Items remarked by * means it was done by someone who is not student team members.
Project Design
The initial idea of doing a project on catnip came from our advisor *Xuan Wang who mentioned to us the fact that catnip can be used as a green pesticide. Alexis Zeng did further research and saw the possibility of using a co-culture system for manufacturing. Lucinda Lin When we search for strategies to optimize the microbial production, our primary PI *Dr. Haoqian Zhang recommended the use of TALE stabilized promoters.
Lab
-Geraniol Production:
Design: Alexis Zeng
Molecular Cloning: Tara Yuan, Leo Li, Alexis Zeng, Leo Li, Rocky Yu, *Genscript (construction of pMVA-GPPS-GES)
Shake-flask fermentation: Alexis Zeng, Jesse Sun
GC Characterization: Sean Yao, Charles Wei
-pTALE Promoters:
Design: Alexis Zeng, *Boxiang Wang
Molecular Cloning: Sean Yao, Rocky Yu, Tara Yuan, *Boxiang Wang (built the promoter library with us by SOE PCR and Golden Gate)
Flow Cytometry Characterization: Tara Yuan, Sean Yao, Charles Wei
Genome Integration: Sean Yao, Alexis Zeng, *Yiming Dong (provided us with plasmids, taught us the usage, and performed PCR), Rocky Yu
-Yeast Gene Deletion:
Design: Tara Yuan, Alexis Zeng, Charles Wei, *Boxiang Wang (taught Tara and Alexis principles for designing sgRNA and homologous arm)
Molecular Cloning: Alexis Zeng, David Yang, Tara Yuan, Leo Li, Rocky Yu, Charles Wei
Verification: Alexis Zeng, *Xuanyu Zhao (deleted OYE2 by CRISPR while we achieved the same result by homologous recombination
-Nepetalactol Production:
Design: Alexis Zeng, *Boxiang Wang (proposed a new strategy using biobrick assembly when we failed to construct the yeast vector using Gibson Assembly)
Shake-flask fermentation: Sean Yao, *Boxiang Wang (helped us to feed the yeast geraniol during night)
GC Characterization: Sean Yao, Tara Yuan, Charles Wei, Alexis Zeng, Rocky Yu
-Interlab:
Interlab:Sean Yao, Charles Wei, David Yang
Human Practice
-Meet up:
Alexis Zeng, Lucinda Lin, and Sean Yao went to the iGEM Southern China Regional Meeting hosted by team SZU
Lucinda Lin and Sean Yao took part in the 5th Conference of China iGEMer Community
Alexis Zeng and Lucinda Lin organized the Shenzhen High School iGEM Meetup
Alexis Zeng, Lucinda Lin, Wade Xiao, Charles Wei, Rocky Yu participated the EurAsian Meet up
-Integrated Human Practice:
Interview with Fenghua Li: Lucinda Lin, Rocky Yu, Wade Xiao
xfactory presentation: Lucinda Lin, Alexis Zeng
Costal City Interview: Eden Yu, Rocky Yu, Luncinda Lin, Alexis Zeng
Green Drinks Workshop: Eden Yu, Rocky Yu, Alexis Zeng
Interview with government: Rocky Yu
-HP documentary:
Director: Rocky Yu
Participated: Lucinda Lin, Alexis Zeng, Eden Yu, Charles Wei, Leo Li, Tara Yuan, *Boxiang Wang, *Yiming Dong
-Public Engagement:
Makers Fair: Eden Yu, Alexis Zeng, Rocky Yu, Charles Wei
Maker space: Alexis Zeng, Lucinda Lin
Interview with neighborhood: Alexis Zeng
-Applied Design:
Design: Alexis Zeng, *Boxiang Wang, Charles Wei
3D model: Eden Yu
Construction: Eden Yu
Model
Lucinda Lin: wrote the ODE equations
Wade Xiao: researched the possible range of parameters
Eden Yu: carried out sensitivity analysis
*Alicia Graham: taught us how to use Matlab and the basics of modeling
*Honghao Su: helped us to research Flux Balance Analysis, attempted to use CellNetAnalyzer find out the optimum expression level of GPPS and GES.
Art Design
Marie Wei: drew wiki illustration, designed postcards, poster, and banner.
David Yang: designed team uniform, wiki layout
Katrina Zhuo: designed team logo
Wiki Construction
Lucinda Lin
Charles Wei
Acknowledgment:
The journey of iGEM wasn’t an easy one, and GreatBay_China has received lots of help from many people. Here we would like to thank specially to the following people who have given us the kindest support:
Boxiang Wang
As a teacher in Bluepha Lab, Boxiang Wang offered us project-oriented training and taught us a set of courses on Molecular Biology, Synthetic Biology, Biosafety, and Ethics. Also as an iGEM coach, he gave us advice on project design and experiment planning, helped troubleshooting experiments, shared external resources, and attended our weekly meetings.
Xuanyu Zhao
Xuanyu Zhao helped us to pick up many important habits for scientific research such as making strain lists and having standardized experiment records. Also by frequent discussions with us, she guided us through the difficulties encountered in experiments, for example, modifying the method to delete yeast genes.
Yiming Dong
Yiming Dong has given us numerous useful tips on molecular cloning experiments. She provided us with the plasmid to perform genome insertion. Also, she shot some video with Fenghua Li for us, and this video later became essential materials of our documentary.
Li Yu and John Henry
Li Yu and John Henry from xFactory offered keen guidance to help us design the cat shelter “Kitty Wonderland”. John Henry taught Eden Yu how to use the laser cut-out machine to prepare materials for constructing the cat shelter.
Honghao Su
Honghao Su helped us with modeling by sharing what he has learned about Flux Balance Analysis, and has attempted to use FBA for predicting the optimum expression level of GPPS and GES.
Fenghua Li and members of her animal rescue team
Fenghua Li kindly allowed us to film her and the cats she rescued. Through direct interview and in-depth conversation, she and the members of her animal rescue team offered us an insight into the current situation of and difficulties faced by feral cat rescue nowadays, which was crucially important guidance for our human practice. They also reviewed our design of cat shelter and gave us suggestions to modify the shelter.
Dr. Junbiao Dai
Dr. Junbiao Dai has given us lots of advice on yeast gene deletion and vector construction, which was a timely help as we didn’t have any experience working with yeast before.
Dr. Christopher Voigt
The excellent work of Dr. Christopher Voigt truly inspired us and encouraged us to explore more about the TALE stabilized promoters. During the 4th Synthetic Biology Young Scholar Forum, he answered our questions about the usage of the TALEsp and discussed with us the application of the TALEsp to metabolic engineered. After, Dr. Christopher Voigt kindly commended our project. His warm encouragement has made us more motivated in the journey of discovery about synthetic biology.
Pre-iGEM training & project start:
Bluepha Lab offers synthetic biology education in the forms of winter camps and summer camps. The course syllabus and materials are not freely available online. In February 2018, majority members of GreatBay_China took part in the Cell Factory winter camp held in Bluepha Lab which lasted for five days and was taught by Boxiang Wang. It was during the winter camp that we first started brainstorming. The project started in March and the lab began in April.
