Team:TU Delft/Project/introduction

From 2010.igem.org

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In summary, this approach will enable efficient hydrocarbon utilization under non-standard conditions. The chassis, in the form or BioBricks®, will facilitate the construction of strains with sustainable applications in the fossil fuel industry.
In summary, this approach will enable efficient hydrocarbon utilization under non-standard conditions. The chassis, in the form or BioBricks®, will facilitate the construction of strains with sustainable applications in the fossil fuel industry.
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# '''Aleksic J, Bizzari F, Cai Y et al.''' (2007) Development of a novel biosensor for the detection of arsenic in drinking water, ''Synthetic Biology'', IET 1: 87–90.
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# '''Halper, M.''' (2006) Saving Lives And Limbs With a Weed, Time [http://www.time.com/time/magazine/article/0,9171,1565508,00.html#ixzz0geEjnTG1 link]
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# '''Achenbach, J.''' (2010) Oil-spill flow rate estimate surges to 35,000 to 60,000 barrels a day, The Washington Post. [http://www.washingtonpost.com/wp-dyn/content/article/2010/06/15/AR2010061504267.html link]
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# '''Patton, J.S. et al.''' (1981) Ixtoc 1 oil spill: flaking of surface mousse in the Gulf of Mexico, Nature 290, 235-238

Revision as of 15:38, 10 September 2010

Contents

Synthetic biology

After more than 3 billion years of evolution, with slow pace of change and isolated species a new era has dawned. Synthetic Biology, an engineering approach to life intersecting biology, chemistry and physics, defines a new way of developing life. Although still in its infancy, its potential applications are enormous. Synthetic Biology research comprises a full spectrum of challenging topics, for example the biological production of existing and novel materials, including food and biofuels. In the field of health care scientists focus on diagnostics, drugs and vaccines, an already existing example is the production of the antimalarial medicine artemisinin. A team from the University of Edinburgh has designed and engineered bacteria to function as a biological sensor of arsenic in water (1). In Denmark genetically engineered Arabidopsis thaliana was developed that changes color when exposed to landmine degradation product (2). This year a team of students from the TU Delft will design a biological system to treat oil-contaminated environments. This essay will cover the ethical issues surrounding this synthetic bioremediation technology.

The project is part of the International Genetically Engineered Machines (iGEM) competition, annually held at the Massachusetts Institute of Technology (MIT). The competition challenges students from around the world to develop new basic biological building blocks, called “bio-bricks”. These biobricks are used to assemble biological systems in model organisms that do not occur naturally, such as oil-degradation pathways.

The problem (oil in water)

Bioremediation is defined as the use of biological systems for the treatment of environmental contaminants. All around the world pollution threatens habitats of animals and people. Accidental oil spills are among the most notorious causes of pollution, and afflict major damage to ecosystems, businesses and communities. Currently one of the greatest ongoing pollutions is the BP Gulf oil spill, caused by the sinking of the drilling platform Deepwater Horizon. Flowing at up to 2,500,000 gallons (3) of crude oil per day, this disaster will soon outrank the biggest accidental oil spill so far (Ixtoc Oil Spill, 1979, 138 million gallons (4)). Taking the size of these catastrophes into account, one can imagine the need for effective and large-scale remediation technologies.

Our solution (strategy)

In order to solve the problem of oil in water, as seen in the Oil Sands tailing waters, the iGEM TU Delft 2010 team has designed a strategy composed of various parts. Each part focuses on a certain challenge faced when removing hydrocarbons from aqueous environments. Together, these subparts form a complete chassis for a hydrocarbon-degrading microorganism. Our general strategy is to create BioBricks® that will facilitate each sub-part of our project within E.coli. This will be done by taking specific genes from various organisms from nature and placing them in a BioBrick®, after which there functioning can be evaluated within E.coli.

Part I – Alkane degradation

First and foremost the organism will have to be able to degrade oil. Oil consists of various hydrocarbon types and sizes, and for this challenge we decided to start with alkanes. There are a number of microorganisms that are known to degrade alkanes, and of these, genes from three different organisms will be used for the conversion of short chain alkanes, long chain alkanes and long chain alcohols and aldehydes, the latter two being intermediates of the long chain alkane degradation pathway. For the further degradation we will rely on the in-house genes of E.coli such as the β-oxidation pathway.

Part II – Tolerance

Hydrocarbons and salts in too high concentrations are known to be toxic to cells. It was found that organisms that are naturally hydrocarbon tolerant produce chaperones that maintain the cellular activity. There are also numerous organisms that can live in salty environments. By using genes from these organisms we hope to create BioBricks® that will facilitate salt tolerance as well as hydrocarbon tolerance.

Part III - Solubility

Oil and water don’t mix; the low solubility of hydrocarbons in water very likely could form a challenge for a hydrocarbon-degrading organism. To overcome this challenge a BioBrick® will be made containing genes encoding for an emulsifier that will increase the solubility.

Part IV – Genetic regulation

In order to have efficient cell growth, it is important to develop a system that activates gene expression at the optimal moment in time. An alkane sensing mechanisms described in literature will be adapted and incorporated using the BioBrick® format. This system will be coupled to the ‘in‐house’ catabolic repression system (crp) generating energy efficient cell growth under glucose conditions as well as produce enzymes for hydrocarbon degradation when needed.

In summary, this approach will enable efficient hydrocarbon utilization under non-standard conditions. The chassis, in the form or BioBricks®, will facilitate the construction of strains with sustainable applications in the fossil fuel industry.

  1. Aleksic J, Bizzari F, Cai Y et al. (2007) Development of a novel biosensor for the detection of arsenic in drinking water, Synthetic Biology, IET 1: 87–90.
  2. Halper, M. (2006) Saving Lives And Limbs With a Weed, Time link
  3. Achenbach, J. (2010) Oil-spill flow rate estimate surges to 35,000 to 60,000 barrels a day, The Washington Post. link
  4. Patton, J.S. et al. (1981) Ixtoc 1 oil spill: flaking of surface mousse in the Gulf of Mexico, Nature 290, 235-238