Team:UC Davis/Attributions

Cyantific: UC Davis iGEM 2016


As a small team of five students we each filled a critical role in the project, and worked together with our advisors and sponsers to bring about Cyantific.

Primary Contributions:

Samir Akre: iGEM team-member Samir took on a highly interdisciplinary role within our project; Samir took a lead on our iGEM Match website and on our Wiki page, also frequently providing assistance to members working on E. coli and B. subtilis. From a website standpoint, Samir developed the entire Wiki site, populated this site with team developed content, and debugged any issues that arouse. In terms of iGEM Match, Samir contacted numerous participating iGEM institutions to invite them to the platform and facilitate collaborative efforts across iGEM teams. In wet-lab, Samir assisted with E. coli and B. subtilis experimentation through regular assistance with PCR’s, gel electrophoresis trials, cloning, bacterial cell culture, and others.

Jonathan Chen: iGEM team-member Jon took the lead on E. coli work. Jon was involved in the entire E. coli experimentation process through primer designs, genetic circuit construction, E. coli strain identification, mini-prep, PCR’s, gel-electrophoresis, cloning, bacterial cell culture, and others. Jon provided some assistance for B. subtilis experimentation, working to develop compatible parts across E. coli and B. subtilis, namely HO, PcyA, and B0015, where both genetic segments could be used within both expression chassis under appropriate Golden Gate primer design.

Brent Weyers: iGEM team-member Brent took the lead on B. subtilis work. Brent worked closely with the Bacillus Genetic Stock Center to identify optimal strains for high CBCR expression and minimal chances of protease-related protein degradation; such strains were chosen to maximize opportunity for successful NPF expression in B. subtilis . Brent was involved in the entire B. subtilis experimentation process through primer designs, RBS special considerations, genetic circuit construction, PCR’s, gel-electrophoresis, bacterial cell culture, transformation protocol identification, and promoted science collaboration with the UC Santa Cruz iGEM team. Brent also prepared content for the iGEM presentation, Wiki content and editing, and developed the team poster for presentation at the Jamboree.

Amanda Everitt: iGEM team-member Amanda took on a highly versatile role for the team’s project. Amanda developed our GAF protein characterization model, which uses protein sequence alignments and profile Hidden Markov Models, to predict what color GAF domains are likely to reflect. Amanda took a lead on identifying isolation and purification methods for the GAF protein domains as well as CBCR-GAF domain spectral analysis. Amanda additionally took the primary role on developing the iGEM team’s presentation for the Jamboree and contributed extensively to the Wiki content.

Alexis Caligiuri: iGEM team-member Alexis took a full lead on our human-practices considerations for our project. Alexis meticulously considered the relation between society and our science, and the synergistic interplay between these two domains. Alexis performed Institutional Review Board (IRB) approved surveys, identified company practices and regulations, and delved into congressional legislation, in order to thoroughly assess policies and consumer viewpoints. Through this research, Alexis identified essential aspects, upon the juxtaposition of our science and society, which merit careful consideration.

Project support and advice:

Colin Milburn: Served as an advisor for our team, meeting with us weekly for progress check-in’s. Dr. Milburn reviewed all of our work, however placed particular emphasis on advising human practice work. He worked very closely with Alexis to establish human practice considerations and review her work. Dr. Milburn provided thorough recommendations and alternative viewpoints to consider on human practices work.

Marc Facciotti: Served as an advisor for our team, meeting with us weekly for progress check-in’s and routinely assisting our team in lab with advice. Dr. Facciotti did not contribute any physical wet-lab work, however assisted us with his expertise for potential protocols and other directions to look when work was not turning out as expected. Dr. Facciotti provided us with recommendations on Wiki content, iGEM Match, and on all wet-lab work. He carefully assessed ‘gaps’ in student knowledge and worked to provide students with the necessary instruction so that they could be competent in the work that they were performing.

Justin Siegel: Served as an advisor for our team, meeting with us weekly for progress check-in’s. Dr. Siegel carefully reviewed our data, presentation content, iGEM Match, and Wiki content on a weekly basis to provide feedback for potential improvement and new methods and protocols to try in lab. Assisted our team in diagnosing issues when lab work did not turn out as expected.

Matthias Hess: Served as an advisor for our team, meeting with us weekly for progress check-in’s. Dr. Hess carefully reviewed all our work and provided us with routine feedback on where to improve and develop to be a stronger team. Dr. Hess organized meeting locations and logistical items, such as printer posting, for our team.

Andrew Yao: Served as a graduate-student advisor for our team. Worked closely with wet-lab work as a supervisor. Andrew verified DNA sequences we wished to order, provided us with a host of lab protocols to implement for our work, and helped our team members debug issues as they arose in experimentation. Organized flight and conference details and ensure that lab reagent and equipment stocks were appropriately maintained.

Nathan Rockwell and Clark Lagarias: Served as a resource for information on the purification and expression of the GAF domain of CBCR's.

Fundraising help and advice:

Monsanto Company, a publicly traded American multinational agrochemical and agricultural biotechnology company, provided our team with some monetary support and welcomed us on a tour of their facilities. We met scientists, learned about their company operations, and were offered support for the science in our project if requested. Their local address is 37437 State Highway 16, Woodland, CA 95695.


Lab support:

Special thanks to the advisors Marc Facciotti and Andrew Yao for frequent check-ins and advice during lab and supporting the team with stocked equipment and reagents.

Wiki support:

Samir Akre - See Primary Contributions section

Human Practices support:

Alexis Caligiuri - See Primary Contributions section