Team:Rice University/RESULTS

From 2008.igem.org

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(A. Genetic Engineering and Part Construction)
(C. HPLC Data)
 
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[[Image:ProjectTitle.jpg]] <BR>
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[[Team:Rice_University/OUR TEAM|OUR TEAM]] :::
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[[Team:Rice_University|SUMMARY]] :::  [[Team:Rice_University/BACKGROUND|INTRODUCTION]] :::  [[Team:Rice_University/STRATEGY|STRATEGY]] :::  [[Team:Rice_University/RESULTS|RESULTS]] :::  [[Team:Rice_University/CONCLUSIONS|ONGOING WORK]]  
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[[Team:Rice_University/OUR TEAM|OUR TEAM]]:::[[Team:Rice_University|SUMMARY]] :::  [[Team:Rice_University/BACKGROUND|BACKGROUND]] :::   
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[[Team:Rice_University/STRATEGY|STRATEGY]] ::: [[Team:Rice_University/CONSTRUCTS|CONSTRUCTS]] :::  [[Team:Rice_University/RESULTS|RESULTS]] :::  [[Team:Rice_University/CONCLUSIONS|ONGOING WORK]]
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=== A. Genetic Engineering and Part Construction===
=== A. Genetic Engineering and Part Construction===
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    <p>''Saccharomyces cerevisiae'' are widely used for baking and brewing, and they are particular useful for synthesizing metabolites under fermentation conditions which prevent the air oxidation of many useful compounds. To achieve our project and expand the synthetic biology toolbox for programming yeast, we have introduced into the iGem registry BioBricks encoding 3 yeast promoters, 3 yeast terminators, a two micron origin of replication, 2 selectable markers, 2 enzymes, and a yeast integration plasmid. In addition, we have generated seven constructs using these parts.  Furthermore, we have submitted two additional parts representing a foundational tool, including a gene encoding an amber suppressed RFP biobrick for screening of SupF+ (Amber suppressor) genotype and an amber suppressor tRNA biobrick. <br />
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A detailed summary of parts, design considerations, and genetic engineering progress can be accessed at the [[Team:Rice_University/CONSTRUCTS|CONSTRUCTS]] page.
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    </p>
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    <h2>Yeast Regulator Biobricks</h2>
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    <p>Three unique constitutive and repressible yeast promoters were introduced into the registry. </p>
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    <table width="756" border="1">
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  <caption>
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        Yeast Promoters
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      </caption>
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      <tr>
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        <td width="120">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122000 BBa_K122000]</td>
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        <td width="118">pPGK1</td>
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        <td width="466">This is the 1500 bp upstream of the PGK1 coding region in an industrial yeast strain. Constitutive promoter. </td>
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        <td width="24">1497</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122002 BBa_K122002]</td>
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        <td>pADH1</td>
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        <td>700bp upstream of ADH1 promoter region  containing RBS. Constitutive promoter.</td>
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        <td>701</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122001 BBa_K122017]</td>
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        <td>pGAL1 + tetO</td>
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        <td>The GAL1 promoter which is highly repressed by glucose. An additional  tetracycline operator site was included upstream of the RBS to allow  repression by tetR.</td>
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        <td>484</td>
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      </tr>
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    </table><BR>
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    <p>Four additional yeast terminators were introduced into the registry. </p>
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    <table width="756" border="1">
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    <caption>
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        Yeast Terminators
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      </caption> <tr>
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        <td width="115">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122003 BBa_K122003]</td>
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        <td width="74">tCYC1</td>
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        <td width="493">300bp downstream the CYC1 coding region in a standard yeast strain.</td>
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        <td width="46">300</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122004 BBa_K122004]</td>
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        <td>tADH1</td>
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        <td>300bp downstream the ADH1 coding region in a standard yeast strain.</td>
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        <td>300</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122013 BBa_K122013]</td>
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        <td>tPGK1</td>
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        <td>1000bp downstream the PGK1 coding region in an industrial yeast strain.</td>
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        <td>1000</td>
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      </tr>
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    </table>
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    <p>&nbsp;</p><BR>
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    <h2>Selectable Markers</h2>
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    <table width="756" border="1">
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      <caption>
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        Selectable Markers
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      </caption>
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      <tr>
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        <td width="115">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122001 BBa_K122018]</td>
