Team:ITESM-CEM/Project/Experiments

From 2014.igem.org

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       <sub2></sub2><sub2></sub2><sub2></sub2><sub2></sub2>
       <sub2></sub2><sub2></sub2><sub2></sub2><sub2></sub2>
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       <sub2><a href="#One" style="color: #FFF;">One</a></sub2>
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       <sub2><a href="#One" style="color: #FFF;">PCR's</a></sub2>
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       <sub2><a href="#Two" style="color: #FFF;">Two</a></sub2>
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       <sub2><a href="#Two" style="color: #FFF;">Mammalian Cell Transfection</a></sub2>
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      <sub2><a href="#Three" style="color: #FFF;">Three</a></sub2>
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       <sub2><a href="#Four" style="color: #FFF;">Protein Expression</a></sub2>
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       <sub2><a href="#Four" style="color: #FFF;">Four</a></sub2>
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       <sub2><a href="#Five" style="color: #FFF;">NeoR Characterization</a></sub2>
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       <sub2><a href="#Five" style="color: #FFF;">Five</a></sub2>
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     </ul></td>
     </ul></td>
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<br>
<br>
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<h2>The Experiments</h2>
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      <p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.<br><br></p>
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<a name="One"><h2>Experiment One</h2></a>  
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<a name="One"><h2>PCR for sequence isolation.</h2></a>  
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       <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus fringilla porta nisi sed dictum. Aliquam at rutrum nisl. Ut eros quam, condimentum sed pretium et, euismod vitae tellus. Curabitur eu blandit massa. Vestibulum at euismod purus. Sed quis pretium ligula. Cras non tristique nulla. Nunc finibus risus non purus malesuada viverra. Cras bibendum augue eu lorem faucibus, nec auctor mi iaculis. Vivamus sagittis, mi non gravida accumsan, odio dui pellentesque leo, a varius dui mauris eu diam. Maecenas laoreet tellus sed porta efficitur.</p>
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<gotop><a href="#top">Back to top</a></gotop><br><br>
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<h4>PCR 25 ul Mix for Mammalian expression Biobricks</h4>
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<p style="text-align: justify; text-justify: inter-word;">
 +
-6.75 µl – Molecular grade water<br>
 +
-1 µl – DNA template (1 ng)<br>
 +
-1.25 µl – Primer F (100 uM)<br>
 +
-1.25 µl – Primer R (100 uM)<br>
 +
-2.25 µl – DMSO 99%<br>
 +
-12.5 µl – NEB Q5 High Fidelity 2X Master Mix</p><br>  
 +
<h4>PCR programs</h4>
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<a name="Two"><h2>Experiment Two</h2></a>
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<p style="text-align: justify; text-justify: inter-word;">
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      <p>Etiam tempus mi pulvinar purus iaculis bibendum. Vivamus vel risus eu enim volutpat finibus. Nullam bibendum est sit amet arcu lobortis, id laoreet ex vestibulum. Curabitur fringilla eleifend lacus, nec ornare nibh imperdiet sed. Maecenas vel velit consectetur, tempus libero quis, consectetur ex. Nulla porttitor pharetra velit. Curabitur tristique, dolor ut sodales euismod, diam diam ultricies arcu, at tincidunt tellus neque in felis. Etiam ut tempor ligula. Sed at dui sapien.<br><br></p>
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NeoR</p><br>
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<a name="Three"><h2>Experiment Three</h2></a>
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<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/c/cf/PCR_cycle_2.jpg" width="600" height="235" hspace="20" BORDER=10></p><br>
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      <p>Proin aliquam nibh id elementum pellentesque. Suspendisse mollis est ut felis sagittis mollis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Etiam accumsan ex ante, quis lobortis erat fermentum ac. Sed et egestas libero. Donec id diam vitae leo consequat interdum. Ut in sem in quam pretium finibus vitae non lectus.<br><br></p>
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<a name="Four"><h2>Experiment Four</h2></a>
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<p style="text-align: justify; text-justify: inter-word;">
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      <p>Curabitur sed erat ante. Maecenas viverra odio sit amet ultrices facilisis. Nullam lobortis mi quam, sit amet placerat erat eleifend eget. Mauris commodo sem tortor, quis blandit orci laoreet vel. In hac habitasse platea dictumst. Curabitur molestie eu dolor ac bibendum. Duis fermentum tellus et dui dapibus, sed feugiat dolor sollicitudin. Nulla malesuada, tortor quis blandit dictum, odio risus rutrum sapien, varius pharetra dui tellus sed lectus. Sed eget magna at justo tempus hendrerit. Nulla in odio nec libero maximus finibus.<br><br></p>
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F1Ori</p><br>
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<a name="Five"><h2>Experiment Five</h2></a>  
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<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/4/43/PCR_cycle_3.jpg" width="600" height="235" hspace="20" BORDER=10></p><br>
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       <p>Praesent molestie consectetur nunc eu gravida. Praesent imperdiet quam vitae erat dapibus sagittis vitae id libero. Etiam vitae tortor massa. Donec vehicula lacus non sem eleifend, sed commodo nunc lobortis. Nulla vitae volutpat mi. Donec vestibulum ultrices lectus, in venenatis elit luctus sit amet. Aliquam eget lacus accumsan, dictum dolor accumsan, venenatis lectus. Ut eget mi facilisis, accumsan odio ac, viverra ipsum. Integer efficitur massa sit amet cursus ultrices. Etiam porta, nisl et tristique egestas, lectus augue convallis nulla, ut ultrices odio dui nec lectus. Morbi facilisis tortor aliquet sagittis auctor. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Etiam tincidunt aliquet sem id lobortis. Nam tincidunt ultrices lorem dictum pretium.
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<br><br><br>
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<p style="text-align: justify; text-justify: inter-word;">
 +
CMV</p><br>
 +
 
