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Held: Thursday, 8 September 2011
Today we begin to delve more deeply into reasons and techniques for aligning
sequences, particularly DNA sequences.
- For Tuesday, respond to Altschul et al. 1990. This paper is particularly complex, so it's okay if you don't understand everything.
- For Tuesday, start considering the Needleman-Wunsch algorithm.
- The On-Your-Own Project 2.6 is due next Thursday.
- Sam updated the office hours on the course front door.
- EC for Teriak Koscik talk, Thursday, 4:30, Science 3821.
- EC for Football, Saturday, 1 p.m.
- EC for Les Duke, Saturday.
- EC for Volleyball, Saturday at Noon, 4 p.m.
- EC for Men's Soccer, Sunday, 2pm, Coe.
- Biology picnic Friday!
- If you choose to participate in the '80's party, please don't try to replicate the excesses of the '80's.
- Chapter 2 Programming Lab.
- The Sequence Explosion.
- Aligning Sequences: A Biological Perspective.
- Bacteria and Antibiotic Resistance.
- Do the programming lab for chapter 2.
- Keep your groups from Tuesday!
- Most of the questions ask you to design an algorithm and then give you a
Python-based implementation. Please spend the time thinking about how
you would write the algorithm before you look at the code!
- Tons of sequence data! With exponential growth.
- Many model systems
- E. Coli and other bacteria
- Yeast - a single cell eucaryote
- Sequencing the model systems helped us build technoogies that helped with
the Human Genome Project
- Biological techniques.
- Computational techniques.
- Whose DNA is in the human sequence?
- Why should one care about aligning sequences?
- It's up to students to answer this question.
- Side note: 90% of our cells are bacteria (gut, skin, etc.)
- Until this century, many people died from bacterial infection
- Bacteria use our bodies as hosts, reproduce, and kill you
- But they can't kill you too quickly, or it won't spread
- Diarrhea helps bacteria spread quickly, as they get into
the water supply
- Some genes in our genome seem to have been selected b/c they
support bacterial resistance.
- Side note: Allelle that makes you resistant to ___ virus
also makes you more succeptable to West nile.
- In 1929, Fleming identified a fungus that produced an antimicrobial
agent (that we call penicllin)
- Lots of research to efficiently get penicillin
- Rare enough at first that they would harvest the urine of those
treated with penicillin and then re-extract the penicillin
- A variety of Nobel prizes related to penicillin
- Dorothy Crowfoot Hodgkin (1964) - Figured out the crystal structure
- A few more people who helped in designing the technology
- What happens when we apply penicillin to a colony of bacteria?
- Most die
- A few, somewhat resistant ones, survive
- Bacteria duplicate quickly
- These bacteria don't have a lot of competition
- So you get a lot of resistant bacteria
- What does Erythromycin do?
- Binds to ribosome
- Prevents creation of protein
- So, if you change the ribosome a bit (gene ermB), it may
- With any antibiotic, the regular bodily defense systems also
- You want to take the full course of antibiotic to kill as
much as you can, including partially resistant
- You hope the body takes care of the rest
- Danger! Antibiotics invoke SOS responses in bacteria: Higher
rate of mutation.
- Going beyond inheritance: Vertical transfer takes some time, so how do we
get so much transmission
- The environment?