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        <td width="74">ZeoR</td>
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        <td width="493">Zeocin Resistance Gene</td>
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        <td width="46">300</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122008 BBa_K122008]</td>
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        <td>BleoR</td>
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        <td>Bleocin Resistance Gene under pTet promoter</td>
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        <td>800ish</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122014 BBa_K122014]</td>
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        <td>ORI+HisTag</td>
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        <td>2 Micron ORI and Histadine Tag </td>
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        <td>&lt;9000</td>
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      </tr>
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    </table>
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    <p>&nbsp;</p><BR><BR>
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    <h2>Project Specific Constructs</h2>
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This year's project involved the integration of 4-coumarate:coenzyme A ligase/ stilbene synthase fusion protein, a tyrosine ammonia lyase, and a zeocin resistance selectable marker. For more information, please visit [[Team:Rice_University/STRATEGY|Strategy]].
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Please visit our [[Team:Rice_University/NOTEBOOK|Notebook]] for a summary of labwork and protocols.<BR><BR>
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<BR>
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    <table width="756" border="1">
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      <tr>
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        <td width="113">[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122001 BBa_K122001]</td>
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        <td width="451">[pGAL1][tetO][ZeoR]</td>
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        <td width="74">[[Image:C2.jpg|120px]]</td>
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        <td width="90">&nbsp;</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122005 BBa_K122005]</td>
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        <td>Tyrosine Ammonia Lyase</td>
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        <td>[[Image:TAL.jpg|50px]]</td>
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        <td>&nbsp;</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122010 BBa_K122010]</td>
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        <td>4CL:STS</td>
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        <td>[[Image:4CL.jpg|50px]]</td>
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        <td>&nbsp;</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122012 BBa_K122012]</td>
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        <td>[pPGK1][4CL:STS][tCYC1]</td>
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        <td>[[Image:C1.jpg|150px]]</td>
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        <td>&nbsp;</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122015 BBa_K122015]</td>
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        <td>[pGAL1][tetO][ZeoR][tADH1]</td>
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        <td>[[Image:C2.jpg|150px]]</td>
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        <td>&nbsp;</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122021 BBa_K122021]</td>
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        <td>[pADH1][TAL][tPGK1]</td>
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        <td>[[Image:C3.jpg|150px]]</td>
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        <td>&nbsp;</td>
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      </tr>
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      <tr>
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        <td>[http://partsregistry.org/wiki/index.php?title=Part:BBa_K122016 BBa_K122019]</td>
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        <td>[pPGK1][4CL:STS][tCYC1][pGAL1][tetO][ZeoR][tADH1]</td>
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        <td>[[Image:C1C2C3.jpg|350px]]</td>
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        <td>&nbsp;</td>
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      </tr>
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    </table>
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    <p>&nbsp;</p><BR>
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    <h2>Additional Bacterial Parts</h2>
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<BR>
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Novel Zero Leak Inverter Concept
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[[Image:arfp_spun_down.jpg|300px|left]]
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[[Image:arfp_spun_down_fluorescence.jpg|300px|center]]
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<center>wtRFP in SupF- / ARFP in SupF- /wtRFP in SupF+ / ARFP in SupF+</center>
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<BR>
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    <h2><br />
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    </h2><BR>
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Please visit our [[Team:Rice_University/NOTEBOOK|Notebook]] for a summary of labwork, protocols, and overviews of progress.<BR>
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=== B. Yeast Transformation ===
=== B. Yeast Transformation ===
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We are currently accumulating data for plasmid transformations into our brewing strain, SAB-Hefe. Data will be updated soon. <BR><BR>
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=== C. HPLC Data===
=== C. HPLC Data===
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To analyze our beer samples for resveratrol content, be will be using '''H'''igh '''P'''erformance '''L'''iquid '''C'''hromatography (HPLC), which will allow us to separate the metabolites produced by the yeast and analyze these compounds by spectrophotometry. By comparing HPLC chromatogram peaks of metabolites produced by our yeast with a resveratrol-only standard, we can identify if resveratrol is being produced, and at what quantities. Below, we show our initial data for HPLC calibration curves using known quantities of resveratrol and p-coumaric acid standards and test chromatograms using extracts from different wine samples.
