Notebook dave

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<h1>Dave's Research</h1>

<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>
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    <p>Lucas Argueso claims that this is quite easy.</p>
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<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> 
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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>
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    <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.jcat.de/">Another tool</a> for analyzing the codon bias of a given protein strand in a specific organism.</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>
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<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>
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<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>
    
    

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