Difference between revisions of "Team:Vanderbilt/Practices/Collaborations"
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| − | <p> | + | <p><font color="758a87"> |
Our team had many productive collaborations with universities across the world. We were especially excited by the number of teams who approached us out of interest in the numerous mutation-reducing tools that our team has developed. We were happy to give these teams free access to our optimization techniques, which not only helped our collaborators to improve the stability of their genetic elements, but also helped us expand our techniques to new applications and even new organisms.</p> | Our team had many productive collaborations with universities across the world. We were especially excited by the number of teams who approached us out of interest in the numerous mutation-reducing tools that our team has developed. We were happy to give these teams free access to our optimization techniques, which not only helped our collaborators to improve the stability of their genetic elements, but also helped us expand our techniques to new applications and even new organisms.</p> | ||
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| − | <p>University of Paris-Bettencourt:</p> | + | <p><font color="758a87">University of Paris-Bettencourt:</p> |
| − | <ul> The team at Paris-Bettencourt approached us out of concern for the stability of their genetically engineered fermenting microbes. Given the importance of strict quality control and long-term stability in the applications that their team was envisioning for their project, they had a keen interest in making their genes more stable. We offered to optimized their fermentation genes using our computational algorithm. As their team did not have sufficient time to synthesize the genes we sent them, we also provided them with statistics on how many mutation-prone sites their original genes had and how much they can be improved for stability. </ul> | + | <ul> <font color="758a87">The team at Paris-Bettencourt approached us out of concern for the stability of their genetically engineered fermenting microbes. Given the importance of strict quality control and long-term stability in the applications that their team was envisioning for their project, they had a keen interest in making their genes more stable. We offered to optimized their fermentation genes using our computational algorithm. As their team did not have sufficient time to synthesize the genes we sent them, we also provided them with statistics on how many mutation-prone sites their original genes had and how much they can be improved for stability. </ul> |
| − | <p>University of Georgia:</p> | + | <p><font color="758a87">University of Georgia:</p> |
| − | <ul> We participated in the Archae interlab study hosted by the University of Georgia's team, during which we measured red fluorescent proteins for them</ul> | + | <ul><font color="758a87"> We participated in the Archae interlab study hosted by the University of Georgia's team, during which we measured red fluorescent proteins for them</ul> |
| − | <p>Vilnius-Lithuania:</p> | + | <p><font color="758a87">Vilnius-Lithuania:</p> |
| − | <ul>After hearing about their project through our mutation survey, we gave the Vilnius-Lithuania iGEM team statistics on how mutation-prone their two most important gene sequences were. We divided these mutation spots into categories so that their team could consider the potential contributions of different sources of mutagens. </ul> | + | <ul><font color="758a87">After hearing about their project through our mutation survey, we gave the Vilnius-Lithuania iGEM team statistics on how mutation-prone their two most important gene sequences were. We divided these mutation spots into categories so that their team could consider the potential contributions of different sources of mutagens. </ul> |
| − | <p>University of California at San Franscisco:</p> | + | <p><font color="758a87">University of California at San Franscisco:</p> |
| − | <ul>After hearing about their project through our mutation survey, we offered the analyze the genetic circuits that the UCSF team engineered. We have arranged to analyze their full circuit sequences through our circuit-optimization software, in order to determine the risk mutation would pose in their paritcular situation. </ul> | + | <ul><font color="758a87">After hearing about their project through our mutation survey, we offered the analyze the genetic circuits that the UCSF team engineered. We have arranged to analyze their full circuit sequences through our circuit-optimization software, in order to determine the risk mutation would pose in their paritcular situation. </ul> |
| − | <p>Washington University at St. Louis:</p> | + | <p><font color="758a87">Washington University at St. Louis:</p> |
| − | <ul>Early on in our project, we contacted WashU's iGEM team to ask for their assistance in characterizing one of our optimized RFP constructs. Their team graciously offered to measure the fluorescence of two of our RFP constructs. In addition to their standard measurement protocol, their team also had the foresight to ask for our measurement protocol, which they replicated in detail in their lab. From the data they generated, we were able to resolve two issues- first, the cross-compairison between WashU's protocol and our own demonstrated that our initial mesaurement protocol was not fully optimized. With their protocol, which they gave our team in detail, fluoresecnce measurements were much more consistant. In addition to this valuable finding, which has caused our lab to change our measurement protocol, they also validated our finding that the K314100 promoter was not reliable with expression. On the contrary, with the R0010 promoter, our engineered RFP had good fluorescence signal- thus giving us independent confirmation from a second lab that our optimized RFPs were still expressed well. </ul> | + | <ul><font color="758a87">Early on