ENCODE Criticism: Made an effort to look for protein binding data in many cell lines, but made no effort to make sure those cell lines all came from the same person.
Finished class with GWAS (Genome Wide Association Studies).