Team:UCSF/Collaborations1

From 2013.igem.org

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<h2><center> Collaborations and Interactions with Other iGEM Teams </center></h2>
<h2><center> Collaborations and Interactions with Other iGEM Teams </center></h2>
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<li><h3>UC Davis Promoter Characterization</h3>
 
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<p2>The UC Davis iGEM team asked us to help in producing a multi-lab, extensive characterization of a commonly used part library - from the iGEM part kit! The team provided us with a protocol and a list of promoters from the parts registry. One of our team members (David Dinh) resuspended these parts from the kit, transformed them into DH5alpha cells and grew them according to their suggested protocol. RFP expression was collected from a plate reader and sent to the UC Davis team. The data we collected is also available <a href="https://static.igem.org/mediawiki/2013/9/98/092013_Davis_Promoter.xls" target="_blank">here.</p2>
 
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<li><h3>UC Davis Promoter Characterization</h3>
 
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<p2>The UC Davis iGEM team asked us to help in producing a multi-lab, extensive characterization of a commonly used part library - from the iGEM part kit! The team provided us with a protocol and a list of promoters from the parts registry. One of our team members (David Dinh) resuspended these parts from the kit, transformed them into DH5alpha cells and grew them according to their suggested protocol. RFP expression was collected from a plate reader and sent to the UC Davis team. The data we collected is also available <a href="https://static.igem.org/mediawiki/2013/9/98/092013_Davis_Promoter.xls" target="_blank">here.</p2>
 
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<font face="arial" size = "3"><b>UC Davis Promoter Characterization</font></b> <br>
 
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<font face="arial" size = "3">The UC Davis iGEM team asked us to help in producing a multi-lab, extensive characterization of a commonly used part library - from the iGEM part kit! The team provided us with a protocol and a list of promoters from the parts registry. One of our team members (David Dinh) resuspended these parts from the kit, transformed them into DH5alpha cells and grew them according to their suggested protocol. RFP expression was collected from a plate reader and sent to the UC Davis team. The data we collected is also available <a href="https://static.igem.org/mediawiki/2013/9/98/092013_Davis_Promoter.xls" target="_blank">here.</a><span> </font>
 
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<font face="arial" size = "3"><b>TU/Eindhoven: Synthetic Facts Project</font></b> <br>
 
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<font face="arial" size = "3">This summer, the TU/Eindhoven team made a website which they hoped would serve as "a Fact Checker to help members of the general public associate with the field of synthetic biology. (Their) Fact Checker will become available online and will allow users to both view and submit facts of their own.  Each submitted “fact” will be reviewed and commented on by respected sources. This way it is hoped that (they) can prove or disprove a number of myths about synthetic biology and thereby promote the idea of synthetic biology to the general public." To help the team, we researched one fact that can now be found on their site by clicking the badge below. </font>
 
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<a href="http://syntheticfacts.tue.nl/index.php?i=CheckedFacts&author=UCSF" target="_blank"><img src="http://syntheticfacts.tue.nl/badge.php?author=UCSF" style="width: 240px; height: 80px; margin-left:350px; margin-top:10px"  /></a>
 
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<font face="arial" size = "3"><b>University of East Anglia (Norwich, England) Project</font></b> <br>
 
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<font face="arial" size = "3">The University of East Anglia team asked for help obtaining soil and sediment samples from various locations around the world. The team wanted to use the samples to test a biosensor that they are developing for their iGEM project. Our team member, David Dinh, went to Crissy Field and Heron's Head Park in San Francisco and dug up sediment samples that were then mailed to the East Anglia iGEM team. We hope the soil samples were useful in the team's work this summer!</font>
 
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<font face="arial" size = "3"><b>University of Nevada, Reno - Meet-up</font></b> <br>
 
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<font face="arial" size = "3">We were visited by members of the University of Nevada, Reno (UNR) iGEM team at the beginning of the summer and were able to talk about our preliminary project ideas. We also had a brainstorming session for our human practices projects so that we could share with the UNR team our method of coming up with and narrowing down our ideas. </font>
 
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<font face="arial" size = "3"><b>NorCal iGEM Team Meet-up</font></b> <br>
 
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<font face="arial" size = "3">This summer the UC Davis iGEM team hosted a meet-up with other local iGEM teams. We were very excited to attend and had a great time meeting the other teams and hearing about their projects. We received a lot of great feedback and also had fun bowling together after!</font>
 