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To analyze our beer samples for resveratrol content, be will be using '''H'''igh '''P'''erformance '''L'''iquid '''C'''hromatography (HPLC), which will allow us to separate the metabolites produced by the yeast and analyze these compounds by spectrophotometry. By comparing HPLC chromatogram peaks of metabolites produced by our yeast with a resveratrol-only standard, we can identify if resveratrol is being produced, and at what quantities. We will be monitoring the production of resveratrol and the consumption of ''p''-coumaric acid, which will only be added to the media for the 4CL::STS-integrated yeast; the 4CL::STS+TAL will produce resveratrol without the need for supplemented ''p''-coumaric acid (see [[Team:Rice_University/STRATEGY|STRATEGY]]). Below, we show our initial data for HPLC calibration curves using known quantities of ''trans''-resveratrol and ''p''-coumaric acid standards and test chromatograms using extracts from different wine samples.
{|align="center" style="background-color:#FFFF99; text-align:left" border="1" cellpadding="0" width="50%"
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:'''HPLC Parameters'''<BR>
:'''HPLC Parameters'''<BR>
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::''Instrument'': Shimadzu LC-10AT liquid chromatography unit, SPD-10A UV-vis detector, and SCL-10A system controller.
::''Column'': Agilent Eclipse XDB-C18, 5uM (9.4x250mm)<BR>
::''Column'': Agilent Eclipse XDB-C18, 5uM (9.4x250mm)<BR>
::''Mobile Phases'':  
::''Mobile Phases'':  
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::''Absorbance monitoring'': 290nm
::''Absorbance monitoring'': 290nm
::''Sample injection volume'': 25 microliters
::''Sample injection volume'': 25 microliters
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|}<BR>
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[[Image:HPLC_RSV_example.jpg|center|thumb|600px|Figure C1. Example HPLC chromatogram of a resveratrol standard.]]
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[[Image:HPLC_RSV_example.jpg|center|thumb|700px|'''Figure C1. Example HPLC chromatogram of a ''trans''-resveratrol standard.''']]
 +
<BR>
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===== HPLC: Calibration Standards=====
 +
[[Image:RSV_standards.jpg|center|thumb|700px|'''Figure C2: ''trans''-resveratrol standards (Sigma).''' Different serial dilutions are shown: 20 ug/mL (red), 10ug/mL (purple), 5ug/mL (blue), 2.5ug/mL (green). The inset shows the calibration curve (Peak area vs. Concentration).]]<BR>
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===== HPLC: Calibration=====
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[[Image:Coumaric_standards.jpg|center|thumb|700px|'''Figure C3:  ''p''-coumaric acid standards (Sigma).''' Different serial dilutions are shown: 18.5ug/mL (red), 9.25ug/mL (purple), 4.63ug/mL (blue), 2.3ug/mL (green). The inset shows the calibration curve (Peak area vs. Concentration).]]<BR>
 +
[[Image:RSVandCoumaric.jpg|center|thumb|700px|'''Figure C4: ''trans''-resveratrol and ''p''-coumaric acid have different retention times.''' This separation will allow us to resolve both molecules in a complex mixture, such as a yeast extract. Shown is 18.5ug/mL of ''p''-coumaric acid and 20ug/mL of ''trans''-resveratrol.]]<BR>
===== HPLC: Wine Extract Tests=====
===== HPLC: Wine Extract Tests=====
 +
:* All wine samples were extracted using 6 volumes of ethyl acetate. The ethyl acetate extracts were then evaporated under vacuum and resuspended with 70% methanol. Samples were kept in light-protected tubes until analysis.
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:* The results clearly show that red wines (Fig. C5) contain ''trans''-resveratrol in significant amounts, whereas white wines (Fig. C6) do not, as expected.
 +
<BR>
 +
[[Image:Red_Wine_Samples.jpg|center|thumb|700px|'''Figure C5: Red wine extracts analyzed by HPLC.''' A)Chromatogram of the red wine extracts; the different wines shown are a Merlot from ''Australia'' (red), a Shiraz from ''Australia'' (green), and a Primitivo from ''S. Italy'' (purple). Also shown is a ''trans''-resveratrol standard (10ug/mL, blue dotted line). B)Zoomed-in view of the resveratrol peak region.]]
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<BR>
 +
[[Image:White_Wine_Samples.jpg|center|thumb|700px|'''Figure C5: White wine extracts analyzed by HPLC.''' A)Chromatogram of the white wine extracts; the different wines shown are a Sauvignon Blanc from ''France'' (red) and a Chardonnay from ''N. California'' (purple). Also shown is a ''trans''-resveratrol standard (10ug/mL, blue dotted line). B)Zoomed-in view of the resveratrol peak region.]]
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<BR>
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[[Image:Wine_graph.jpg|center|thumb|500px|'''Figure C6: Resveratrol amounts as calculated using the above chromatograms and the calibration curve.''' Red wine samples are shown in red, white wine samples in yellow. The Chardonnay sample produced no detectable ''trans''-resveratrol peak.]]
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<BR>
 +
<BR>
 +
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===== HPLC: ''beta''-Glucosidase treated samples=====
 +
:*Some papers show that treatment of wine samples by ''beta''-glucosidase increases the amount of resveratrol detected by converting glycosylated resveratrol (aka piceid) into its aglycone form.
 +
:*Our experiments indicate a marginal increase in ''trans''-resveratrol detection by HPLC after treatment with 500U of beta-glucosidase (Fisher). Other wine varieties may contain a greater percentage of resveratrol in piceid form.
 +
<BR>
 +
[[Image:glyco-RSV.jpg|center|thumb|700px|'''Figure C7. ''beta''-glucosidase treatment of wine samples.''' Shown is a Shiraz wine extract treated with ''beta''-glucosidase (purple) or untreated (red). Also shown is a ''trans''-resveratrol standard (10ug/mL, blue dotted line).]]
 +
<BR><BR>
===== HPLC: Fermenation batches=====
===== HPLC: Fermenation batches=====
 +
We are currently in the process of transforming our yeast strain; HPLC data of the extracts for this strain will be added soon.
 +
<BR><BR>
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=== Fermentation ===
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=== D. Fermentation Experiments ===
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[[Image:Lab17.jpg|center|thumb|400px|'''Figure D1. Test beer fermentation using the SAB-hefeweizen brewing strain provided by Saint Arnold Brewery (Houston, TX)'''.]]
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Coming Soon. For a sneak preview, check out the [[Team:Rice_University/GALLERY|Gallery]]
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<BR>
 +
More experimental data coming soon. For a sneak preview, check out the [[Team:Rice_University/GALLERY|Gallery]]
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Latest revision as of 05:22, 30 October 2008


