Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started...
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![Page 1: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/1.jpg)
Melbourne Uni
2008
![Page 2: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/2.jpg)
What is iGEM?•International Genetically
Engineered Machine competition
•Started in 2003 within MIT
![Page 3: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/3.jpg)
What is iGEM?•Now a global competition
•54 teams, 750 students, 19 countries
![Page 4: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/4.jpg)
What is iGEM
•Teams of students use principles of synthetic biology to create biological systems
![Page 5: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/5.jpg)
What is Synthetic Biology?
•Builds on genetic engineering technologies
•Adds a set of guiding principles to aid coordination of activities
•Standardisation
•Abstraction
![Page 6: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/6.jpg)
Lego Brick BioBrick
Standardisation
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Abstraction
![Page 8: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/8.jpg)
2008 Team ProjectBioClock
![Page 9: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/9.jpg)
BioClock•A customisable regulatory system
•One signal switches between multiple states
Signal
1 2 3
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Input
Output
Logic
BioClockSystem State
2
State 3
State 1
t=1
t=2
t=3
123
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How will it work?•Two methods currently being looked
at
•Ideal implementation through a binary counting system
•Contingency plan using a linear system
•Both will have the similar components, with different interactions
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Linear ModelSignal
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Signal
State 1 Mechanis
m
State 2 Mechanis
m
State 3 Mechanis
m
State 1 Mechanis
m
SignalSignal
State 2 Mechanis
m
Signal
Linear Model
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Linear ModelSignal
State 1 Mechanis
m
State 2 Mechanis
m
State 3 Mechanis
m
State 1 Mechanis
m
SignalSignal
State 2 Mechanis
m
State 1 Mechanis
m
SignalSignal
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Linear ModelSignal
State 1 Mechanis
m
State 2 Mechanis
m
State 3 Mechanis
m
State 2 Mechanis
m
State 3 Mechanis
m
Signal
State 2 Mechanis
m
![Page 16: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/16.jpg)
Design•Small teams researching different
parts of system
•Signaling
•Riboswitch
•Positive feedback
•Modeling
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Signal Sensor
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Riboswitch
RiboLock RiboKey
![Page 19: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/19.jpg)
Positive Feedback•Feedback loop that upregulates itself
P(tetR)C luxR luxPR luxI
GFP
AHL
Coactivates
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Signal
State 1 Mechanis
m
State 2 Mechanis
m
State 3 Mechanis
m
State 1 Mechanis
m
SignalSignal
State 2 Mechanis
m
Signal
Where they fit inSignal Sensor Riboswitch
Positive Feedback
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Binary ModelRed GreenBlue
0 0 0
R B G
0 0 1
0 1 0
0 1 1
1 0 0
1 0 1
1 1 0
1 1 1
Correspond toTime
0
1
2
3
4
5
6
7=22 + 21 + 20
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Binary Model
Sg0
On0
On1
Tr0
Tr1
Off
Green Globe Off
Red GreenBlue
0 0 0
R B GCorrespond toTime
0
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Binary Model
Sg1
On0
On1
Tr0
Tr1
Off
Green Globe On
Red GreenBlue R B G
0 0 1 1
Correspond toTime
![Page 24: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/24.jpg)
Binary Model
Sg2
On0
On1
Tr0
Tr1
Off
Green Globe Off
TriggerBlueLight
Red GreenBlue R B GCorrespond toTime
0 1 0 2
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Binary Model
Sg0
On0
On1
Tr0
Tr1
Off
Green Globe Off
![Page 26: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/26.jpg)
Genetic map from circuit
Receptor Riboswitch Positivefeedback loop
![Page 27: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/27.jpg)
Binary ModelEx: Counting to seven with three-color system
Goal
![Page 28: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/28.jpg)
Time Division Tasking Time
0
1
2
3
4
5
6
7
First T1/2, do task 1
Second T1/2, do task 2
Red GreenBlue
![Page 29: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/29.jpg)
Time Division Tasking Time
0
1
2
3
4
5
6
7
1st T1/4, do task 1
Red GreenBlue
2nd T1/4, do task 2
3rd T1/4, do task 3
4th T1/4, do task 4
![Page 30: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/30.jpg)
Modeling with two colours
Currently outputs GFP, RFP
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Modeling with two colours•Current output of two colour model
QuickTime™ and a decompressor
are needed to see this picture.
QuickTime™ and a decompressor
are needed to see this picture.
![Page 32: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/32.jpg)
Goal•We want to count as high as possible in binary
•Example with two colour system:
![Page 33: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/33.jpg)
Sensitivity Analysis•Code program that will produce
sensitivity plot
•Plot sensitivities against each kinetic parameter to to select best proteins
![Page 34: Melbourne Uni 2008. What is iGEM? International Genetically Engineered Machine competition Started in 2003 within MIT.](https://reader035.fdocuments.in/reader035/viewer/2022062804/5697bf821a28abf838c85e65/html5/thumbnails/34.jpg)
Timeline
March April May June
July AugustSeptemb
erOctober
Sensitivity testing of modelSensitivity testing of model
Kinetic testing of Kinetic testing of componentscomponents
AssembleAssemble
SystemsSystems Test systemsTest systems
Prepare for JamboreePrepare for Jamboree
Post resultsPost results
November 8-9
2008
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BudgetLab Expenses $10,000
Sequencing 3,000
Synthesising 3,000
SELEX 3,000
Consumables 1,000
Jamboree Expenses $22,000
iGEM Registration $1,000
Jamboree Fee $1,000
Accommodation $2,000
Flights $18,000
Total $32,000
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Questions
2008