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<h3>Teaching Synthetic Biology to High School Students</h3>
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<li><h3>UC Davis Promoter Characterization</h3></li>
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<p2>A common misunderstanding held by proponents of organic food, is that once genetically modified organisms (GMOs) are incorporated into our food supply, they will become undetectable, and cannot be differentiated from other foods. To educate their peers, students in the Biotechnology Academy at Abraham Lincoln High School in San Francisco offered to teach their fellow students in the school’s ecological Green Academy how to test for, and recognize, genetically modified food ingredients. Additionally, we taught our peers about some of the beneficial real-world applications of GMOs.<br><br>
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<p2>The UC Davis iGEM team asked us to help in producing a multi-lab, extensive characterization of a commonly used part library - from the iGEM part kit! The team provided us with a protocol and a list of promoters from the parts registry. One of our team members (David Dinh) resuspended these parts from the kit, transformed them into DH5alpha cells and grew them according to their suggested protocol. RFP expression was collected from a plate reader and sent to the UC Davis team. The data we collected is also available <a href="https://static.igem.org/mediawiki/2013/9/98/092013_Davis_Promoter.xls" target="_blank">here.</a></p2>
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Our educational program included a pre-learning survey, direct instruction by our biotechnology teacher, George Cachianes, and a series of three lab exercises in which the iGEM/biotech students taught the Green Academy students how to recognize genetically modified foods using common biotech lab techniques. Afterwards, a post learning survey assessed the knowledge of the Green Academy students to see if their attitude and knowledge about GMOs had shifted.</p2>
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Revision as of 15:38, 28 October 2013

Collaborations and Interactions with Other iGEM Teams

The UC Davis iGEM team asked us to help in producing a multi-lab, extensive characterization of a commonly used part library - from the iGEM part kit! The team provided us with a protocol and a list of promoters from the parts registry. One of our team members (David Dinh) resuspended these parts from the kit, transformed them into DH5alpha cells and grew them according to their suggested protocol. RFP expression was collected from a plate reader and sent to the UC Davis team. The data we collected is also available here.
A pre-lab survey measured the Green Academy students'knowledge of, and attitudes toward, genetically modified food. Before the lectures and lab activities, the majority of the student had heard of genetically modified food crops (77.8%) and could identify corn as a crop likely to be genetically modified (66.6%). 85.2% of the students felt that GMOs should be labeled. About half of the students (48.1%) said they would avoid eating GMOs (66.7%) and would pay extra to avoid them (18.5%). After the unit, one student said he learned “that a lot of what we eat is genetically modified”. Another echoed that statement, “I learned that a lot of the food we eat are made from GMOs,” and went on to explain, “I also learned that we can check if they contain GMOs by a process that we learned in this biotech class.”

In search of two genes

In order to find out if GMOs were present in common, every-day foods, such as tortilla chips and papaya, we tested these common foods for the presence of two genes: CaMV35S, which codes for a promoter, and NOS, which codes for a terminator. We specifically looked for the presence of promoter and terminator genes instead of the actual functional genes themselves because the functional gene may vary from organism to organism, depending on what qualities of the organism are being altered. In order to determine which of our samples were GMOs and which were not, we used some very common lab techniques including Polymerase Chain Reaction (PCR), which amplifies a certain piece of DNA.


Choosing the foods

We chose to use a variety of food, including fresh soy beans, tortilla chips, Fritos corn chips, papaya and a organic corn snack that claims it is made from an ancient variety of corn. We tested some foods that were labeled “non-GMO” and some that weren’t labeled at all.


Testing

We crushed up samples of each food up with a mortar and pestle, while adding small amounts of water to make a slurry. We then placed each sample into a microcentrifuge tube containing InstaGene, a chelating agent that helps to remove metal ions. We have to use this because it ensures that the PCR will be free of metal ions. After adding our samples to InstaGene, we shook the tubes and placed them into a 95°C water bath for 5 minutes. Afterwards, we centrifuged them for 5 minutes at the maximum speed, and then refrigerated them.

The next day, we removed the samples from the refrigerator and placed them on ice. We added all of the essential ingredients for PCR into a PCR tube, in addition to DNA from the samples we had centrifuged the previous day. After mixing the contents of the tube, we placed them into the thermal cycler. Finally, we used gel electrophoresis to see if fragments of DNA that would indicate that the sample is a GMO were present in the samples or not.
To detect if the food products were GMOs, we analyzed the samples by gel electrophoresis and looked for the CaMV35S promoter and NOS terminator base on the base pair size of each gene. If a food was genetically modified, it showed a 203 bp band of CaMV35S promoter and a 225 bp band of NOS terminator. Whereas, a non-GMO food would not have these two bands. During the course of the lab we tested eight foods: Fritos brand corn chips, Hawaiian papaya, Inka Roasted Corn snack food, Santitas brand tortilla chips, raw soy beans, soy crisp snack chips (brand unknown), Bob’s Red Mill Cornmeal (labeled “all natural”) and Bob’s Red Mill Cornbread Mix. Four of these eight foods proved to contain the CaMV35S promoter and the NOS terminator: Fritos, papaya, tortilla chips, and the “all natural” cornmeal. The students were surprised to find no proof of genetic modification in fresh soy beans or soy crisp snack chips, even though some sources claim that 91% of the U.S. soybean crop is genetically modified. However, in testing the soy foods, the CaMV35S and NOS terminator bands did not appear. Interestingly enough, the cornbread mix did not show evidence of genetic modification while the same-brand cornmeal did. Please see the full data represented in the chart below:

Results from PCR analysis of food products
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