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OUR TEAM:::SUMMARY ::: BACKGROUND ::: STRATEGY ::: CONSTRUCTS ::: RESULTS ::: ONGOING WORK

Contents

A. Genetic Engineering and Part Construction

A detailed summary of parts, design considerations, and genetic engineering progress can be accessed at the CONSTRUCTS page.

Please visit our Notebook for a summary of labwork and protocols.

B. Yeast Transformation

We are currently accumulating data for plasmid transformations into our brewing strain, SAB-Hefe. Data will be updated soon.

C. HPLC Data

To analyze our beer samples for resveratrol content, be will be using High Performance Liquid Chromatography (HPLC), which will allow us to separate the metabolites produced by the yeast and analyze these compounds by spectrophotometry. By comparing HPLC chromatogram peaks of metabolites produced by our yeast with a resveratrol-only standard, we can identify if resveratrol is being produced, and at what quantities. We will be monitoring the production of resveratrol and the consumption of p-coumaric acid, which will only be added to the media for the 4CL::STS-integrated yeast; the 4CL::STS+TAL will produce resveratrol without the need for supplemented p-coumaric acid (see STRATEGY). Below, we show our initial data for HPLC calibration curves using known quantities of trans-resveratrol and p-coumaric acid standards and test chromatograms using extracts from different wine samples.

