Team:Johns Hopkins-BAG/Synthetic Yeast Genome Project

From 2009.igem.org

(Difference between revisions)

Revision as of 12:58, 21 September 2009

Hello, interchangeable part: Meet your new chassis

Yes, we have quite a collection of interchangeable biological parts for this and that. And sure, they can light up, detect, act, react, and do all sorts of biological gymnastics that would make any biologist feel all warm and fuzzy. However, we need a good chassis to put all these goodies in. iGEM needs a sleek, efficient, and advanced host to showcase all the newly derived luxury, sport, and tow packages. This is where JHU Build-A-Genome's custom Saccharomyces cerevisiae, Sc2.0 comes in. Harnessing the power of undergrad labor, the genome is being synthesized from scratch. A few liberties have been taken in removing junk DNA, and introns to see if these features are really needed. Also, this strain of yeast has been redesigned from the ground up to act as a biological 'goal seek' to find all of the solutions to the fabled minimal genome. The driving force for minimization is supplied by the addition of numerous loxPsym sites between genes throughout the genome. LoxPsym sites act like couplers between train cars allowing additions, deletions, and general reordering of the yeast genes. Cre recombinase acts on loxPsym sites and, depending on local geometry and more likely random chance, allows recombination to occur between any pair of sites. We employ a very specialized engineered Cre-ER chemically regulated by the human sex hormone estradiol so the process can be controlled at will. (Those who attended iGEM2008 will know the JHU Team has a tradition of always inserting the word SEX into its presentations). Such genome reorganization allows for a staggering number of permutations. Most of the genomes in this “swarm” will not survive, but the ones that do can be analyzed. Commonalities and linkages can be drawn by what genes are commonly left behind, with which other genes, and a huge linkage map can be made. This map can lead to the minimal genome as well as the discovery of genes related by their presence in a biological pathway.

An entire chromosome arm “9R” has been synthesized according to our mad scheme and successfully inserted into yeast. Moreover, the native chromosome 9R can be trashed and the cell continues to smile and happily reproduce ad infinitum. Initial testing of the Cre-ER system strongly suggests that recombination occurs when estradiol is added. However, a more visual test is appropriate. A FLO8 gene has been added; this gene allows yeast to grow and organize into “fuzzy” structures similar to mold, technically referred to as pseudohyphae. We are doing experiments to initiate recombination in the presence of both FLO8 and the synthetic chromosome, which contains a number of genes required for fuzziness. A control group of fuzzy yeast (with no synthetic chromosome) should not respond to the addition of hormone. The experimental group should show a reduction in colony count, varying colony size, as well as a mix of fuzzy and non-fuzzy colonies. This should show that recombination is occurring and can be controlled.

@@ Line 1: / Line 1: @@
 {{Template:JHU_BAG_Top}}
 {{Template:JHU_BAG_SideBar}}
-==Building Blocks: A revolution==
+==Hello, interchangeable part:  Meet your new chassis==
-The Johns Hopkins team presents the work of a Build-a-Genome course that fabricates synthetic yeast genome Sc2.0 and provides students tools to meld seamless arrays of DNA into redesigned synthetic chromosomes. Our team is part of a larger effort to develop new technologies and standards for synthetic genomic construction allowing for the production of longer more complicated DNA sequences without certain constraints of current Biobrick standards. By using overlap assembly PCR, followed by Uracil Specific Excision Reaction (USER), and finally, multiple rounds of homologous recombination we create pieces of chromosomes and finally full chromosomes, efficiently and cheaply. We will present improved methodology for building block synthesis, the software created to aid in our synthesis, and applications of the yeast genome redesign, focusing on the implications the Build-a-Genome course has on future genomic technologies that rely on and teach students.
+Yes, we have quite a collection of interchangeable biological parts for this and that.  And sure, they can light up, detect, act, react, and do all sorts of biological gymnastics that would make any biologist feel all warm and fuzzy.  However, we need a good chassis to put all these goodies in.  iGEM needs a sleek, efficient, and advanced host to showcase all the newly derived luxury, sport, and tow packages.  This is where JHU Build-A-Genome's custom Saccharomyces cerevisiae, Sc2.0 comes in.  Harnessing the power of undergrad labor, the genome is being synthesized from scratch.  A few liberties have been taken in removing junk DNA, and introns to see if these features are really needed.  Also, this strain of yeast has been redesigned from the ground up to act as a biological 'goal seek' to find all of the solutions to the fabled minimal genome.  The driving force for minimization is supplied by the addition of numerous loxPsym sites between genes throughout the genome.  LoxPsym sites act like couplers between train cars allowing additions, deletions, and general reordering of the yeast genes.  Cre recombinase acts on loxPsym sites and, depending on local geometry and more likely random chance, allows recombination to occur between any pair of sites.  We employ a very specialized engineered Cre-ER chemically regulated by the human sex hormone estradiol so the process can be controlled at will. (Those who attended iGEM2008 will know the JHU Team has a tradition of always inserting the word SEX into its presentations). Such genome reorganization allows for a staggering number of permutations.  Most of the genomes in this “swarm” will not survive, but the ones that do can be analyzed.  Commonalities and linkages can be drawn by what genes are commonly left behind, with which other genes, and a huge linkage map can be made.  This map can lead to the minimal genome as well as the discovery of genes related by their presence in a biological pathway.
+An entire chromosome arm “9R” has been synthesized according to our mad scheme and successfully inserted into yeast. Moreover, the native chromosome 9R can be trashed and the cell continues to smile and happily reproduce ad infinitum. Initial testing of the Cre-ER system strongly suggests that recombination occurs when estradiol is added.  However, a more visual test is appropriate.  A FLO8 gene has been added; this gene allows yeast to grow and organize into “fuzzy” structures similar to mold, technically referred to as pseudohyphae.  We are doing experiments to initiate recombination in the presence of both FLO8 and the synthetic chromosome, which contains a number of genes required for fuzziness.  A control group of fuzzy yeast (with no synthetic chromosome) should not respond to the addition of hormone.  The experimental group should show a reduction in colony count, varying colony size, as well as a mix of fuzzy and non-fuzzy colonies.  This should show that recombination is occurring and can be controlled.
 {{Template:JHU_BAG_Bottom}}