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First Institute of Higher Education in Modern China Since 1895. A World-class, Progressive, and Multidisciplinary Research University. Construction of Our Teams. Undergraduates. 30. 10. Teams. 3. Facts. Graduates. 6. 111. Teachers. Foundations. Peking University.
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First Institute of Higher Education in Modern China Since 1895 A World-class, Progressive, and Multidisciplinary Research University
Construction of Our Teams Undergraduates 30 10 Teams 3 Facts Graduates 6 111 Teachers Foundations
Peking University Tsinghua University Tianjin University USTC China workshop
China workshop "Engineering RNA Devices as Communication and Control Systems " "Building an Infrastructure for Metabolic Engineering" "Synthetic Biology, A System for Engineering Biology" "Building A Constructive Culture, The Ethics of Synthetic Biology"
TTT workshop Peking University Virginia Bioinformatics Institute Tsinghua University Davidson College Tianjin University USTC Chiba University National Yang Ming University Hong Kong University of Science and Technology Melbourne University
TTT workshop “Standard and Synthetic Biology” “How to construct an iGEM team” “iGEM Resources and Expectations” “An iGEM summer example” Reports of Peking, Tsinghua, USTC, NYMU, TJU, VT, Melbourne, Chiba, HKUST, Davidson .
Brainstorm B Workshops C Design A E D Simulation Experiment Our teams Process
Bio-Diode RS Flip-Flop Symbiotic System Symbiotic System Vitamin Beer Our projects
Basic components Integrated circuit Computer Too hard for one cell E.coli Four gene circuits act modular to form a bio-circuit
Bio-generator Generator Amplifier Block Lamp Wires Culture medium Current Flux of AHL Light GFP Bio-diode Bio-lamp Design Diode in electronic circuit Bio-Diode in Biology circuit Positive-biased Negative-biased
Generator cell Block cell function Amplifier cell Generator cell Lamp cell Amplifier cell Block cell Generator cell Lamp cell Block cell Amplifier cell Lamp cell Generator cell Generator cell Generator cell Block cell Amplifier cell Block cell Amplifier cell Block cell Amplifier cell break down Dark Light Lamp cell Lamp cell Lamp cell Positive-biased Negative-biased
Generator Amplifier Block Lamp Biobrick design
Immobilize cells & Equipment Immobilization: Generator Amplifier Block
amplifier cell Block cell generator cell output concentration output concentration output concentration generator generator generator flux flux flux Unamplified Break down amplifier cell block cell generator cell output of positive-biased output of negative-biased output concentration output concentration output concentration generator flux amount of G generator generator flux flux flux Simulation of the whole system Positive-biased Negative-biased
1000 Block Fluorescence (A.U.) 500 Generator Amplifier Amplifier+AHL 0 0 2 4 6 8 Time (h) Test result
Test result 500 400 300 Fluorescence/(A.U.) control 200 +AHL +IPTG 100 +IPTG+AHL 0 0 1 2 3 4 Time/h
500 400 G+B G+B+A 300 G+A+B G + A G + A( NO IPTG ) 200 fluorescence 100 G 0 Final result Positive-biased pass through Negative-biased blocked
Model Predicting potential performance of our modules and guiding experiments • Design • A bio-circuit • containing a bio-diode • placed in • designed equipment • Goal • Building a dynamic biology • circuit • made up of • different modules Experiment Testing our design and verifying the result of model Summary
Genetical RS Flip-Flop
R & & Q J & Q & CP Q Q & K & Q D & Q & EN S & & 1 WHAT? The concept of enable control
Master-slave JK flip-flop CP J K Q HOLD FLIP-FLOP POPS POPS Falling-edge trigger 1 A B A B 0 0 1
Biological circuit & Multiple functions PoPS PoPS (IPTG) (GFP) WHY? Instead of simulating electric circuit through the interactions between complicate logic gates we use the biological delay, and gene regulation to realize the function of complex circuits with simple biological systems.
We are LuxR. DESIGN We are LacI. LuxI PCI CI PLac LuxR LuxPR GFP
AHL AHL AHL AHL AHL CI CI IPTG IPTG comes to save you LuxR LuxR LuxR LuxR LacI LacI CI LuxR PLac LuxI PCI LuxPR GFP
AHL AHL AHL AHL AHL AHL AHL LuxR LuxR LuxR LuxR CI CI GFP GFP GFP GFP GFP GFP LuxR PCI PLac CI LuxI LuxPR GFP
SoGFPonly expresseswhen input signal changes. LuxR Our system takes advantage of delay existing in biology systems-the degradation period of protein. TIME-DELAY GFP
MODELCONSTRUCTION Mathematical Model of genetic circuit is constructed based on ordinary differential equation
Rising-edge Falling-edge AHL 30 30 CI AHL LuxR CI AHL-LuxR 20 20 LuxR GFP AHL-LuxR GFP 10 10 0 0 0 100 200 300 400 0 50 100 150 200 250 Time(min) Time(min)
Generating AHL BBa_R0040 Function of CI protein BBa_P0412 √ √ BBa_R0010 Leaky expression BBa_C0261 BBa_Q04510 ? BBa_A340620 BBa_E0840
800 control t=6.67h 1mM IPTG t=6.67h 1mM IPTG (supplement) 600 GFP 400 200 0 6 8 10 12 14 16 18 Time /h SYSTEMTESTING We optimized the most suitable condition for addition of IPTG—OD600=0.2~0.3, C=0.5μM. The function of trigger
FINALRESULTS 1000 Inhibition of LuxR 800 Intensity of GFP are different, but both tend to be stable. 600 GFP 400 AHL Difference 200 0 5 10 15 Time (h) GFP (t=4.66h 0.6μM AHL) GFP (t=4.66 0.5mM IPTG) GFP (t=4.66 0.5mM IPTG , t=6.67 aiia) AHL (t=4.66 0.5mM IPTG) AHL (t=4.66 0.5mM IPTG , t=6.67 aiia)
GFP M AHL M AHL E GFP E Time/h FOR FUTURE Contrast between model and experiment GFP easily to decompose Various signals such as pH、Temp. Response to different intensity of inputs For more advanced biological circuits
Conclusion • Two circuits have been constructed, a biological circuit and a genetic circuit • The mathematical models are used to optimize our original design • Results of experiment successfully verify our design.
Acknowledgement • Advisors: Prof. Yingjin Yuan Prof. Xueming Zhao Prof. Pingsheng Ma Prof. Jianping Wen Sponsors: Tianjin University National Natural Science Foundation of China