Get Started in Synthetic Biology: Anggoro Wiseso Ui Synbio Club - Class 2015

GET STARTED IN SYNTHETIC
BIOLOGY
Anggoro Wiseso
UI SynBio Club Class 2015
Outline
Introduction (definitions and history)
Fundamentals of molecular biology
Comparing Synthetic Biology with their friends
Application of Synthetic Biology
Fascinating Project in SynBio
Disclaimer
This is NOT a comprehensive look at Synthetic
Biology.just an introduction
It may not be *everything* you need to know, but Ill try to
get close
For everything else, theres Wikipedia
For more detailed topics, other people will be a much better
source of information:
Transcriptional control strategies, the Registry, and knowledge about
what types of parts are possible: Sean Kearney

Lab Equipment: Jenna Rickus and Rickus lab grad students
Cloning particulars/Reagents: Dow AgroSciences
What is synthetic biology (synbio)?

Synthetic Biology is:
The design and construction of new biological parts, devices, and
systems, and
The re-design of existing, natural biological systems for useful
purposes.
(from SyntheticBiology.org)
Basically, its genetic engineering (aka molecular biology)
for practical purposes

Try to look at genetics from engineering paradigm
Genes and different genetic components = parts
Groups of components = devices
Model devices as circuits
What is synthetic biology (synbio)?

Engineering Goal:
To build components that can be reliably and predictably

assembled into ever more complicated systems
Whos in charge?
The Biobricks Foundation (BBF) is one of the biggest
initiatives worldwide driving the development of synbio

Goals of the BBF:
Educate the public about synbio and biotechnology
Make biotech simple to do and available to the public
Define ethical concerns and practices in synbio
The BBF developed and maintains the Parts Registry
DNA Construction = #1 Tech. of 21st Ctry.

From absract
information to
physical,
living DNA
designs.
TAATACGACTCACTATAGGGAGA
2004: 10,000 bp
2010: 1,000,000 bp
2016: 100 million?
Outline

.or What makes up a device?
For this section, I drew a lot of basic information from the
Registry: http://partsregistry.org
You can also find most of this (minus the synbio-specific
terminology) in any genetics or biochemistry textbook (or

Wikipedia)
Some of this is probably review, but I figured it would be
better to include too much rather than too little
Synbio jargon
A part is a DNA sequence encoding some part of the genetic
machinery, including but not limited to:

Promoters
Ribosome binding sites (RBS)
Protein coding regions
Terminators
A device is a group of parts that work together for specific
functions, such as:

Protein production
Sensing/reporting
Measurement
Signal inversion
Cell signaling
Cell motility
More jargon
A chassis is the organism (host) containing the devices
Usually E. coli or S. cerevisiae (yeast)
Also can be bacteriophage (virus), plants, mammals, etc
anything, really
Cloning does not refer to Dolly the sheep!
Refers to manipulation of recombinant DNA
How do I make my device?

Lots of ways to do it, but there are two I would specifically
recommend:
3A Assembly (similar to Standard Assembly)
Based on traditional cloning methods
If a part is designed to work with these methods, it is said to be a Biobrick
Gibson Assembly
Developed recently
Rapidly becoming one of the methods of choice
The next few slides will give you an idea of both methods,
but first lets talk about some of the tools you will be using
Enzymes
Plasmids
Outline
Problem
Electrical
Engineering
Mechanical Engineering
water = weight
water<weight
Biological Engineering
Biological Engineering
rDNA
Sequencing
PCR
A LIVING HOUSE Terreforms Fab Tree

Hab
How is Synthetic Biology Different? Synthetic biology uses
four principles not typically found in genetics, genomics,

or molecular biology:
abstraction,
modularity,
standardization,
design and modeling.
Abstraction:
Abstraction - you can use parts/devices/systems without
having to worry about how they work.

