Team:Alberta/Project/Bioinformatics
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- | <h1>Genome | + | <h1>Why a Minimal Genome?</h1> |
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- | <P>One of the most useful applications of the BioBytes assembly method is | + | <P>One of the most useful applications of the BioBytes assembly method is the production of entire genomes. This brings the synthetic biology research community closer to one of its holy grails, the production of a viable synthetic minimal organism. For this reason the BioBytes team has attempted to create the tools and design principles needed to produce a minimal genome.</P> |
- | A minimal genome provides many benefits to the scientific community. Genomes are extremely complex. Producing a minimal genome allows for a better understanding of the function and interaction of cellular components. | + | |
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+ | A minimal genome provides many benefits to the scientific community.</P> | ||
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+ | <li>Genomes are extremely complex. Producing a minimal genome allows for a better understanding of the function and interaction of key cellular components needed for life.</li> | ||
+ | <li>A minimal cell provides a chassis for future research with minimal intracellular inteferents. This makes it the optimum research vector. As <i>Escherichia coli</i> is the most common research vector in modern biology, it only makes sense to attempt to produce a minimal <i>E. coli</i> cell.</li> | ||
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+ | <h2>Genome Design</h2> | ||
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+ | Due to complexity of producing a minimal genome, its development has been shortened into three sections: | ||
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<li>The selection of essential genes to be used in the genome | <li>The selection of essential genes to be used in the genome |
Revision as of 00:43, 21 October 2009
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Why a Minimal Genome?One of the most useful applications of the BioBytes assembly method is the production of entire genomes. This brings the synthetic biology research community closer to one of its holy grails, the production of a viable synthetic minimal organism. For this reason the BioBytes team has attempted to create the tools and design principles needed to produce a minimal genome. A minimal genome provides many benefits to the scientific community.
Genome DesignDue to complexity of producing a minimal genome, its development has been shortened into three sections:
For additional information on Bioinformatics please continue reading, to skip to information on recombination click on the Chromosome Assembly section. The E. coli bacterium (strain MG1655) was chosen as the model organism for the production of this essential genome. Although there many other organisms that have smaller genomes (E. coli contains over 4500 genes) Escherichia coli has been one of the most commonly used laboratory organisms and is very well understood. This will make an E. coli minimal genome more useful to the scientific community than some other organism. |
Determining Essential GenesE. coli has over 4,500 genes. The size and complexity of this genome makes it almost impossible to manually process. An ''in silico'' approach allows for this complex data to be more easily collected, manipulated, and interpreted. Bioinformatics has aided us in accomplishing the following:
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Gene SelectionIn order to produce a preliminary genome list, various databases and papers were used. These were determined through a variety of different experimental methods and have very limited overlap. Each gene must was carefully considered and a gene list of 332 genes was produced. Additionally, 29 genes were found to be essential for the RNA's. |
Metabolic ModelingTo verify that all genes necessary for metabolism are included in our essential gene list, a computer model was used. The Model was produced by the Palson group at the University of San Diego and was used in conjunction with the Cobra Toolbox developed by the System's Biology Research Group. It provides a new "in silico" approach to identifying essential genes. The results from the computational analysis suggests that many more genes are required in order to produce a viable minimal genome. This added an additional 118 essential genes. Together with the Literature Research, 450 genes were found to make up our essential gene list. In order to accomplish this a series of programs were developed to be used with the Cobra Toolbox. These programs allow for '''the determination of any organism's minimal metabolic network.''' The results of the metabolic modeling is currently being researched in the wetlab to demonstrate its accuracy. |