Synthetic Biology I
The Programming of Cells
Nawwaf Kharma & Luc Varin
Artificial Life Group
Elec. & Comp. Engineering and Biology Departments
Concordia University, Montréal (QC), Canada
kharma@ece.concordia.ca
Synthetic Biology- What & Why
• It is an emerging area of research
that combines science and engineering
to envision, design and realize novel
structures and functions (mainly in cells)
by (primarily) modifying the genome
(within the cells)
• Cells have advantages:
• They have/can have built-in
interfaces, to sense and produce
many substances
• They are easy to mass produce,
store and distribute
• They are generally more robust than
man-made systems
• They are optimizable via directed
evolution
Artificial Life Group
The Programming of Cells
2
Biological Refresher:
Flow of genetic information
DNA 
Transcription
 RNA
RNA 
Translation
 Protein
Proteins 
Can interact with
each other
Artificial Life Group
The Programming of Cells
3
Basic Paradigm:
From the ground up
• First: Basic Components
Combinatorial & Sequential
• Second: Larger Circuits
With more/larger components and/or more functionality
• Third: Communications & Pattern Formation
Leading to even greater functionality
>> Finally, future Challenges that must be met if
the field is to advance >>>
Artificial Life Group
The Programming of Cells
4
Combinatorial Components I:
Promoter-based Regulation
Artificial Life Group
The Programming of Cells
Kaern et al. (2003)
5
Combinatorial Components II:
siRNA-based Regulation
Artificial Life Group
The Programming of Cells
Deans et al. (2007)
6
Combinatorial Components III:
Ribozyme-based Regulation
Artificial Life Group
The Programming of Cells
Win et al. (2008)
7
Sequential Components I:
First Toggle
Artificial Life Group
The Programming of Cells
Gardner et al. (2000)
8
Sequential Components II:
Various Oscillators
Artificial Life Group
The Programming of Cells
Elowitz et al. (2000)
Wong et al. (2006)
9
Sequential Components III:
Mammalian Memory
Artificial Life Group
The Programming of Cells
Ajo-Franklin et al. (2007) 10
Sequential Components IV:
Pulsers & Delays
Delays using repressors only- how?
Artificial Life Group
The Programming of Cells
Kaesling et al. (2006)
11
Summary 1
of 3
Combinatorial Components include:
 Switches
 Inverters
 Logic Gates


Sequential Components include:
 Oscillators
(ON-OFF-ON-OFF-…)
 Toggles
(ON or OFF, depending on Input & State)
 1-bit Memory
(ON or OFF, depending on Input)
 Pulse-rs
(ON for a short while, then auto-OFF)
 Delays
(Output follows Input after a Delay)
Next: Scale-up & combine components to build
circuits
Artificial Life Group
The Programming of Cells
12
Larger Circuits I:
Combinatorial Logic
Artificial Life Group
(4 inputs/1 output)
The Programming of Cells
Rinaudo et al. (2007)
13
Artificial Life Group
The Programming of Cells
Rinaudo et al. (2007)
14
Larger Circuits II:
Sequential Logic (multi-bit memory)
Artificial Life Group
The Programming of Cells
Ham et al. (2008)
15
Larger Circuits III:
Modular Design
(- also involving intercellular communication)
Artificial Life Group
The Programming of Cells
Kobayashi et al. (2004)
16
Summary 2

of 3
Ex1: Larger Combinatorial Circuit with:
 Multi-input Logic Function with
 4 (and 5) inputs and 1 output

Ex2: Multi-bit Memory that:
 Set precisely using a series of inputs
 Grows exponentially with no. of invertases

