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Transition from a prokaryotic bacteria to yeast.
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2. Codon bias. | 2. Codon bias. | ||
| - | The issue in Codon bias is that different organisms can produce different RNA's much easier. If the RNA used in a codon is uncommon, it is likely to die off. Using the codon bias tools below, there is a strong indication that the Bio-brick UW developed last year uses a lot of RNA uncommon in yeast. It is likely that this strain will die out in yeast very quickly. However, the Codons can be altered to use more common RNA, which would make the odds of replication greater. An optimized sequence is given by the final two links, and I am now investigating methods of synthesizing such a sequence. | + | The issue in Codon bias is that different organisms can produce different RNA's much easier. If the RNA used in a codon is uncommon, it is likely to die off as was shown in the following Stanford research paper: |
| + | [http://www.annualreviews.org/doi/pdf/10.1146/annurev.genet.42.110807.091442 Codon bias]. Using the codon bias tools below, there is a strong indication that the Bio-brick UW developed last year uses a lot of RNA uncommon in yeast. It is likely that this strain will die out in yeast very quickly. However, the Codons can be altered to use more common RNA, which would make the odds of replication greater. An optimized sequence is given by the final two links, and I am now investigating methods of synthesizing such a sequence. | ||
[http://www.genscript.com/cgi-bin/tools/rare_codon_analysis This is a tool for analyzing the codon bias of a given protein strand in a specific organism]. | [http://www.genscript.com/cgi-bin/tools/rare_codon_analysis This is a tool for analyzing the codon bias of a given protein strand in a specific organism]. | ||
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[http://www.encorbio.com/protocols/Codon.htm This gives optimized nucleic acid sequence for a given amino acid sequence]. | [http://www.encorbio.com/protocols/Codon.htm This gives optimized nucleic acid sequence for a given amino acid sequence]. | ||
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3. Secreting enzyme into beer. | 3. Secreting enzyme into beer. | ||
Revision as of 18:00, 8 June 2012
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Currently I'm looking into 3 aspects of the transition to yeast:
1. Subcloning into a yeast expression plasmid.
Lucas Argueso claims that this is quite easy.
2. Codon bias.
The issue in Codon bias is that different organisms can produce different RNA's much easier. If the RNA used in a codon is uncommon, it is likely to die off as was shown in the following Stanford research paper: Codon bias. Using the codon bias tools below, there is a strong indication that the Bio-brick UW developed last year uses a lot of RNA uncommon in yeast. It is likely that this strain will die out in yeast very quickly. However, the Codons can be altered to use more common RNA, which would make the odds of replication greater. An optimized sequence is given by the final two links, and I am now investigating methods of synthesizing such a sequence.
This is a tool for analyzing the codon bias of a given protein strand in a specific organism.
Another tool for analyzing the codon bias of a given protein strand in a specific organism.
This gives optimized nucleic acid sequence for a given amino acid sequence.
3. Secreting enzyme into beer.
Steven is currently taking the lead on this research. See his page for more information, but a useful background article is given below.
https://static.igem.org/mediawiki/2008/2/27/JHU_0708_paper_ForeignGeneExpression.pdf
