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Notebook dave
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<h1>Dave's Research</h1> | <h1>Dave's Research</h1> | ||
<p>Currently I'm looking into 4 aspects of the transition to yeast:</p> | <p>Currently I'm looking into 4 aspects of the transition to yeast:</p> | ||
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<h2>1. Subcloning Into a Yeast Expression Plasmid</h2> | <h2>1. Subcloning Into a Yeast Expression Plasmid</h2> | ||
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<p>Lucas Argueso claims that this is quite easy.</p> | <p>Lucas Argueso claims that this is quite easy.</p> | ||
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<h2>2. Codon Bias</h2> | <h2>2. Codon Bias</h2> | ||
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<p>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 this <a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev.genet.42.110807.091442">Stanford research paper</a> on codon bias.</p> | <p>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 this <a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev.genet.42.110807.091442">Stanford research paper</a> on codon bias.</p> | ||
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<p>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.</p> | <p>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.</p> | ||
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<ol> | <ol> | ||
<li><a href="http://www.genscript.com/cgi-bin/tools/rare_codon_analysis">This</a> is a tool for analyzing the codon bias of a given protein strand in a specific organism.</li> | <li><a href="http://www.genscript.com/cgi-bin/tools/rare_codon_analysis">This</a> is a tool for analyzing the codon bias of a given protein strand in a specific organism.</li> | ||
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<li><a href="http://www.encorbio.com/protocols/Codon.htm">This</a> gives optimized nucleic acid sequence for a given amino acid sequence.</li> | <li><a href="http://www.encorbio.com/protocols/Codon.htm">This</a> gives optimized nucleic acid sequence for a given amino acid sequence.</li> | ||
</ol> | </ol> | ||
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<h2>3. Gene Synthesis</h2> | <h2>3. Gene Synthesis</h2> | ||
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<p>Chemical synthesis is done by chemically creating the desired sequence. There is a lab on campus which would do this for us if we so desired: <a href="http://www.pmf.colostate.edu/genomics_pricing.html">Chemical Synthesis at CSU</a>.</p> | <p>Chemical synthesis is done by chemically creating the desired sequence. There is a lab on campus which would do this for us if we so desired: <a href="http://www.pmf.colostate.edu/genomics_pricing.html">Chemical Synthesis at CSU</a>.</p> | ||
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<h2>4. Secreting enzyme into beer.</h2> | <h2>4. Secreting enzyme into beer.</h2> | ||
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<p>Guy has done quite a bit of research on secretion/expression vectors. See his page for more information, but here's a useful <a href="https://static.igem.org/mediawiki/2008/2/27/JHU_0708_paper_ForeignGeneExpression.pdf">background article</a>.</p> | <p>Guy has done quite a bit of research on secretion/expression vectors. See his page for more information, but here's a useful <a href="https://static.igem.org/mediawiki/2008/2/27/JHU_0708_paper_ForeignGeneExpression.pdf">background article</a>.</p> | ||
Latest revision as of 23:09, 20 July 2012
|
Edit page
Dave's Research
Currently I'm looking into 4 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 this Stanford research paper on 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. Gene Synthesis
Chemical synthesis is done by chemically creating the desired sequence. There is a lab on campus which would do this for us if we so desired: Chemical Synthesis at CSU.
4. Secreting enzyme into beer.
Guy has done quite a bit of research on secretion/expression vectors. See his page for more information, but here's a useful background article.
