2012 5 September

Matters Arising

1. Good work on the student notes, people!
2. ...but you have to log in to Wikia so I know who gets the credit for editing
3. Textbook availability?
4. Issues, difficulties and questions from students
5. What do you think of the collaborative work on problems?
6. Are we nearly done with Chapter 1?

Review of student contributions

1. Introduction to The Randomizer of Doom
2. Round 1 : Show us something that you've done.

Group Activity (in class)

• My Twitter feed is full of news about ENCODE today. What's going on?
• Do Twitter search #ENCODE
• Identify about 6 subtopics
• Write draft version of one section (student pairs)
• Present to class

Assignments

1. Finish up any remaining work on Chapter 1
2. Edit the ENCODE page that we started in class and turn it into a definitive, up-to-date Wikipedia-style page, complete with references and useful information on useful applications for ENCODE
3. Read Chapter 2 (Download here)
4. Continue adding content to wiki, focusing on Class Notes, and Concepts & Jargon. Feel free to add to other areas where you have interest and/or expertise.
5. Continue editing wiki pages that already have some content.
6. Start on Chapter 2 exercises, problems and weblems
7. Start thinking about the writing project on YFG, and be prepared to discuss your ideas during the next week

Class Notes

The Randomizer of Doom: Class discussed individual contributions to wiki site.

• Chimera: J.Burke added a second paragraph on recombinant DNA technology. We discussed that Chimeras are different than polyploids in that polyploids are meant to have 2 or more chromosomal sets. The offspring of polyploids will have the same chromosomal ploidy, while chimeras, although carrying more than a set of chromosomes, would not naturally inherit the same ploidy. Chimeras are commonly used in lab experiments when cloning or for protein isolation (e.g. HIV proteins). The term chimera is also in regrd to recombinant DNA. In this sense, a chimeric DNA molecule results from enzymatic joining of DNA from one species (e.g. a human) to that of another species (e.g. a cloning vector derived from a bacterial plasmid).
• Transgenic Organism: An organism that contains 1 or more artificially inserted genes. Provides the ability for an organism to express a trait that it normally would not.
• Cancer Genome: Depending on site of cancer genome can be very different to another cancer genome from that sema site. For example, its been studied that Sarcome has little variation across vcancer genomes, however skin neoplams is higly variable.
• model organism: it is possible to use model organisms for more studies, not only for studies of one subset. Model organisms, used for studies with relevance to human beings, are mice, pigs and chimpanzees. Experiments with chimpanzees are very expensive, it is impossible to do experiments with a larger number of animals and there is an obvious ethical problem in their usage. Pigs are used as model organisms for human studies based on the fact, that they are fyziologically and anatomically simillar to humans. Mice are the most commonly used model organisms. Important factors to consider when using a model organism are: (1) Level of inbreeding, (2) time to reproductive age, (3) generation turnover, (4) money, and (5) moral implications.
• To by-pass the high costs of animal research, some pharmaceuticals with approved drugs invest in "repurpose of drugs" research. This is when it is tested if drugs that have already been tested on animals for human use can be useds towards other issues/diseases.
• ENCODE - Encyclopedia of DNA elements. The goal of the projects is to identify all functional elements in the human genome. On September 5, 2012, ENCODE published 30 papers on their findings that were created by ~440 different scientists. A summary of all their work can be found in the journal Nature.
• Exercises: Question 1.5. In the book, Box 1.1 on p.6, was misleading with their genetic code diagram. It is meant to match RNA sequences not DNA sequences. ie. substitute a u in for all t's. This question was answered correctly on the wiki page.
• ....