Post on 06-May-2015
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iGEM Buenos Aires 2012
Manuel Gimenez
Luciano Morosi
Verónica Parasco
Ma. Alejandra Parreño
Mario Rugiero
iGEM is the international Genetically Engineerd Machines competition
• Meant for students from all around the world
• To share freely
• To combine
• To contribute
• To learn
• To solve
Some projects over the past years UT Austin 2004
University of Washington 2011
UC Berkeley 2007
Biosensors Cambridge 2009
Groningen 2009
Ar(III), Cu(I o II), Zn(II)
Arsenic conc. (ppb) pH Colony colour
0 9.5 none
5 7 none
10 7 green
20 4.5 green
30 4.5 red
Edinburgh 2006
iGEM and BioBricks
Why synthetic biology in Argentina and Latin America?
• New ways of solving practical problems
• Standardization & knowledge sharing
• Old iGEM projects might have immediate application in our country
• Free and public access technology
• Technology independence
Our project is “Tunable Synthetic Ecology”
Goal:
Co-culture genetically engineered machines at tunable proportions
while using re-utilizable and well-characterized parts and modules
Uses elements from
Ecology Classic Genetics Bioinformatics
Molecular Genetics Synthetic Biology
Systems Biology
Or... Synthetic Design of Communities
Color Palette
Synthetic Oenology
Optimization of Bioreactor Output
Circuit Isolation
Circuit Integration
To co-culture several strains in tunable proportions has interesting applications
To co-culture several strains allows to break the “6 promoters barrier”
Purnick, P.E. and R. Weiss, The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol, 2009. 10(6): p. 410-22.
To co-culture several strains introduces a new layer of modularity
Andrianantoandro, E., et al., Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol, 2006. 2: p. 2006 0028.
A
Rhl R Rhl I
I R
E Prhl
R
E
C4HSL
B
Las R Las I
I R
E Plas
R
E
3OC12HSL
Design 1: Independent Population Control
Pros and cons: + The system is already implemented for one
strain and can be re-utilized. + Easily scalable, as many strains as
independent QS systems can be added. + The system can be set with a small initial
inoculum of each strain. + Stabilization at sub-saturation OD could be
achieved. - A new QS mechanisms is required for each strain.
3OC12HSL
A
Rhl I
I
C4HSL
B
Las I
I
A
B
C
A
B
C
Design 2: Cross-Population Control
Pros and cons:
+ Required parts are available and well characterized.
+ Stabilization at sub-saturation OD could be achieved.
+ Should work in complex mediums. + Interesting dynamics as oscillations could
arise. - A new QS mechanisms is required for each strain. - Not scalable, modifications to several or all strains are required each time a new strain is added. - A minimum OD is required for the system to work.
-LYS
+TRP
Lysine
Tryptophane
+LYS
-TRP Export
Export A
B
Design 3: Crossfeeding
Pros and cons: + Relatively easy to implement, but new parts would need to be created. + Feasible based on previous studies (Shou et. al., 2006) + Easily scalable, as many strains as initial amino acid auxotrophies can
be added - Doesn’t work at very low or very high cell densities. - Only works in synthetic defined mediums. - A considerable initial cell density is required to start the system
A B States
A B
Ener
gy
Lan
dsc
ape
States
Gene A P(A)
Gene B P(B)
Gene A P(A)
Gene B P(B)
Ener
gy
Lan
dsc
ape
Design 4: Stochastic States Transitions
Pros and cons: + Completely independent of cell density.
+ If a rare state induces death, a slow population growth could be
achieved - All components need to be incorporated in the same strain, thus no
circuit integration or isolation is possible (see applications section).
Acknowledgments
• UNU BioLAC • FCEN UBA • Advisors German Sabio Alan Bush • Instructors Alejandro D. Nadra Ignacio E. Sánchez • External advisors Raik Grümberg Fernan Federici