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From 2010.igem.org

Project

This year's TU Delft team worked on the biological conversion of hydrocarbons in aqueous environments, e.g. biological degradation of oil particulates in oil sands tailing waters. The project addresses one of the more considerable challenges in this branch of industry. Addressing the issue through a biological means required an interdisciplinary approach. The broad range of scientific fields to which we have been exposed throughout our studies will provide the knowledge and experience to formulate an efficient solution for this issue. Besides competing in iGEM, the team also contributed to future research into oil utilization and create new possibilities for sustainable developments in the fossil fuel industry.

Read our Abstract or full Introduction.

Team

The members of the TU Delft team carry a broad range of multidisciplinary assets, but it should be noted that there is a large focus on wet lab work, due to the large number of students from Life Science and Technology. This study is collaboration of two top universities in the Netherlands, the Leiden University (molecular genetics and medicine) and the Technical University of Delft ((bio-)chemical and process engineering), combining fundamental research and applied sciences.

Continue to our Team Page.

Sub projects

The basis of the 2010 TU Delft iGEM team's project is the generation of a biological chassis for the conversion of hydrocarbons. The conversion system will be implemented and characterized using the well-studied cellular environment of Escherichia coli, the workhorse for genetic and metabolic engineering. To tackle the important aspects faced when using biological systems for oil utilization, we are focusing on the following features:

Alkane degradation

The aerobic alkane conversion pathways of medium and long chain (<C36) alkanes from Gordonia sp. TF6 and Geobacillus thermodenitrificans is the basis of our parts. These pathways are implemented using the BioBrick principle and characterized in detail with respect to single enzyme activities and affinity. Using these measurements the efficiency of different enzymes can easily be compared.

Read more about Alkane Degradation.

Hydrocarbon & Salt tolerance

Hydrocarbons are known to damage the cell membrane and some essential cell proteins. It was found that organisms which are naturally hydrocarbon tolerant produce chaperons and other proteins, which maintain the cellular activity. We implemented this type of hydrocarbon by generating the respective BioBricks.

High salt concentrations, as can be found in tailing waters and other aqueous environments contaminated with oil, are also toxic to many microorganisms. Our aim was to create a BioBrick which will facilitate cell growth at increased salt concentrations.

Read more about Salt & Solvent Tolerance.

Hydrocarbon Solubility

An engineering challenge faced in oil bio-conversions is the low solubility of hydrophobic molecules in water. In order to overcome this mass‐transfer limitation we will clone two genes encoding for proteins with emulsifying properties. It is expected that these proteins will increase the solubility of hydrocarbons, which can be then converted more efficiently into potentially valuable products. Additionally, these emulsifiers are promising reagents for oil extraction from sands making the process cheaper and more sustainable.

Read more about Solubility.

Sensing

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 mechanism 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.

Read more about Sensing.

Genome‐scale modeling

Modeling approaches are used to explore the possibilities of valuable product formation from hydrocarbons. The model will be based on the MetaCyc pathway database, which contains pathway information of many sequenced organisms, covering a broad range of products such as biofuels, bioplastics and other fine chemicals.

Read more about Modeling.

RBS Characeterization

Read more about RBS Characterization.

Ethics and Education

Also the ethical and safety issues posed by our synthetic biology project were considered. The synthesis of a DNA strand representing a set of genes arbitrarily chosen by the designer, and its insertion in a living cell will, in general, provide the host cell, with new emerging properties that were not present in the original organisms. This poses several challenges in terms of safety and ethics that need to be addressed within the project.

Read more about Ethics & Safety or Education.