Rewirable circuit - Main Page - 2014.igem.org
Transcript of Rewirable circuit - Main Page - 2014.igem.org
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Rewirable circuitAn elegant means of system integration
iGEM HZAU-China!October 31, 2014
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Disordered parts
TT
TT T
Duplicated the existing parts
Overlapping module
TT T
TT
Natural biological system
Standard parts
Logic elements
Small modules
Synthetic systems vs Natural systems
Synthetic biological system
Background
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BackgroundAdaptability—what synthetic biological systems lack
One module, one function.
How to process different information with one module?
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• Host overload
• Crosstalk
As the complexity increases
Intuitive solution: Combining circuitsBackground
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Our Solution: The rewirable circuit
What if we can alter regulatory pathways and reuse existing parts?
Rewirable circuit
Our approach
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Our approachAdvantages
• Eliminating crosstalk between processing modules.
More adaptive with fewer parts used.!Less is more!
• Choosing specific processing modules when needed
• Reducing workload
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Viability of our design
Repressilator
T TT lacI cItetR T TlacI cI
Toggle switchlox66lox71
T TT lacI cItetR
Our rewirable circuit
Information processing
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lox66lox71
T TT lacI cItetR
Our rewirable circuit
Our Biobricks:BBa_K1368000! BBa_K1368002
Viability of our designInformation processing
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Preliminary works
Parameter Valueβ0 0.03
Kdp 0.0069Kdm 0.347Ktl 6.93··· ···
Data collection Characterization
Information processing
Modeling
d[BmRNA]dt
= β0 +βKn
K n + An− Kdm[BmRNA]
d[B]dt
= Ktl[BmRNA]− Kdp[B]
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Parameter scanning and dynamic analysis
Limit cycle attractor
Fixed point attractor
An attracting limit cycle emerges as the promoter strength increases.Strength of promoter AStrength of promoter B
Stre
ngth
of p
rom
oter
C
Information processing
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Preconditions to implement both oscillation and bistability
• To implement oscillation
• To implement bistability
The weakest promoter must be strong enough.
Two promoters’ strength must be approximately equal.
Information processing
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Simulation resultsInformation processing
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Another rewirable circuit design
luxpRluxpL
T TT luxI luxRaiiAluxpLluxpR
Our Biobricks:BBa_K1368004! BBa_K1368005! BBa_K1368006
AHL
Information processing
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Results from fluorescence microscope
Positive feedback stage Negative feedback stage
TGFPluxpR
LuxI
LuxR-‐AHL complex
AiiA LuxI
LuxR-‐AHL complex
AiiA
Information processing
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Results:experimental results were consistent with our expectationsResults from multifunctional microplate reader
Information processing
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Information processingDesign procedures
• Design fitness functions
• Scan the topological space
A
BC
Topology
0
@0 0 �1�1 0 00 �1 0
1
A
A B CABC
Matrix
FitnessA=0.7891
FitnessB=0.8915…
• Match topological structures
• Sort and select
More details can be found in our modeling part
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Potential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
Information processing
• …
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Plenty of time for comparisonLeave it to nature
Information processingPotential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
• …
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Maintain homeostasisMake next decision
Information processingPotential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
• …
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Positive feedback: !increase efficiency
Negative feedback:!maintain the lower steady state
PollutionFunction!proteins
Information processingPotential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
• …
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Potential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
Information processing
• …
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Improvements in I/O modules Lower the leakage of recombinase
Our Biobricks:BBa_K1368007! BBa_K1368009! BBa_K1368013!BBa_K1368015
Tcre
Tcre
Problem: leakage
Input
taRNA
cre
Solution: riboregulator
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Riboregulator assay
1 !71
1.9 Fold 2.5 Fold 5.5 Fold
Positive control
Negative control
Experimental group
Improvements in I/O modules
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Increase response rates in output module
FluorophoreRNA aptamer
+
Fluorescent protein
Improvements in I/O modules
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RNA level fluorescence
DMHBI DMHBI + !13-2 RNA
DMHBI + !control RNA
Population levelOur Biobricks:BBa_K1368010! BBa_K1368011
Single cell level
Improvements in I/O modules
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Elegant designHighlights
• Carefully arranging the order of parts
• Reusing the existing parts and pathways
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Balance of biology and engineeringBiological modules:overlapping and closely related
Module A
Module BM
odule C
Module A
Module B
Module C
Engineering modules: independent
Highlights
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Balance of biology and engineering
Module A
Module BM
odule C
time
• Simplified like the biological modules
• Independent like the engineering modules
Highlights
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Synthetic biological system with rewirable circuits is like Transformer!
Highlights
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—Other implications of the Rewirable Circuits
Giving circuit adaptability is like giving it intelligence. What if it suddenly begins making variations of its own?
Policy & Practices
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Policy & PracticesWhose Intellectual Property Right?
•Circuit designer
•Circuit user
•…Nobody?
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A model providing stimulus for thinking
Awareness
PositiveNegative
StagePositive
Negative
2nd-dimension 3rd-dimension 4th-dimension
A 4-Dimensional model to help iGEMers think:
Policy & Practices
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OutreachPolicy & Practices
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Achievements
• Our input module, processing module and output module worked as we expected.
• We documented and submitted 13 new standard parts.
• We improved the characterization of 3 existing BioBrick Parts.
• Our team and HUST-China helped each other in lab work.
• We held a meetup this August in which 15 teams took part.
• We proposed a concept of rewirable circuit which can process different information with one module.
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Acknowledgement
Instructors:Sponsors and departments:
Advisors:
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AcknowledgementOur Team!
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Thanks