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.

{|
 * align="center" style="background:#f0f0f0;"|Gene
 * align="center" style="background:#f0f0f0;"|Modification
 * X||Extract from gene II.
 * VII||Separate from gene IX.
 * VIII||Separate from gene IX.
 * -}
 * VIII||Separate from gene IX.
 * -}
 * -}

{|
 * align="center" style="background:#f0f0f0;"|Abstraction (Functional Unit)
 * align="center" style="background:#f0f0f0;"|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
 * -}
 * A Portion of the Life Cycle||The genes responsible for a certain part of the life cycle
 * -}
 * -}