Ex3: Modular Circuit with:
 3 intra-cellular modules that
Sense, Process, and Output information
 It also communicates with other cells
Artificial Life Group
The Programming of Cells
17
Advanced Topics I:
Pattern Formation (using inter-cellular communications)
Artificial Life Group
The Programming of Cells
Basu et al. (2005)
Bernhardt et al. (2007) 18
Advanced Topics II:
Inter-kingdom Communications
(using another kind of inter-cellular communications)
Artificial Life Group
The Programming of Cells
Weber et al. (2007)
19
Advanced Topics II continued
Inter-kingdom Communications
Artificial Life Group
The Programming of Cells
Weber et al. (2007)
20
Advanced Topics III:
Applications
Artificial Life Group
The Programming of Cells
Rodrigo et al. (2007)
21
Summary 3

of 3
Ex1: Pattern Formation
 Is necessary for autonomous
differentiation of large collections of cells

Ex2: Inter-cellular Communications
 Is necessary for coordinated action by
larger collections of cells

Ex3: Applications
 Necessary to justify the significant cost
of investment in “blue-sky” research
Artificial Life Group
The Programming of Cells
22
Future
Challenges I:
Reliable WellCharacterized
Modules
Artificial Life Group
The Programming of Cells
Canton et al. (2008)
23
Future Challenges II:
Synchronization & Communications
How can a large number of
components communicate and work
synchronously across large distances?
Possible answers include:
A. A large number of freely-diffusing
signals
B. A much smaller number of shortdistance signals
C. Isolated channels (e.g. neurons)
that pass signals
As to operating synchronously:
simulations have been made but
no implementations yet!
Artificial Life Group
The Programming of Cells
Garcia-Ojalvo et al. (2004) 24
Future Challenges III: Interfacing
with Electro/Optical Components
How can electronic devices be
interfaced to the new cellular
devices? Possibilities include:
A. Light at different frequencies
B. Electric field
C. Chemical reactions, such as:
A mammalian cell-based frequency
generator: DC power converts
ethanol into acetaldehyde, which
dose-dependently triggers
expression of the BMP-2 in
engineered rat cardiomyocytes
(AIRNRC-BMP-2) and increases the
contraction frequency
Artificial Life Group
The Programming of Cells
Weber et al. (2009) 25
Final Summary
Cells are not like human-engineered machines
Cells, if fully understood, may be treated as machines
Cells are not fully understood or characterized
Researchers are starting to see potential in manipulating the
genome of cells
And they are continuing to expand the frontier while
simultaneously improving the reliability of existing components
There has been great progress, but still more needs to be done to:
A. Build a basic repertoire of reliable well-characterized combinatorial &
sequential components
B. Communicate and synchronize across large distances and in different
mediums
C. Establish controllable methods for growing large patterns of inter-acting
cells
Artificial Life Group
The Programming of Cells
26
Artificial Life Group
The Programming of Cells
27
References
Kaern et al. (2003): Mads Kærn,William J Blake, and J J Collins. “The Engineering of Gene
Regulatory Networks.” Annual Review of Biomedical Engineering 5:179–206.
Deans et al. (2007): Tara L Deans, Charles R Cantor & James J Collins. “A Tunable Genetic
Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in
Mammalian Cells.” Cell 130, 363–372.
Win et al. (2008): Maung Nyan Win & Christina D Smolke. “Higher-Order Cellular Information
Processing with Synthetic RNA Devices.” Science vol. 322, 456-460.
