Rewirable circuit An elegant means of system integration iGEM - - PowerPoint PPT Presentation
Rewirable circuit An elegant means of system integration iGEM HZAU-China October 31, 2014 Background Synthetic systems vs Natural systems Synthetic biological system Natural biological system T T T T T Small modules Overlapping
An elegant means of system integration iGEM HZAU-China October 31, 2014
Disordered parts
T T T T T
Duplicated the existing parts Overlapping module
T T T T T
Natural biological system Standard parts Logic elements Small modules
Synthetic systems vs Natural systems
Synthetic biological system
Adaptability—what synthetic biological systems lack
One module, one function. How to process different information with one module?
As the complexity increases
Intuitive solution: Combining circuits
Our Solution: The rewirable circuit
What if we can alter regulatory pathways and reuse existing parts? Rewirable circuit
Advantages
processing modules.
More adaptive with fewer parts used. Less is more!
modules when needed
Viability of our design
Repressilator
T T T
lacI cI tetR
T T
lacI cI
Toggle switch
lox66 lox71
T T T
lacI cI tetR
Our rewirable circuit
lox66 lox71
T T T
lacI cI tetR
Our rewirable circuit
Our Biobricks: BBa_K1368000 BBa_K1368002
Viability of our design
Preliminary works
Parameter Value β0 0.03 Kdp 0.0069 Kdm 0.347 Ktl 6.93 ··· ···
Data collection Characterization
Modeling
d[BmRNA] dt = β0 + β K n 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.
S t r e n g t h
p r
e r A Strength of promoter B Strength of promoter C
Preconditions to implement both
The weakest promoter must be strong enough. Two promoters’ strength must be approximately equal.
Simulation results
Another rewirable circuit design
luxpR luxpL
T T T
luxI luxR aiiA
luxpL luxpR
Our Biobricks: BBa_K1368004 BBa_K1368005 BBa_K1368006 AHL
Results from fluorescence microscope
Positive feedback stage Negative feedback stage
T
GFP
luxpR
LuxI
LuxR-‑AHL ¡complex
AiiA LuxI
LuxR-‑AHL ¡complex
AiiA
Results:experimental results were consistent with our expectations Results from multifunctional microplate reader
Design procedures
A B C
Topology
−1 −1 −1
A B C A B C
Matrix FitnessA=0.7891 FitnessB=0.8915 …
More details can be found in our modeling part
Potential applications
Plenty of time for comparison Leave it to nature
Potential applications
Maintain homeostasis Make next decision
Potential applications
Positive feedback: increase efficiency Negative feedback: maintain the lower steady state Pollution Function proteins
Potential applications
Potential applications
Lower the leakage of recombinase
Our Biobricks: BBa_K1368007 BBa_K1368009 BBa_K1368013BBa_K1368015
T
cre
T
cre
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
Increase response rates in output module
Fluorophore RNA aptamer
Fluorescent protein
RNA level fluorescence
DMHBI DMHBI + 13-2 RNA DMHBI + control RNA
Population level
Our Biobricks: BBa_K1368010 BBa_K1368011
Single cell level
Elegant design
Balance of biology and engineering
Biological modules:
Module A Module B Module C Module A Module B Module C Engineering modules: independent
Balance of biology and engineering
Module A Module B Module C
time
like the biological modules
like the engineering modules
Synthetic biological system with rewirable circuits is like Transformer!
—Other implications of the Rewirable Circuits
Giving circuit adaptability is like giving it
variations of its own?
Whose Intellectual Property Right?
A model providing stimulus for thinking
Awareness Positive Negative Stage Positive Negative
2nd-dimension 3rd-dimension 4th-dimension A 4-Dimensional model to help iGEMers think:
Outreach
worked as we expected.
different information with one module.
Instructors: Sponsors and departments: Advisors:
Our Team!