Davidson 2006
From 2006.igem.org
Macampbell (Talk | contribs) (→'''Project Description''') |
Macampbell (Talk | contribs) (→'''Project Description''') |
||
| Line 61: | Line 61: | ||
'''Biology''' | '''Biology''' | ||
| - | • <u>ERIN</u> How can we turn Hin off (using CRE or mutating HIX so that they stop after one reversal)?<br> | + | • <u>ERIN</u> How can we turn Hin off quickly (using CRE or mutating HIX so that they stop after one reversal)?<br> |
| + | • Do we want to be able to turn Hin on and off more than once?<br> | ||
• Should we create a transgenic E. coli with Hin and/or Cre in the chromosome so we won't need so many plasmids?<br> | • Should we create a transgenic E. coli with Hin and/or Cre in the chromosome so we won't need so many plasmids?<br> | ||
• How can we count the number of Flips? (even vs. odd only?)<br> | • How can we count the number of Flips? (even vs. odd only?)<br> | ||
| - | • <u>SABRIYA</u> Does CRE flip once and is then done with that pancake | + | • <u>SABRIYA</u> Does CRE flip once and is then done with that pancake, or will it be excised the next time?<br> |
| - | + | ||
• How many flips would the normal negative supercoiling of a plasmid in ''E. coli'' allow? <br> | • How many flips would the normal negative supercoiling of a plasmid in ''E. coli'' allow? <br> | ||
• Can we alter the amount of negative supercoiling and thus the number of flips if necessary? <br> | • Can we alter the amount of negative supercoiling and thus the number of flips if necessary? <br> | ||
Revision as of 01:04, 30 May 2006
Contents |
Students
• Sabriya Rosemond [1] is a rising junior biology major at Hampton University in VA.
• Erin Zwack [2] is a rising junior biology major at Davidson College in NC.
• Lance Harden [3] is a rising sophomore at Davidson College, who might major in math.
Faculty
• A. Malcolm Campbell [http://www.bio.davidson.edu/campbell Department of Biology], [4]
• Laurie J. Heyer [http://www.davidson.edu/math/heyer/ Department of Mathematics], [5]
Papers of Interest
• [http://www.bio.davidson.edu/courses/synthetic/papers/Sanders_04.pdf Stepwise Dissection of the Hin-catalyzed Recombination Reaction from Synapsis to Resolution. Erin R. Sanders and Reid C. Johnson]
• [http://www.molcells.org/home/journal/article_read.asp?volume=16&number=3&startpage=377 The Effects of Ethidium Bromide and Mg++ Ion on Strand Exchange in the Hin-mediated Inversion Reaction. Hee Jung Lee et al.]
• [http://www.jbc.org/cgi/reprint/267/16/11183 The Effects of Symmetrical Recombination Site hixC on Hin Recombinase Function. Heon Man Lim et al.]
• [http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=3457367 The role of the loxP spacer region in P1 site-specific recombination. Ronald H.Hoess et al.]
• [http://www.biomedcentral.com/1471-2164/7/73 A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination. Perseus I Missirlis et al.]
• [http://nar.oxfordjournals.org/cgi/content/full/30/13/2764 Non-contact positions impose site selectivity on Cre recombinase. Andreas W. Rufer and Brian Sauer]
Project Description
Questions to Resolve
General
• What is our team name and project name?
• What is HU?
• What is the recombinase enhancer (RE; function, sequence, usual position, relationship with HU, etc.)?
• What sort of spacing can RE allow and still work?
• Will we need more than one RE to accomplish recombination at all positions?
Math
• What is the problem we are solving?
• Can we determine more than just Even/Odd number of flips?
• Can we model the distance of RE from pancake vs. time or number of flips
• Can we model the kinetics of n flips?
• Is it possible to simulate the impact of one-time flipping lox/hix sites?
• Help us design the fewest number of constructs that will allow us to scale up the number of flips in our constructs (1, 2, 3, 4...n)
Biology
• ERIN How can we turn Hin off quickly (using CRE or mutating HIX so that they stop after one reversal)?
• Do we want to be able to turn Hin on and off more than once?
• Should we create a transgenic E. coli with Hin and/or Cre in the chromosome so we won't need so many plasmids?
• How can we count the number of Flips? (even vs. odd only?)
• SABRIYA Does CRE flip once and is then done with that pancake, or will it be excised the next time?
• How many flips would the normal negative supercoiling of a plasmid in E. coli allow?
• Can we alter the amount of negative supercoiling and thus the number of flips if necessary?
• What happens to supercoiling if we make the plasmid larger?
• What happens to supercoiling during the stationary phase, relax?
• Can we apply EtBr to relax the number of supercoils and thus stop recombination?
• What should we use as the reporters? Fluorescent vs. Resistant pancake or combinations?
• Possible detection delays for both methods and how to minimize the delays
• Where would biobricks be located?
• How can we gradually scale up the number of flips with the fewest number of constructs?
• Can we use mutated lox or hix sites that will allow single flips?
• Will a segment flip multiple times or will the enzymes move to new sites?
Here's what we'd like to see on your wiki page(s):
- A list of all team members, their roles, and email addresses
- Overview of project(s), including schematics and figures
- Ongoing data/updates about project(s), including schematics, figures, test data, and biobrick parts used
- Some photos of your team, facilities, institution, etc.
- Optionally, anything that broadcasts your team's personality, spirit, sense of fun, or coolness...