DNA
makes parts.
Parts
into devices.
Devices
connected to make systems.
Modularity:
parts, devices and systems - connected as self-
contained units and combined in any combination you

want
Standardization:
All the Tab As fit into all the Slot Bs.
An everyday example - all light bulbs fit into any socket!
Designing and modeling

build a model
test the devices capacity
improves design
tests basic biological assumptions that could be false
Registry of Standard biological Parts

http://partsregistry.org/Main_Page
DNA is DNA
E. Coli is our chassis
Can use parts from any organism
Can use parts made by a computer
Abstraction Hierarchy
a human invention designed to assist
people in engineering complex systems
Assemblies of devices
make a system
Assemblies of parts
make up devices
Sequences of DNA
encode parts
Part sequence of DNA with human defined function
AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTC
AACGCCGCCCGTTATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAAC
GGAGCCGAATCGCGCCTGGTTCCAGGTGGAAGATGACGGTCCGGGAA
TTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGTTTGTCCGCGGCG
ACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGC
AGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCG
AGCGGGGCGGGCTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACG
CGGGCGCAGGGCATGACAAAAGAAGGGTAATCTAGAGGCATCAAATAA
AACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTT
GTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC
Parts assembled into Devices
Parts assembled into Devices
DEVICE TO SYSTEM
Plasmids and Transformation
Outline

Naturally Replicating Rubber for Tires
Delivering Economic, Renewable BioAcrylic
Making Green Chemicals from Agricultural Waste
Vaccine Development
Developing a Suite of Biobased Products and
Services
Biosensor for many sensoring problems
Producing Biofuels and Renewable Chemicals as
Petroleum Alternatives
Increasing Efficiency in Bioprocessing of
Pharmaceuticals
Outline
Cornell
Hong Kong
CUHK
Paris
Bettencourt
Slovenia
Visible, Applicative, Valuable, Prospective

mahal, tidak jatuh dari langit
CORNE
Membuat biosensor
kualitas air di wilayah
eksplorasi minyak
LL
lapisan pasir.
Racun seperti arsenik
dan naftalena dapat
menerobos isolasi
menuju lingkungan
bebas.
Pemantauan kualitas
air penting dan
memerlukan sampel
banyak.
Biosensor baru
berbeda dari
biosensor yang sudah
dikembangkan
sebelumnya
(fluorosensi, pH,
CORN
ELL
Sistem memberi data

tanpa perlu
interpretasi lab
(seperti yang
dihasilkan dari
fluorosensi misalkan),
wireless, kontinyu
dan real-time.
Menggunakan
Shewanella
oneidensis MR-1
sebagai chassiss.
MtrB
MtrB
arsR
arsR
MtrB
CUHK
Membuat bakteri
yang dapat
melihat.
Bakteri
mengekspresikan
rhodopsin yang
peka cahaya.
Mengendalikan
gerakan dan
ekspresi gen.
Dibandingkan
biosensor lain, tim
membuat
Membuka peluang aplikasi

lain seperti :
Light-directed bacteria
sorter
Metal ions collection
SR utk
keberlangsungan
hidup archaea.
SRI dan
transdusernya
(HtrI) untuk
fototaksis positif
bagi sinar dengan
panjang
gelombang
kurang dari 500
nm.
SRII dan HtrII

untuk fototaksis
negatif
sinar
Mengintegrasikan sensory rhodopsin ke
dalambagi
E.coli
dengan
E.Coli secara alami memiliki Tsr dan Tar
untuk panjang
kemotaksis m
gelombang lebih
dari 500 nm.
CUHK
negatif
positif
Cahaya Biru
Adapted from
Janie Brennan. 2012. Synthetic Biology. Purdue University
Syntheticbiology.org

Get Started in Synthetic Biology: Anggoro Wiseso Ui Synbio Club - Class 2015

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GET STARTED IN SYNTHETIC

For more detailed topics, other people will be a much better

what types of parts are possible: Sean Kearney

What is synthetic biology (synbio)?

Basically, its genetic engineering (aka molecular biology)

for practical purposes

What is synthetic biology (synbio)?

To build components that can be reliably and predictably

initiatives worldwide driving the development of synbio

DNA Construction = #1 Tech. of 21st Ctry.

Fundamentals of molecular biology

terminology) in any genetics or biochemistry textbook (or

better to include too much rather than too little

machinery, including but not limited to:

A device is a group of parts that work together for specific

functions, such as:

How do I make my device?

A LIVING HOUSE Terreforms Fab Tree

How is Synthetic Biology Different? Synthetic biology uses

four principles not typically found in genetics, genomics,

having to worry about how they work.

contained units and combined in any combination you

Designing and modeling

Registry of Standard biological Parts

Part sequence of DNA with human defined function

Parts assembled into Devices

Parts assembled into Devices

Application of Synthetic Biology

Visible, Applicative, Valuable, Prospective

Sistem memberi data

Membuka peluang aplikasi

SRII dan HtrII

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