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/d/df/PCR_cycle_4.jpg" width="600" height="235" hspace="20" BORDER=10></p><br>
 +
 
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">
 +
BGHPA</p><br>
 +
 
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/a/af/PCR_cycle_5.jpg" width="600" height="235" hspace="20" BORDER=10></p><br>
 +
 
 +
 
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 +
<gotop><a href="#top">Back to top ↑</a></gotop><br><br>
 +
 
 +
<a name="Two"><h2>Mammalian Cells Transfection</h2></a>  
 +
 
 +
       <p style="text-align: justify; text-justify: inter-word;">Add 50µl of OPTI-MEM (GIBCO) and 12 µl of Lipofectamine2000 Invitrogen reagent to a microtube. (Solution 1). Incubate at room temperature for 5 minutes.</p><br>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">Add 50µl of Optimen and 40µl (100ng) of plasmid to a microtube (Solution 2). Incubate at room temperature for 5 minutes.</p><br>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">Mix Solutions 1 and 2. Incubate at room temperature for 5 minutes →(Solution 3).</p><br>
 +
 
 +
<h4>Cell preparation.</h4><br>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">
 +
1) Wash MARC145 Cells with OPTI-MEM. Repeat two times.<br>
 +
2) Add 1.8ml of OPTI-MEM to the cells.<br>
 +
3) Mix solution 3 with MARC145 cells solution and incubate 4 hours with 6% CO2.<br>
 +
4) Change medium for 2ml fresh OPTI-MEM medium to eliminate Lipofectamine 2000 Invitrogen.<br>
 +
5) Change to 5ml of complete DMEM-10% neonatal serum and add 12.5 µl Geniticin (100µg/ml).</p><br>
 +
 
 +
<h2>7-dehydratase insertion in pcDNA 3.1 Myc-His A</h2><br>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">7-dehydratase was inserted in pcDNA 3.1 Myc-His A. Since our enzyme sequence design has the iGEM preffix and suffix, the only restriction available to insert it into the plasmid was with NotI. This means that the further ligation can be sense or anti-sense. The correct ligation was corroborated with a restriction and was then transfected in monkey kidney cells. </p><br>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">pcDNA 3.1 Myc-His A is an expression plasmid that contains BGHPA, a constitutive promoter and an origin of replication that work in mammalian cells. To see if the plasmid was working correctly, a cassette was expressed with GFP to see if the plasmid worked in a specific eukaryotic cell line (Marc145), so the enzyme could be inserted and the analysis of functionality of the enzyme by substrate degradation could be started. </p><br>
 +
 
