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• Bruce Blumberg– 2113E McGaugh Hall - office hours Wed 11-12 AM (or by appointment)– phone 824-8573– [email protected]
• TA – Curtis Daly– 2113 McGaugh Hall, 924-6873, 3116
• check e-mail and noteboard daily for announcements, etc..– If you do not have ready access to e-mail or the web speak with me
ASAP– Please use the course noteboard for discussions of the material
• I will post all questions received via e-mail on the course noteboard
• If you object to your question being posted please indicate this clearly in the message..
• lectures will be posted on web pages after lecture – http://eee.uci.edu/04s/05705/ - link only here– http://blumberg-serv.bio.uci.edu/bio145b-sp2004– http://blumberg.bio.uci.edu/bio145b-sp2004
Midterm 40%Final exam 40%Term paper 10%Participation 10%
attendance, class discussion, paper presentation
• 20-30 minute presentation and discussion of a journal article is required• These will be randomly assigned• There are more papers than students – possibility for extra credit
• Meet with me during week 1 or 2 to discuss and get paper topic approved
• Attendance and participation is important• Please come to class having read assigned material
• Final examination will not be cumulative, however, understanding of concepts and techniques from first part of course is required.
• Select a topic related to genomic or proteomic analysis of an interesting problem– Talk with me about your topic
• Write a short paper (~5 pages) in the style of a research grant describing how you will attack this problem (I will post an example).– Specific aims – questions, hypotheses– Background and significance
• What is known, what remains to be learned• why should someone give you money to study this problem?
– Research plan – specific experiments to answer the questions posed in specific aims
Requirements for the oral presentation• Goal – again to get you to think more analytically
– Exposure to literature (classic and current)– Learn critical reading– Discuss practical applications of what we are learning
• Powerpoint (“journal club”) presentation – as a presenter– 20 minutes with time allowed for discussion (max of 15 – 20 slides)– Frame the problem – what is the big picture question?
• What was known before they started? What was unknown?• Present background (few slides), handouts helpful but not
required– What are specific questions or hypotheses to be tested
• Discuss figures– What is the question being asked in each figure or panel?– What experiments did the authors do to answer questions?– Do the data support the conclusions drawn?
» Were controls done?• What did they conclude overall?• What could have been improved?
– Point out a few papers for further reading (reviews, followups, etc)
Lecture Outline 4/6/2004 – Organization and Structure of Genomes
• Today’s topics– Genome complexity– Implications of split genes for protein diversity– Repetitive elements and gene evolution
• The big picture – how are genomes similar and different?
• This week’s papers – Two groups discover introns and win the Nobel prize in Physiology or Medicine (1993)– Authors of your book do not cite either paper - Hmm what’s up
with that?• Beget et al., August (PNAS) (adenovirus)• Chow et al., September (Cell) (adenovirus)• Breathnach et al., November (Nature) (chicken)• Jeffreys and Flavell, December (Cell) (rabbit)
Origins of intron/exon organization• Exon number tends to increase with increasing organismal complexity
– Possible reasons?• Longer time to accumulate introns?• Genomes are more recombinogenic due to repeated sequences?• Selection for increased protein complexity
– Gene number does not correlate with complexity– Ergo, it must come from somewhere
Evolution of gene clusters• Many genes occur as multigene families (e.g., actin, tubulin, globins,
Hox)– Inference is that they evolved from a common ancestor– Families can be
• clustered - nearby on chromosomes (α-globins, HoxA)• Dispersed – on various chromosomes (actin, tubulin)• Both – related clusters on different chromosomes (α,β-globins,
HoxA,B,C,D)– Members of clusters may show stage or
tissue-specific expression • Implies means for coregulation as well