Team:Alberta/Project/Bioinformatics

From 2009.igem.org

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<P>Genomes are complex! Determining how simplified a genome can become enriches our understanding the function and interactions of cellular components. Simplified cells can be used as a well characterized chasses for synthetic biology. Moreover, a simplified cell can be used to study cellular processes in a controlled, characterized genetic background. Finally, developing a minimal genome requires us to develop and optimize molecular methods of genome assembly. These methods can be then applied to other high through put biology. </P>
<P>Genomes are complex! Determining how simplified a genome can become enriches our understanding the function and interactions of cellular components. Simplified cells can be used as a well characterized chasses for synthetic biology. Moreover, a simplified cell can be used to study cellular processes in a controlled, characterized genetic background. Finally, developing a minimal genome requires us to develop and optimize molecular methods of genome assembly. These methods can be then applied to other high through put biology. </P>
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<P> The size and complexity of the genome make bioinformatics analysis essential. We used bioinformatics to accomplish the following: </P>
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<P> - review lists of essential genes in the literature and existing databases and compile a preliminary essential gene list </P>
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<P> - model the metabolic reactions and net growth rate of E.coli with given gene sets. This identified additional metabolic genes essential to a minimal genome. </P>
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<P> - identify knock out combinations that could be tested in the wet lab, to verify the accuracy of our metabolic model. </P>
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<P> - select standardized promoters and terminators that would replace the natural promoters and terminators of essential genes. </P>
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<P> - determine which promoter should be used with which gene, by analyzing expression level data. </P>
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<P> - design primers to amplify all essential genes from genomic DNA. </P>
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<P> These steps have all been completed, and are described on the following pages. </P>

Revision as of 02:47, 11 September 2009

University of Alberta - BioBytes










































































































Why build a minimal genome?

Genomes are complex! Determining how simplified a genome can become enriches our understanding the function and interactions of cellular components. Simplified cells can be used as a well characterized chasses for synthetic biology. Moreover, a simplified cell can be used to study cellular processes in a controlled, characterized genetic background. Finally, developing a minimal genome requires us to develop and optimize molecular methods of genome assembly. These methods can be then applied to other high through put biology.

Presentations

The size and complexity of the genome make bioinformatics analysis essential. We used bioinformatics to accomplish the following:

- review lists of essential genes in the literature and existing databases and compile a preliminary essential gene list

- model the metabolic reactions and net growth rate of E.coli with given gene sets. This identified additional metabolic genes essential to a minimal genome.

- identify knock out combinations that could be tested in the wet lab, to verify the accuracy of our metabolic model.

- select standardized promoters and terminators that would replace the natural promoters and terminators of essential genes.

- determine which promoter should be used with which gene, by analyzing expression level data.

- design primers to amplify all essential genes from genomic DNA.

These steps have all been completed, and are described on the following pages.

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