HPLC Parameters
Instrument: Shimadzu LC-10AT liquid chromatography unit, SPD-10A UV-vis detector, and SCL-10A system controller.
Column: Agilent Eclipse XDB-C18, 5uM (9.4x250mm)
Mobile Phases:
(A) 5% acetonitrile / 0.95% acetic acid
(B) 70% acetonitrile / 0.3% acetic acid
Linear gradient: A to B over 29 minutes
Flow rate: 0.9mL/min
Absorbance monitoring: 290nm
Sample injection volume: 25 microliters

Figure C1. Example HPLC chromatogram of a trans-resveratrol standard.


HPLC: Calibration Standards
Figure C2: trans-resveratrol standards (Sigma). Different serial dilutions are shown: 20 ug/mL (red), 10ug/mL (purple), 5ug/mL (blue), 2.5ug/mL (green). The inset shows the calibration curve (Peak area vs. Concentration).

Figure C3: p-coumaric acid standards (Sigma). Different serial dilutions are shown: 18.5ug/mL (red), 9.25ug/mL (purple), 4.63ug/mL (blue), 2.3ug/mL (green). The inset shows the calibration curve (Peak area vs. Concentration).

Figure C4: trans-resveratrol and p-coumaric acid have different retention times. This separation will allow us to resolve both molecules in a complex mixture, such as a yeast extract. Shown is 18.5ug/mL of p-coumaric acid and 20ug/mL of trans-resveratrol.

HPLC: Wine Extract Tests
  • All wine samples were extracted using 6 volumes of ethyl acetate. The ethyl acetate extracts were then evaporated under vacuum and resuspended with 70% methanol. Samples were kept in light-protected tubes until analysis.
  • The results clearly show that red wines (Fig. C5) contain trans-resveratrol in significant amounts, whereas white wines (Fig. C6) do not, as expected.


Figure C5: Red wine extracts analyzed by HPLC. A)Chromatogram of the red wine extracts; the different wines shown are a Merlot from Australia (red), a Shiraz from Australia (green), and a Primitivo from S. Italy (purple). Also shown is a trans-resveratrol standard (10ug/mL, blue dotted line). B)Zoomed-in view of the resveratrol peak region.


Figure C5: White wine extracts analyzed by HPLC. A)Chromatogram of the white wine extracts; the different wines shown are a Sauvignon Blanc from France (red) and a Chardonnay from N. California (purple). Also shown is a trans-resveratrol standard (10ug/mL, blue dotted line). B)Zoomed-in view of the resveratrol peak region.


Figure C6: Resveratrol amounts as calculated using the above chromatograms and the calibration curve. Red wine samples are shown in red, white wine samples in yellow. The Chardonnay sample produced no detectable trans-resveratrol peak.



HPLC: beta-Glucosidase treated samples
  • Some papers show that treatment of wine samples by beta-glucosidase increases the amount of resveratrol detected by converting glycosylated resveratrol (aka piceid) into its aglycone form.
  • Our experiments indicate a marginal increase in trans-resveratrol detection by HPLC after treatment with 500U of beta-glucosidase (Fisher). Other wine varieties may contain a greater percentage of resveratrol in piceid form.


Figure C7. beta-glucosidase treatment of wine samples. Shown is a Shiraz wine extract treated with beta-glucosidase (purple) or untreated (red). Also shown is a trans-resveratrol standard (10ug/mL, blue dotted line).



HPLC: Fermenation batches

We are currently in the process of transforming our yeast strain; HPLC data of the extracts for this strain will be added soon.

D. Fermentation Experiments

Figure D1. Test beer fermentation using the SAB-hefeweizen brewing strain provided by Saint Arnold Brewery (Houston, TX).


More experimental data coming soon. For a sneak preview, check out the Gallery


OUR TEAM  ::: SUMMARY ::: INTRODUCTION ::: STRATEGY ::: RESULTS ::: ONGOING WORK