Team:SDU-Denmark/labwork/Testing

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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols"><b>mRNA Isolation</b></a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Testing"><b>Growth Curves</b></a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/PCR">PCR</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Testing/InulinStaining">Inulin Staining</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/Miniprep">Miniprep</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/Checkdigest">Check Digest</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/3A">3A-Assembly</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/colpcr">Colony-PCR </a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/Trans">Transformation</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/gel">Gel-electrophoresis</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/revtrans">Reverse Transcriptase</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/mutagen">Mutagenisis</a></td>
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<td><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Protocols/pcrgelclean">PCR-,gel clean-up</a></td>
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<h1> Isolation of mRNA from <i>Helianthus tuberosus</i></h1> </b>
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<h1>Growth curves: SST and FFT</i></h1> </b>
<p>
<p>
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(The procedure we used for mRNA isolation, is a modified version of the Qiagen RNeasy protocol for plant mRNA isolation.)
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<b>Introduction:</b></br>
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This experiment was set up to measure the growth rates of our bacteria, expressing either of the two proteins fructan:fructan fructosyltransferase (FFT) and sucrose:sucrose fructosyltransferase (SST).</br>
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Our hypothesis is, that the growth of the bacteria producing the FFT will be as fast as the top 10 coli (because FFT shouldn't work without SST)and SST bacteria will be near the same speed (maybe a little slower because it converts the sucrose to 1-kestose).<br><br>
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<b>Method:</b></br>
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In order to produce this growth curve we took E.coli top10 transformed with the pJET plasmid containing FFT or SST and grew them in 50 mL fresh LB medium (containing ampicillin).</br>
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We transfered 1 mL of overnight culture (ONC) to the fresh LB medium and measured the optical density (OD) at 600 nm, every hour.</br>
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We also made a negative sample containing 1 mL of ONC with E.coli top10 and 50 mL of LB media (without ampicillin)</br></br>
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<b>Results:</b></br>
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The data is given in a table (table 1) and can also be seen plotted on a logarithmic scale (figure 1). Hour nr. 7 is left out, because it was measured at OD 450 instead of OD 600, hence giving false data.</br></br>
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<center><img src="https://static.igem.org/mediawiki/igem.org/f/fd/SDU-2012-Tabel_til_GC.png" width="100%" /></center>
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<i>Tabel 1</i> <br>
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<center><img src="https://static.igem.org/mediawiki/igem.org/2/2a/SDUiGEM-2012-Graf_GC.png" width="100%" /></center>
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<i>figure 1</i>
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</br></br>
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<p>
<p>
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Small tubers from Helianthus tuberosus were washed with untreated water and cut in rough slices with an everyday boxcutter.</br>
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<b>Discussion:</b></br>
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The slices were distributed in cryotubes and weighed, the weights were noted down, and submerged in liquid nitrogen (flash-freeze at -196 °C). Flash-freezing is necessary to halt all RNase activity. </br>
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As you can see, clearly, SST is decreasing the growth rate of the bacteria. This is most likely because SST produces an indigestible polysaccharide from sucrose, disabling the bacteria in getting the energy. FFT grows as fast as the negative test, which indicates that the protein does not have any disadvantages concerning growth. This is probably because FFT produces a trisaccharide from sucrose, that the bacteria is able to digest. </br></br>
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RLT buffer is mixed at this point, for later use. For each mL RLT, add μL beta-mercaptoethanol. Do this in a fume cabinet, as mercaptoethanol smells really bad and is toxic!</br>
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After 20 minutes 600mg is extracted from the cryotubes, the rest is stored for later use. The 600mg plant material is grinded to a fine dust using a mortar. It is important to keep the plant material frozen during the grinding, to keep the cell wall rigid enough to destroy it.</br>
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<b>Conclusion:</b></br>
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The plant powder is transferred to a tube and dissolved in RLT buffer(450μL buffer op 100mg plant material). We used approx. 3mL for 600mg material.</br>
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SST is decreasing the growth rate of E. coli Top10 but not FFT.</br></br>
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The solution is mixed using a vortex mixer.</br>
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500 μL of the solution is transfered to a 2mL treated with ultrasound to homogenize the content and further disrupt the cell wall. 500 μL is transfered to a 2mL tube as a control.</br>
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The samples are centrifuged at 14.500 rpm for 60 seconds to pellet out large organelles.
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0,5 vol. 96-100% ethanol is added(250μL) to the sample, mixed by pipette. </br>
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Transfer the samples to spin-column (Qiagen RNeasy mini kit, for RNA isolation from animal cells) in a 2mL sampletube and do the following:
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<p>
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<ol>
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<li>Spin at 10.000 rmp for 15s, discard flowthrough
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add 700μL RW1 til spin column </li></br>
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<li>spin at 10.000 rmp for 15s, discard flowthrough
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add 500μL RPE buffer til spin column (RPE buffer = 1:4 vol RPE/96-100% ethanol)</li>
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</li>
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</br>
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<li> spin at 10.000 rmp for 15s, discard flowthrough
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add another 500μL RPE buffer to the spin column (RPE buffer = 1:4 vol RPE/96-100% ethanol)
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</li>
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</br>
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<li> spin at 10.000 rmp for 15s, discard flowthrough
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Transfer the columns to new 2mL centrifuge tubes. Centrifuge at full speed for 1 min.
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Transfer spin columns to new 1.5mL sample tubes </li>
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</br>
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<li> add 30-50μL RNase-free water <p></li>
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<li> spin at 10.000 rpm for 60 seconds <p></li>
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<li> Repeat the prior step once.</li>
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</ol>
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</p>
</p>
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<p>
 
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The mRNA is now isolated in the 60-100μL at the bottom of the collection tubes, and can be stored at -80C
 
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</p>
 
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Latest revision as of 01:49, 27 September 2012

iGEM TEAM ::: SDU-DENMARK courtesy of NIAID


Growth Curves Inulin Staining

Growth curves: SST and FFT

Introduction:
This experiment was set up to measure the growth rates of our bacteria, expressing either of the two proteins fructan:fructan fructosyltransferase (FFT) and sucrose:sucrose fructosyltransferase (SST).
Our hypothesis is, that the growth of the bacteria producing the FFT will be as fast as the top 10 coli (because FFT shouldn't work without SST)and SST bacteria will be near the same speed (maybe a little slower because it converts the sucrose to 1-kestose).

Method:
In order to produce this growth curve we took E.coli top10 transformed with the pJET plasmid containing FFT or SST and grew them in 50 mL fresh LB medium (containing ampicillin).
We transfered 1 mL of overnight culture (ONC) to the fresh LB medium and measured the optical density (OD) at 600 nm, every hour.
We also made a negative sample containing 1 mL of ONC with E.coli top10 and 50 mL of LB media (without ampicillin)

Results:
The data is given in a table (table 1) and can also be seen plotted on a logarithmic scale (figure 1). Hour nr. 7 is left out, because it was measured at OD 450 instead of OD 600, hence giving false data.

Tabel 1
figure 1

Discussion:
As you can see, clearly, SST is decreasing the growth rate of the bacteria. This is most likely because SST produces an indigestible polysaccharide from sucrose, disabling the bacteria in getting the energy. FFT grows as fast as the negative test, which indicates that the protein does not have any disadvantages concerning growth. This is probably because FFT produces a trisaccharide from sucrose, that the bacteria is able to digest.

Conclusion:
SST is decreasing the growth rate of E. coli Top10 but not FFT.

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