CHE.496/2008/Responses/a5

Natural biological parts

• Discussion leader: Patrick Gildea (Discussion guide)

Kevin Hershey's Response

• Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
  • Stahler's main focus in this paper is on the development of in situ microarray analysis. Such examples of these array-derived oligos include the Maskless Array Synthesizer and the use of a microfluidic synthesiser platform. He discusses how this new advancement will allow for cheaper and quicker synthetic biology. However, Stahler's definition of synthetic biology is different from the previous papers discussed in this class. He defines synthetic biology simply as "... the making and use of biosystems founded on the synthesis of the coding DNA (and potentially RNA) based upon chemically synthesised nucleic acids oligonucleotides of programmable sequences." However, even though his definition is different than ours, it is still a useful tool to be used in the practice of synthetic biology for the iGEM competition.
• Codon bias and heterologous protein expression
  • Gustaffson's paper deals with codon bias in organisms. In brief, different organisms have a bias towards codons for protein expression. For example, while two different codons may code for one amino acid, they may each work better in different organisms. While Gustaffson points out some areas in which care should be taken (i.e. repetitive sequences), companies such as DNA2.0 offer free software to easily complete codon optimization.
• KPHershey 22:26, 29 January 2008 (CST)

Eyad's Responses

Another side of genomics - This raeding was pretty dense with biological terms and processes that i had to ask my bio friends for explanation, but the gist i got from the reading is that the field has had recent breakthroughs that will lead to cheaper and more powerful synthesis opportunity. Oligonucleotides being one of the cost constraints apparently there have been break throughs to more easily produce desired oligonucleotides.

Codon bias - Its really interesting to know that we now have the ability to line up codons in any order we want because it truly gives us the ability to create our own brand new unique cells whether they work or not. Although its surprising we have this power its surprising that we dont really understand why certain codon chains produce more reliable and more expresses proteins, it almost seems like we are playing with science that could have bigger repercussions then we understand. although it does seem quite simple when its broken down to a cookie cutter recipe of how to more successfully produce proteins in your cell. Eyad Lababidi 12:50, 30 January 2008 (CST)