First Institute of Higher Education in Modern China Since 1895 A World-class, Progressive, and Multidisciplinary Research University

Construction of Our Teams Teams Undergraduates Graduates Teachers Foundations Facts

China workshop Peking University Tsinghua University Tianjin University USTC

China workshop "Synthetic Biology, A System for Engineering Biology" "Building A Constructive Culture, The Ethics of Synthetic Biology" "Engineering RNA Devices as Communication and Control Systems " "Building an Infrastructure for Metabolic Engineering"

TTT workshop Chiba University Tsinghua University Peking University Tianjin University USTC National Yang Ming University Hong Kong University of Science and Technology Melbourne University Virginia Bioinformatics Institute Davidson College

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.

Our teams Process Workshops A Brainstorm B Design C Simulation D Experiment E

Symbiotic System Our projects Vitamin Beer Symbiotic System Bio-Diode RS Flip-Flop

Bio-Diode

Basic components E.coli Too hard for one cell Four gene circuits act modular to form a bio-circuit Integrated circuit Computer

Design Diode in electronic circuit Current Flux of AHL Bio-Diode in Biology circuit Positive-biased Light GFP Wires Culture medium Negative-biased Generator Amplifier Block Lamp Bio-lamp Bio-diode Bio-generator

Positive- biased Generator cell Amplifier cell Block cell Lamp cell Generator cell Block cell Amplifier cell Lamp cell Generator cell Block cell Amplifier cell Lamp cell Generator cell Amplifier cell Block cell Lamp cell Generator cell Block cell Amplifier cell Lamp cell Generator cell Block cell Amplifier cell Lamp cell Light Dark break down function Negative-biased

Biobrick design GeneratorAmplifierBlockLamp

Immobilize cells & Equipment Immobilization: Generator Amplifier Block Immobilization: Generator Amplifier Block

Simulation of the whole system Positive-biased Negative-biased generator flux output concentration generator cell generator flux output concentration Block cell generator output concentration amplifier cell flux Unamplified generator output concentration generator cell flux generator output concentration amplifier cell flux generator output concentration block cell flux Break down amount of G flux output of positive-biased output of negative-biased

Test result Time (h) Fluorescence (A.U.) Block Generator Amplifier Amplifier+AHL

Time/h Fluorescence/(A.U.) control +AHL +IPTG +IPTG+AHL Test result

G G + A ( NO IPTG ) G + A G+A+B G+B G+B+A fluorescence Final result Positive-biased pass through Negative-biased blocked

Summary Experiment Testing our design and verifying the result of model 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

Genetical RS Flip-Flop

WHAT? R S Q & & Q The concept of enable control J K CP EN Q Q Q Q D & & & & 1 & & & &

Falling-edge trigger A B B A CP J K Q HOLDFLIP-FLOP Master-slave JK flip-flop POPS

PoPS (IPTG) PoPS (GFP) Biological circuit & Multiple functions WHY? we use the biological delay, and gene regulation to realize the function of complex circuits with simple biological systems. Instead of simulating electric circuit through the interactions between complicate logic gates

We are LacI. We are LuxR. GFP LuxI CI P Lac P CI LuxR LuxPR DESIGN

GFP LuxI CI P CI LuxR LuxPR LacI IPTG comes to save you AHL CI P Lac LuxR IPTG

LuxI CI P CI LuxR AHL CI LuxR AHL GFP LuxPR GFP P Lac

GFP TIME-DELAY LuxR Our system takes advantage of delay existing in biology systems-the degradation period of protein. So GFP only expresses when input signal changes.

MODEL CONSTRUCTION Mathematical Model of genetic circuit is constructed based on ordinary differential equation

Rising-edge Falling-edge Time(min) AHL CI LuxR AHL-LuxR GFP Time(min) AHL CI LuxR AHL-LuxR GFP

BBa_R0040 BBa_P0412 BBa_R0010 BBa_C0261 BBa_Q04510 BBa_A BBa_E0840 Function of CI protein Leaky expression Generating AHL

SYSTEM TESTING We optimized the most suitable condition for addition of IPTG—OD 600 =0.2~0.3, C=0.5μM. The function of trigger

Time (h) GFP GFP (t=4.66h 0.6μM AHL) GFP (t= mM IPTG) GFP (t= mM IPTG, t=6.67 aiia) AHL (t= mM IPTG) AHL (t= mM IPTG, t=6.67 aiia) FINAL RESULTS Inhibition of LuxR Intensity of GFP are different, but both tend to be stable. AHL Difference

Contrast between model and experiment FOR FUTURE Time/h AHL M GFP M AHL E GFP E 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