Gardner et al. (2000): Timothy S Gardner, Charles R Cantor & James J Collin. “Construction
of a genetic toggle switch in Escherichia coli.” Nature vol. 403, 339-342.
Elowitz et al. (2000): Michael B Elowitz & Stanislas Leibler. “A synthetic oscillatory network of
transcriptional regulators.” Nature vol. 403, 335- 338.
Wong et al. (2006): W W Wong and J C Liao. “The design of intracellular oscillators that
interact with metabolism.” Cell. Mol. Life Sci. vol. 63:1215–1220.
Ajo-Franklin et al. (2007): Caroline M Ajo-Franklin, David A Drubin, Julian A Eskin, Elaine P S
Gee, Dirk Landgraf, Ira Phillips & Pamela A Silver. “Rational design of memory in
eukaryotic cells.” Genes and Development 21:2271–2276.
Kaesling et al. (2006): http://keaslinglab.lbl.gov/wiki/index.php/Synthetic_Biology__Devices_-_Pulse_Generator
Rinaudo et al. (2007): Keller Rinaudo, Leonidas Bleris, Rohan Maddamsetti, Sairam
Subramanian, Ron Weiss & Yaakov Benenson. “A universal RNAi-based logic evaluator
that operates in mammalian cells.” Nature Biotechnology vol. 25, No. 7: 795-801.
Artificial Life Group
The Programming of Cells
28
References
continued
Ham et al. (2008): Timothy S Ham, Sung K Lee, Jay D Keasling & Adam P Arkin. “Design and
Construction of a Double Inversion Recombination Switch for Heritable Sequential
Genetic Memory.” PloS ONE, vol. 3, No. 7: 1-9.
Kobayashi et al. (2004): Hideki Kobayashi, Mads Kærn, Michihiro Araki, Kristy Chung,
Timothy S Gardner, Charles R Cantor & James J Collins. “Programmable cells: Interfacing
natural and engineered gene networks.” PNAS vol. 101, No. 22: 8414–8419.
Basu et al. (2005): Subhayu Basu, Yoram Gerchman, Cynthia H Collins, Frances H Arnold &
Ron Weiss. “A synthetic multicellular system for programmed pattern formation.” Nature,
vol. 434: 1130-1134. IET Synth. Biol., vol. 1, no. 1–2: 29–31.
Bernhardt et al. (2007): K Bernhardt, E J Carter, N S Chand, J Lee, Y Xu, X Zhu, J W Ajioka, J
M Goncalves, J Haseloff, G Micklem and D Rowe. “New tools for self-organised pattern
formation.”
Weber et al. (2007): Wilfried Weber, Marie Daoud-El Baba & Martin Fussenegger. “Synthetic
ecosystems based on airborne inter- and intrakingdom communication.” PNAS, vol. 104,
no. 25: 10435–10440.
Rodrigo et al. (2007): G Rodrigo, A Montagud, A Aparici, M C Aroca, M Baguena, J Carrera, C
Edo, P Fernandez-de-Cordoba, A Ferrando, G Fuertes, D Gimenez, C Mata, J V Medrano,
C Navarrete, E Navarro, J Salgado, P Tortosa, J Urchueguia and A Jaramillo. “Vanillin cell
sensor.” IET Synth. Biol., vol. 1, no. 1–2: pp. 74–78.
Artificial Life Group
The Programming of Cells
29
References
continued
Alexic et al. (2007): J Aleksic, F Bizzari, Y Cai, B Davidson, K de Mora, S. Ivakhno, S L
Seshasayee, J Nicholson, J Wilson, A Elfick, C French, L Kozma-Bognar, H Ma & A Millar.
” Development of a novel biosensor for the detection of arsenic in drinking water.” IET
Synthetic Biolology, vol. 1, no. 1–2: 87–90.
Canton et al. (2008): Barry Canton, Anna Labno & Drew Endy. “Refinement and
standardization of synthetic biological parts and devices.” Nature Biotechnology, vol. 26,
no. 7: 787-793.
Garcia-Ojalvo et al. (2004): Jordi Garcia-Ojalvo, Michael B Elowitz, and Steven H Strogatz.
“Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing.”
PNAS, vol. 101, no. 30: 10955–10960.
Weber et al. (2009): Wilfried Weber, Stefan Luzi, Maria Karlsson, Carlota Diaz SanchezBustamante, Urs Frey, Andreas Hierlemann & Martin Fussenegger. “A synthetic
mammalian electro-genetic transcription circuit.” Nucleic Acids Research, vol. 37, no. 4.
Artificial Life Group
The Programming of Cells
30