first institute of higher education in modern china since 1895 a world-class, progressive, and...

First Institute of Higher Education in Modern China

Since 1895

A World-class, Progressive, and Multidisciplinary Research

University

Construction of Our TeamsConstruction of Our Teams

30

3

1116

10TeamsTeams

UndergraduatesUndergraduates

GraduatesGraduates

TeachersTeachers

FoundationsFoundations

FactsFacts

China workshopChina workshop

Peking University

Tsinghua University

Tianjin University

USTC

China workshopChina 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 workshopTTT 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 workshopTTT 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 teamsOur teams

ProcessProcess

WorkshopsWorkshops

A

Brainstorm Brainstorm

B

DesignDesignC

SimulationSimulationD

ExperimentExperimentE

Symbiotic System

Our projectsOur projects

Vitamin Beer

Symbiotic System

Bio-DiodeRS Flip-Flop

Bio-Diode Bio-Diode

Basiccomponents

E.coli

Too hard for one cell

Four gene circuitsact modular to

form a bio-circuit

Integratedcircuit

Computer

DesignDesignDiode in

electronic circuit

Current

Flux of AHL

Bio-Diode in Biology circuit

Positive-biasedLight

GFP

Wires

Culture medium

Negative-biased

Generator

Amplifier

Block

LampBio-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 cellLight Darkbreakdown

function

Negative-biased

Biobrick designBiobrick design

Generator

Amplifier

Block

Lamp

Immobilize cells & Equipment

Immobilization:GeneratorAmplifierBlock

Immobilization:GeneratorAmplifierBlock

Simulation of the whole system

Po

sitive-bia

sed

Ne

gative

-bia

sed

generator flux

ou

tpu

t con

cen

tration

generator cell

generator flux

ou

tpu

t con

cen

tration

Block cell

generator

ou

tpu

t con

cen

tration

amplifier cell

flux

Unamplified

generator

ou

tpu

t con

cen

tration

generator cell

fluxgenerator

ou

tpu

t con

cen

tration

amplifier cell

fluxgenerator

ou

tpu

t con

cen

tration

block cell

flux

Breakdown

amount o

f G

flux

ou

tpu

t of p

ositive-b

iased o

utp

ut o

f neg

ative-biased

Test result

0 2 4 6 80

500

1000

Time (h)

Flu

ore

scen

ce (

A.U

.)

Block

Generator

Amplifier

Amplifier+AHL

0 2 4 6 80

500

1000

Time (h)

Flu

ore

scen

ce (

A.U

.)

4J4L8P8P+AHL

0 1 2 3 40

100

200

300

400

500

Time/h

Flu

ore

scen

ce/(

A.U

.)

control+AHL+IPTG+IPTG+AHL

Test result

0

100

200

300

400

500

G

G

+ A

( N

O

IPT

G )

G

+ A

G

+A

+B

G+

B

G+

B+

A

flu

ore

scen

ceFinal 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

SQ

&

&

Q

The concept of enable control

J

KCP

EN

Q

Q

Q

QD &

&

&

&1

&

&

&

&

Falling-edge trigger

A B0 0

1

1

B A

CPJ

K

Q

HOLD FLIP-FLOP

Master-slave JK flip-flop

POPS

POPS

PoPS(IPTG)

PoPS(GFP)

Biological circuit

& Multiple functions

WHY?

we use the biological delay, and gene regulation torealize 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 PLac PCI LuxR

LuxPR

DESIGN

GFP

LuxI CI PCILuxR

LuxPR

LacI

LacI

IPTG comes to save you

AHL

AHL

AHL

AHL

AHL

CICI

PLac

LuxR

LuxR

LuxR LuxR

IPTG

LuxI CI PCI LuxR

AHL

AHL

AHL

AHL

AHL

CICI

LuxR

LuxR

LuxR

LuxRAHL

AHL

GFP

GFP

GFPGFP

GFP

GFP

LuxPR GFP

PLac

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

GkRARA

RA

dt

dG

RAkARkdt

dRA

ARkRk

CCdt

dR

Ckdt

dC

AkAkAkdt

dA

ARkAkAkAkdt

dA

dG

M

dRAin

indR

M

dc

outdooutininoutout

inoutininoutindiin

22

2

1

2

22

222

1

''

22

1

21

2

Mathematical Model of genetic circuit is constructed based on ordinary differential

equation

Rising-edge Falling-edge

0 50 100 150 200 2500

10

20

30

Time(min)

AHLCILuxRAHL-LuxRGFP

0 100 200 300 4000

10

20

30

Time(min)

AHLCILuxRAHL-LuxRGFP

BBa_R0040

BBa_P0412

BBa_R0010

BBa_C0261

BBa_Q04510

BBa_A340620

BBa_E0840

Function of CI

protein Leaky expression

Generating AHL

SYSTEM TESTINGWe optimized the most suitable condition for addition of IPTG—OD600=0.2~0.3, C=0.5μM.

6 8 10 12 14 16 180

200

400

600

800

Time /h

GF

P

controlt=6.67h 1mM IPTG

t=6.67h 1mM IPTG (supplement)

The function of

trigger

5 10 150

200

400

600

800

1000

Time (h)

GF

P

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)

FINAL RESULTSInhibition 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