in our project, we contacted WashU's iGEM team to ask for their assistance in characterizing one of our optimized RFP constructs. Their team graciously offered to measure the fluorescence of two of our RFP constructs. In addition to their standard measurement protocol, their team also had the foresight to ask for our measurement protocol, which they replicated in detail in their lab. From the data they generated, we were able to resolve two issues- first, the cross-compairison between WashU's protocol and our own demonstrated that our initial mesaurement protocol was not fully optimized. With their protocol, which they gave our team in detail, fluoresecnce measurements were much more consistant. In addition to this valuable finding, which has caused our lab to change our measurement protocol, they also validated our finding that the K314100 promoter was not reliable with expression. On the contrary, with the R0010 promoter, our engineered RFP had good fluorescence signal- thus giving us independent confirmation from a second lab that our optimized RFPs were still expressed well. </ul> |
| − | <p>University of Virigina:</p> | + | <p><font color="758a87">University of Virigina:</p> |
| − | <ul>As killswitches were a maor emphasis for our mutation-optimization strategy, we proposed to improve the SacB killswitch that Virigina's iGEM team was using for the engineered probiotics. Using their original part sequence, we generated an optimized version which we then sent their time for synthesizing and testing in their system. We also gave their team the names of Vanderbilt faculty that had legal expertise in the area of probiotic medicine that their team was working on. </ul> | + | <ul><font color="758a87"> As killswitches were a maor emphasis for our mutation-optimization strategy, we proposed to improve the SacB killswitch that Virigina's iGEM team was using for the engineered probiotics. Using their original part sequence, we generated an optimized version which we then sent their time for synthesizing and testing in their system. We also gave their team the names of Vanderbilt faculty that had legal expertise in the area of probiotic medicine that their team was working on. </ul> |
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Revision as of 17:46, 20 November 2015
Demons in the Code
Our team had many productive collaborations with universities across the world. We were especially excited by the number of teams who approached us out of interest in the numerous mutation-reducing tools that our team has developed. We were happy to give these teams free access to our optimization techniques, which not only helped our collaborators to improve the stability of their genetic elements, but also helped us expand our techniques to new applications and even new organisms.
University of Paris-Bettencourt:
- The team at Paris-Bettencourt approached us out of concern for the stability of their genetically engineered fermenting microbes. Given the importance of strict quality control and long-term stability in the applications that their team was envisioning for their project, they had a keen interest in making their genes more stable. We offered to optimized their fermentation genes using our computational algorithm. As their team did not have sufficient time to synthesize the genes we sent them, we also provided them with statistics on how many mutation-prone sites their original genes had and how much they can be improved for stability.
University of Georgia:
- We participated in the Archae interlab study hosted by the University of Georgia's team, during which we measured red fluorescent proteins for them
Vilnius-Lithuania:
- After hearing about their project through our mutation survey, we gave the Vilnius-Lithuania iGEM team statistics on how mutation-prone their two most important gene sequences were. We divided these mutation spots into categories so that their team could consider the potential contributions of different sources of mutagens.
University of California at San Franscisco:
- After hearing about their project through our mutation survey, we offered the analyze the genetic circuits that the UCSF team engineered. We have arranged to analyze their full circuit sequences through our circuit-optimization software, in order to determine the risk mutation would pose in their paritcular situation.
Washington University at St. Louis:
- Early on in our project, we contacted WashU's iGEM team to ask for their assistance in characterizing one of our optimized RFP constructs. Their team graciously offered to measure the fluorescence of two of our RFP constructs. In addition to their standard measurement protocol, their team also had the foresight to ask for our measurement protocol, which they replicated in detail in their lab. From the data they generated, we were able to resolve two issues- first, the cross-compairison between WashU's protocol and our own demonstrated that our initial mesaurement protocol was not fully optimized. With their protocol, which they gave our team in detail, fluoresecnce measurements were much more consistant. In addition to this valuable finding, which has caused our lab to change our measurement protocol, they also validated our finding that the K314100 promoter was not reliable with expression. On the contrary, with the R0010 promoter, our engineered RFP had good fluorescence signal- thus giving us independent confirmation from a second lab that our optimized RFPs were still expressed well.
University of Virigina:
- As killswitches were a maor emphasis for our mutation-optimization strategy, we proposed to improve the SacB killswitch that Virigina's iGEM team was using for the engineered probiotics. Using their original part sequence, we generated an optimized version which we then sent their time for synthesizing and testing in their system. We also gave their team the names of Vanderbilt faculty that had legal expertise in the area of probiotic medicine that their team was working on.