User:Mgethers/2.27.09 Refactoring Work

2.27.09 Refactoring Work

My refactoring work generally followed the guidelines set out by Chan et al's "Refactoring T7". I started by designing [BBa_M31530] directly from the germane promoters, RBSs, and ORFs. As an exercise in abstraction, I then started defining more complex functional units. First I defined a gene with its transcriptional and translational regulatory regions as a part. In this way, I don't have to think about how the gene is expressed so much as the end result. An example is [Gene X (BBa_M31532)]. By the same token, I was able to create functional units of several genes related by their functions. For example, I created [BBa_M31538] which is made of all the genes responsible for gene amplification of M13K07 while in a host and I made [BBa_M31540] for phage coat proteins. Within each of these, I attempted to address the possibility of intergenetic cross-talk by introducing transcriptional terminators between the genes [BBa_0015]. From my work with Heather Keller, I also know that hair pins (5' and 3' UTRs) can play a role in stabilization of DNA and posit that they may be helpful in preventing recombination events. I was unable to locate hairpins as parts in the registry, but I would like to add and make use of them in my refactored M13K07.

Here are a few tables of my work.

Gene	Modification
X	Extract from gene II.
VII	Separate from gene IX.
VIII	Separate from gene IX.

Abstraction (Functional Unit)	Components of Functional Unit
The Regulatory/Coding Region	Strings of DNA
The Gene	The Promoter, RBS, and ORF
A Portion of the Life Cycle	The genes responsible for a certain part of the life cycle