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From 2010.igem.org

Project Description

This year's TU Delft team will be working 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 will require 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 wants to contribute to future research into oil utilization and create new possibilities for sustainable developments in the fossil fuel industry.

The members of the TU Delft team carry a broad range of multidisciplinary assets, especially the master students from Life Science and Technology. This study is collaboration of two top universities in the Netherlands, the Leiden Unversity (molecular genetics and medicine) and the Technical University of Delft ((bio-)chemical and process engineering), combining fundamental research and applied sciences.

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 importan aspects faced when using biological systems for oil utilization, we are focusing on the following features:

• Conversion of hydrocarbons

The aerobic alkane conversion pathways of medium and long chain (<C36) alkanes from Gordoniasp. TF6 and Geobacillus thermodenitrificans will be the basis of our parts. These pathways will be implemented using the Biobrick principle and characterized in detail with respect to signle enzyme activities and affinity. Using these measurments the efficiency of different enzymes can easily be compared.

• Hydrocarbon 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 chaperones and other proteins, which maintain the cellular activity. We will implement this type of hydrocarbon by generating the respective Biobricks.

• Hydrocarbon solubility

In order to overcome the mass‐transfer limitation of hydrocarbons to water we will clone two genes coding for proteins with emulsifying capabilities.

• Halotolerance

High salt concentrations are toxic to many microorganisms. Our aim is to create a biobrick which will facilitate cell growth at increased salt concentrations.

• Genetic regulation

An alkane sensing mechanisms coupled to the catabolic repression system (crp) produces enzymes for hydrocarbon degradation when needed.

• Genome‐scale modeling

Modeling approaches are used to explore the possibilities of valuable product formation from hydrocarbons.

The tasks of the team are roughly be divided into two groups. One group will deal mainly with the aspects related to the modeling and design of the synthetic system. A second group of students will mainly carry out the wet lab work.

Also the ethical and safety issues posed by synthetic biology will be 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.

All registered biobricks will be published here:

Planning

The project can be divided into three phases:

• Brainstorming phase

The team members get to know each other, get a working knowledge of each other’s topic and start generating ideas.

• Design phase

The students define the biological design which they want to carry out, together with the project specifications.

• Production phase

The (wet-lab) realization of the system and the evaluation of its performance.

During the brainstorming phase, the involvement of the students will be part-time. There are weekly meeting to exchange ideas and discuss proposals. For the remaining 6 months covered by the actual project (May-October), the involvement of the team is full time.