first institute of higher education in modern china since 1895 a world-class, progressive, and...
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First Institute of Higher Education in Modern China
Since 1895
A World-class, Progressive, and Multidisciplinary Research
University
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Construction of Our TeamsConstruction of Our Teams
30
3
1116
10TeamsTeams
UndergraduatesUndergraduates
GraduatesGraduates
TeachersTeachers
FoundationsFoundations
FactsFacts
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China workshopChina workshop
Peking University
Tsinghua University
Tianjin University
USTC
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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"
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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
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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 .
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Our teamsOur teams
ProcessProcess
WorkshopsWorkshops
A
Brainstorm Brainstorm
B
DesignDesignC
SimulationSimulationD
ExperimentExperimentE
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Symbiotic System
Our projectsOur projects
Vitamin Beer
Symbiotic System
Bio-DiodeRS Flip-Flop
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Bio-Diode Bio-Diode
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Basiccomponents
E.coli
Too hard for one cell
Four gene circuitsact modular to
form a bio-circuit
Integratedcircuit
Computer
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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
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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
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Biobrick designBiobrick design
Generator
Amplifier
Block
Lamp
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Immobilize cells & Equipment
Immobilization:GeneratorAmplifierBlock
Immobilization:GeneratorAmplifierBlock
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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
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Test result
0 2 4 6 80
500
1000
Time (h)
Flu
ore
scen
ce (
A.U
.)
Block
Generator
Amplifier
Amplifier+AHL
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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
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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
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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
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Genetical
RS Flip-Flop
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WHAT? R
SQ
&
&
Q
The concept of enable control
J
KCP
EN
Q
Q
Q
QD &
&
&
&1
&
&
&
&
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Falling-edge trigger
A B0 0
1
1
B A
CPJ
K
Q
HOLD FLIP-FLOP
Master-slave JK flip-flop
POPS
POPS
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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
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We are LacI.We are LuxR.
GFP
LuxI CI PLac PCI LuxR
LuxPR
DESIGN
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GFP
LuxI CI PCILuxR
LuxPR
LacI
LacI
IPTG comes to save you
AHL
AHL
AHL
AHL
AHL
CICI
PLac
LuxR
LuxR
LuxR LuxR
IPTG
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LuxI CI PCI LuxR
AHL
AHL
AHL
AHL
AHL
CICI
LuxR
LuxR
LuxR
LuxRAHL
AHL
GFP
GFP
GFPGFP
GFP
GFP
LuxPR GFP
PLac
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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.
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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
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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
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BBa_R0040
BBa_P0412
BBa_R0010
BBa_C0261
BBa_Q04510
BBa_A340620
BBa_E0840
Function of CI
protein Leaky expression
Generating AHL
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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
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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
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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
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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.
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Acknowledgement• Advisors:
Prof. Yingjin Yuan
Prof. Xueming Zhao
Prof. Pingsheng Ma
Prof. Jianping Wen
Sponsors:
Tianjin University
National Natural Science Foundation of China