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/2/2a/Dehyd_pcDNA.jpg" width="600" height="213" hspace="20" BORDER=10></p><br>
 +
 
 +
<p><pie><b>Image 1.</b>Cells before (left) and after (right) transfection with plasmid pcDNA 3.1 Myc-His A with 7-dehydratase gene using lipofectamine as a transfecting agent. </p></pie>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">As fluorescence of this enzyme cannot be detected, its characterization is going to be determined by an antibiotic resistance at a certain concentration (Neomycin), where cells are able to keep dividing, except for the ones without the resistance gene.</p>
 +
 
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/8/8f/Dehyd_pcDNA2.jpg" width="350" height="476" hspace="20" BORDER=10></p><br>
 +
<gotop><a href="#top">Back to top ↑</a></gotop><br><br>
 +
 
 +
<a name="Four"><h2>Recombinant Protein Expression</h2></a>
 +
      <p style="text-align: justify; text-justify: inter-word;">Each protein was inserted in Escherichia coli through pPROEX B which is a bacterial expression plasmid. This plasmid was used due to its characteristics, which include TRC promoter inducible by IPTG and has a 6x histidine tag in N-terminal end.<br></p>
 +
 
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/6/64/PPROEXb.jpg" width="593" height="593" hspace="10" BORDER=10></p><br>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">In the case of cholesterol oxidase, the enzyme was successfully introduced in the plasmid mentioned before. The protein wasn’t overexpressed by induction with IPTG, so no further analysis was made because this enzyme is well characterized and there is more information about it in BRENDA Enzymes as EC 1.1.3.6 – cholesterol oxidase, <u>Chromobacterium sp.</u><br><br>
 +
 
 +
<p style="text-align: justify; text-justify: inter-word;">Oxoacyl reductase was analyzed by SDS-PAGE in a 15% acrylamide gel. First, main cultures of the different colonies grown in the plate were inoculated in 40 ml of LB with ampicillin (100 ug/ml). After a few hours in the shaker, optical density was measured repeatedly until it was between 0.5 and 0.65, considering this measurement our time zero. Right after it, IPTG 1 mM was added to start the overexpression of the protein. Each hour, the absorbance of each culture was registered until the time six.<br><br>
</p>
</p>
 +
 +
<p><pie><b>Table 1.</b> Different absorbances measured each hour of the cultures of oxoacyl reductase.</p></pie><br>
 +
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/d/de/OLIALDO_tabla_1.jpg"  width="580" height="180" hspace="10" BORDER=10></p><br>
 +
 +
<p style="text-align: justify; text-justify: inter-word;">The samples taken each hour were centrifuged 5 min/13500 rpm to concentrate the pellet in the bottom of the microtube. The supernatant was thrown into a waste glass, and the pellets were resuspended in different volumes of Laemmli buffer, depending on the value of absorbance obtained. The criteria used to determine the volume of buffer, was taking into consideration the absorbance of the time zero, which would represent the 100 percent of buffer added (100 ul in this sample), and going up or down depending of the absorbances of the other samples. The different volumes are now shown.</p><br>
 +
 +
<p><pie><b>Table 2.</b> Volumes of Laemmli buffer depending of the absorbance value of each sample. </p></pie><br>
 +
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/d/dc/CaroDany_tabla_2.jpg" width="580" height="180" hspace="10" BORDER=10></p><br><br>
 +
 +
<gotop><a href="#top">Back to top ↑</a></gotop><br><br>
 +
 +
<a name="Five"><h2>NeoR characterization</h2></a>
 +
 +
<p style="text-align: justify; text-justify: inter-word;"> The scope of our project is to express a new synthetic pathway  in mammalian cells in order to make them able to metabolize 7-ketocholesterol. Just like bacteria, mammalian cells also have a selective gene to identify successfully transformed organisms. NeoR is a gene that encodes an aminoglycoside 3'-phosphotransferase enzyme, which provides a resistance to Neomycin and its derivatives. The antibiotic that will be used to select the successfully transformed mammalian cells is G418®, a Neomycin derivative which only affects mammalian cells. <br><br>
 +
 +
However, this exceeded the possibilities given the time constrains. Therefore a characterization in a mammalian cell culture was not done due to time limitations. The NeoR gene was characterized using an <u>E.coli</u> culture and Neomycin as selective antibiotic. The NeoR gene was obtained by PCR from pcDNA3.1(-)/ Myc-His A, and following iGEM instructions, the gene was introduced in the plasmid pSB1C3 as it is shown in the following picture.<br></p>
 +
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/e/ef/Plasmido_BBa_K1313004.jpg" width="443" height="351" hspace="20"></p>
 +
 +
<h4>Procedure</h4>
 +
      <p style="text-align: justify; text-justify: inter-word;">The characterization was made using two groups: the samples and a control group. The samples were made using an <u>E.coli</u> DH5-α inoculum, transformed with the NeoR gene inserted in psB1C3 using the constitutive promoter BBa_K823012. The control group used an untransformed <u>E.coli</u> DH5-α inoculum. <br><br>
 +
 +
Both groups consisted on thirteen essay tubes with 5 ml of LB media each one with a different concentration on Neomycin as shown in table 1 and 2. The tubes were cultured on a shaker for 18 hours at 250 rpm/37ºC. Afterwards, each tube had its optical density measured at 600 nm using as LB media as a blank with the same antibiotic concentration. Five neomycin concentrations were chosen to perform petri dish cultures but only with the trouble group to perform a C.F.U. count.
 +
</p>
 +
<p><pie><b>Table 1.</b> Control group without neomycin</p></pie><br>
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/a/a7/ControlTable.jpg" height="366" width="700" align="middle" hspace="10" BORDER=10><br></p><br>
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 +
<p><pie><b>Table 2.</b> Positive Group with neomycin</p></pie><br>
 +
<p class="centeredImage"><img src="https://static.igem.org/mediawiki/2014/1/1d/NeoR_positivo.jpg" height="411" width="700" align="middle" hspace="10" BORDER=10><br></p><br>
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<gotop><a href="#top">Back to top ↑</a></gotop><br><br>
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<br><br><br>
<!--FIN CONTENIDO-->
<!--FIN CONTENIDO-->

