Embed Size (px)
Citation preview
Rewirable circuitAn elegant means of system integration
iGEM HZAU-China!October 31, 2014
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
BackgroundAdaptability—what synthetic biological systems lack
One module, one function.
How to process different information with one module?
• Host overload
• Crosstalk
As the complexity increases
Intuitive solution: Combining circuitsBackground
Our Solution: The rewirable circuit
What if we can alter regulatory pathways and reuse existing parts?
Rewirable circuit
Our approach
Our approachAdvantages
• Eliminating crosstalk between processing modules.
More adaptive with fewer parts used.!Less is more!
• Choosing specific processing modules when needed
• Reducing workload
Viability of our design
Repressilator
T TT lacI cItetR T TlacI cI
Toggle switchlox66lox71
T TT lacI cItetR
Our rewirable circuit
Information processing
lox66lox71
T TT lacI cItetR
Our rewirable circuit
Our Biobricks:BBa_K1368000! BBa_K1368002
Viability of our designInformation processing
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]
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
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
Simulation resultsInformation processing
Another rewirable circuit design
luxpRluxpL
T TT luxI luxRaiiAluxpLluxpR
Our Biobricks:BBa_K1368004! BBa_K1368005! BBa_K1368006
AHL
Information processing
Results from fluorescence microscope
Positive feedback stage Negative feedback stage
TGFPluxpR
LuxI
LuxR-‐AHL complex
AiiA LuxI
LuxR-‐AHL complex
AiiA
Information processing
Results:experimental results were consistent with our expectationsResults from multifunctional microplate reader
Information processing
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
Potential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
Information processing
• …
Plenty of time for comparisonLeave it to nature
Information processingPotential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
• …
Maintain homeostasisMake next decision
Information processingPotential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
• …
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
• …
Potential applications
• Living therapeutics
• Environment improvement
• Circuit design in synthetic biology
Information processing
• …
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
Riboregulator assay
1 !71
1.9 Fold 2.5 Fold 5.5 Fold
Positive control
Negative control
Experimental group
Improvements in I/O modules
Increase response rates in output module
FluorophoreRNA aptamer
+
Fluorescent protein
Improvements in I/O modules
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
Elegant designHighlights
• Carefully arranging the order of parts
• Reusing the existing parts and pathways
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
Balance of biology and engineering
Module A
Module BM
odule C
time
• Simplified like the biological modules
• Independent like the engineering modules
Highlights
Synthetic biological system with rewirable circuits is like Transformer!
Highlights
—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
Policy & PracticesWhose Intellectual Property Right?
•Circuit designer
•Circuit user
•…Nobody?
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
OutreachPolicy & Practices
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.
Acknowledgement
Instructors:Sponsors and departments:
Advisors:
AcknowledgementOur Team!
Thanks
