Lecture 8 Flashcards
Synthetic Biology 3 research programmes
Rational design of genetic logic devices from modular DNA parts
Production of commodity chemicals through redesign of metabolic pathways
Large scale synthesis of microbial genomes
How is Synthetic Biology different? Synthetic biology uses four principles not typically found in genetics, genomics, or molecular biology:
abstraction
modularity
standardisation
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
Designing and modeling
build a model
test the devices capacity
improves design
tests basic biological assumptions that could be false
Universal DNA
DNA works across host organisms - chassis
Can use parts from any organism
Can use parts made by a computer
Repressilator
case study
Repressilators were first reported in a paper[2] by Michael Elowitz and Stanislas Leibler in 2000. This network was designed from scratch to exhibit a stable oscillation which is reported via the expression of green fluorescent protein, and hence acts like an electrical oscillator system with fixed time periods. The network was implemented in Escherichia coli using standard molecular biology methods and observations were performed that verify that the engineered colonies do indeed exhibit the desired oscillatory behavior.
The repressilator consists of three genes connected in a feedback loop, such that each gene represses the next gene in the loop, and is repressed by the previous gene. In addition, green fluorescent protein is used as a reporter so that the behavior of the network can be observed using fluorescence microscopy.
Repressilator
oscillations are favored by Strong promoters Efficient ribosome-binding sites Tight transcriptional repression Comparable protein and mRNA decay rates
Need for biofuels
Energy security
Economic development
Mitigation of climate change
Biofuel Ethics
Biofuels development should not be at the expense of people’s essential rights
Biofuels should be environmentally sustainable.
Biofuels should contribute to a net reduction of total greenhouse gas emissions and not exacerbate global climate change.
Biofuels should develop in accordance with trade principles that are fair
Costs and benefits of biofuels should be distributed in an equitable way.
If 1-5 then there is a duty to develop such biofuels.
AMYRIS
Amyris’s trans-β-Farnesene is produced through fermentation of sugars by yeast. Target genes are selected to change the yeast’s metabolism, converting the yeast from an ethanol-producing organism into a hydro-carbon producing organism.
Amyris’s platform enables the production of selected molecules at high purity levels. It also provides three distinct advantages over the existing sources: first, it efficiently produces compounds that can’t be made by chemical synthesis;
second, it replaces compounds typically derived from plant sources that can’t be extracted reliably; and third, it replaces compounds made from petrochemicals, with renewable compounds.
Amyris pathway to beta-farnesene
Farnesene production begins with sugarcane grown in Brazil, which is fermented and uses yeast to convert the sugar feedstock into ethanol. The company engineers the yeast to convert the sugar into isoprenoids, including farnesene, which separates and is recovered from the fermented sugar. The farnesene is then “finished” to be used in a variety of different products. This is preferable to the previous sources of Farnesene which have primarily been controversial shark liver and the somewhat limited supply of olive oil.
BIOFUELS MARKET
Because fuels are low-margin commodities, biofuel companies need to produce at large volumes to make a profit.
Commercial plants can cost on the order of hundreds of millions of dollars.
Oil price crash from 2014 make it not economically viable
Artemesinin production
In 2015, there were an estimated 429 000 malaria deaths
Artemisinin-based combination therapies (ACTs) are recommended by WHO as the first-line treatment for uncomplicated P. falciparum malaria
Derived from Artemesia annua, sweet wormwood
Fluctuating harvest levels each year
Artemisia annula
The plant Artemisia annua (pictured being harvested in Tanzania) was the only source of artemisinin before biochemists invented a synthetic route