Latest revision as of 03:54, 18 October 2014

TEC-CEM | Project

ITESM-CEM | Enzy7-K me

Project 3014

 

PCR for sequence isolation.

PCR 25 ul Mix for Mammalian expression Biobricks

-6.75 µl – Molecular grade water
-1 µl – DNA template (1 ng)
-1.25 µl – Primer F (100 uM)
-1.25 µl – Primer R (100 uM)
-2.25 µl – DMSO 99%
-12.5 µl – NEB Q5 High Fidelity 2X Master Mix


PCR programs

NeoR



F1Ori



CMV



BGHPA



Back to top ↑

Mammalian Cells Transfection

Add 50µl of OPTI-MEM (GIBCO) and 12 µl of Lipofectamine2000 Invitrogen reagent to a microtube. (Solution 1). Incubate at room temperature for 5 minutes.


Add 50µl of Optimen and 40µl (100ng) of plasmid to a microtube (Solution 2). Incubate at room temperature for 5 minutes.


Mix Solutions 1 and 2. Incubate at room temperature for 5 minutes →(Solution 3).


Cell preparation.


1) Wash MARC145 Cells with OPTI-MEM. Repeat two times.
2) Add 1.8ml of OPTI-MEM to the cells.
3) Mix solution 3 with MARC145 cells solution and incubate 4 hours with 6% CO2.
4) Change medium for 2ml fresh OPTI-MEM medium to eliminate Lipofectamine 2000 Invitrogen.
5) Change to 5ml of complete DMEM-10% neonatal serum and add 12.5 µl Geniticin (100µg/ml).


7-dehydratase insertion in pcDNA 3.1 Myc-His A


7-dehydratase was inserted in pcDNA 3.1 Myc-His A. Since our enzyme sequence design has the iGEM preffix and suffix, the only restriction available to insert it into the plasmid was with NotI. This means that the further ligation can be sense or anti-sense. The correct ligation was corroborated with a restriction and was then transfected in monkey kidney cells.


pcDNA 3.1 Myc-His A is an expression plasmid that contains BGHPA, a constitutive promoter and an origin of replication that work in mammalian cells. To see if the plasmid was working correctly, a cassette was expressed with GFP to see if the plasmid worked in a specific eukaryotic cell line (Marc145), so the enzyme could be inserted and the analysis of functionality of the enzyme by substrate degradation could be started.



Image 1.Cells before (left) and after (right) transfection with plasmid pcDNA 3.1 Myc-His A with 7-dehydratase gene using lipofectamine as a transfecting agent.

As fluorescence of this enzyme cannot be detected, its characterization is going to be determined by an antibiotic resistance at a certain concentration (Neomycin), where cells are able to keep dividing, except for the ones without the resistance gene.


Back to top ↑

Recombinant Protein Expression

Each protein was inserted in Escherichia coli through pPROEX B which is a bacterial expression plasmid. This plasmid was used due to its characteristics, which include TRC promoter inducible by IPTG and has a 6x histidine tag in N-terminal end.


In the case of cholesterol oxidase, the enzyme was successfully introduced in the plasmid mentioned before. The protein wasn’t overexpressed by induction with IPTG, so no further analysis was made because this enzyme is well characterized and there is more information about it in BRENDA Enzymes as EC 1.1.3.6 – cholesterol oxidase, Chromobacterium sp.

Oxoacyl reductase was analyzed by SDS-PAGE in a 15% acrylamide gel. First, main cultures of the different colonies grown in the plate were inoculated in 40 ml of LB with ampicillin (100 ug/ml). After a few hours in the shaker, optical density was measured repeatedly until it was between 0.5 and 0.65, considering this measurement our time zero. Right after it, IPTG 1 mM was added to start the overexpression of the protein. Each hour, the absorbance of each culture was registered until the time six.

Table 1. Different absorbances measured each hour of the cultures of oxoacyl reductase.



The samples taken each hour were centrifuged 5 min/13500 rpm to concentrate the pellet in the bottom of the microtube. The supernatant was thrown into a waste glass, and the pellets were resuspended in different volumes of Laemmli buffer, depending on the value of absorbance obtained. The criteria used to determine the volume of buffer, was taking into consideration the absorbance of the time zero, which would represent the 100 percent of buffer added (100 ul in this sample), and going up or down depending of the absorbances of the other samples. The different volumes are now shown.


Table 2. Volumes of Laemmli buffer depending of the absorbance value of each sample.




Back to top ↑

NeoR characterization

The scope of our project is to express a new synthetic pathway in mammalian cells in order to make them able to metabolize 7-ketocholesterol. Just like bacteria, mammalian cells also have a selective gene to identify successfully transformed organisms. NeoR is a gene that encodes an aminoglycoside 3'-phosphotransferase enzyme, which provides a resistance to Neomycin and its derivatives. The antibiotic that will be used to select the successfully transformed mammalian cells is G418®, a Neomycin derivative which only affects mammalian cells.

However, this exceeded the possibilities given the time constrains. Therefore a characterization in a mammalian cell culture was not done due to time limitations. The NeoR gene was characterized using an E.coli culture and Neomycin as selective antibiotic. The NeoR gene was obtained by PCR from pcDNA3.1(-)/ Myc-His A, and following iGEM instructions, the gene was introduced in the plasmid pSB1C3 as it is shown in the following picture.

Procedure

The characterization was made using two groups: the samples and a control group. The samples were made using an E.coli DH5-α inoculum, transformed with the NeoR gene inserted in psB1C3 using the constitutive promoter BBa_K823012. The control group used an untransformed E.coli DH5-α inoculum.

Both groups consisted on thirteen essay tubes with 5 ml of LB media each one with a different concentration on Neomycin as shown in table 1 and 2. The tubes were cultured on a shaker for 18 hours at 250 rpm/37ºC. Afterwards, each tube had its optical density measured at 600 nm using as LB media as a blank with the same antibiotic concentration. Five neomycin concentrations were chosen to perform petri dish cultures but only with the trouble group to perform a C.F.U. count.

Table 1. Control group without neomycin




Table 2. Positive Group with neomycin




Back to top ↑