Team:TU Delft/Project

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===Alkane degradation===
===Alkane degradation===
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The aerobic alkane conversion pathways of medium (C<sub>5</sub>-C<sub>13</sub>) and long chain (C<sub>15</sub>-C<sub>36</sub>) alkanes from ''Gordonia sp. TF6'' and ''Geobacillus thermodenitrificans'' were the basis for the [[Team:TU_Delft/Project/alkane-degradation/parts|alkane degradation parts]]. These pathways were implemented in ''E.coli'' using the BioBrick principle and [[Team:TU_Delft/Project/alkane-degradation/characterization|characterized]] in detail with respect to single enzyme activities and affinity. Using these measurements the efficiency of different enzymes can easily be compared.'''The characterization showed that ... '''
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The aerobic alkane conversion pathways of medium (C<sub>5</sub>-C<sub>13</sub>) and long chain (C<sub>15</sub>-C<sub>36</sub>) alkanes from ''Gordonia sp. TF6'' and ''Geobacillus thermodenitrificans'' were the basis for the [[Team:TU_Delft/Project/alkane-degradation/parts|alkane degradation parts]]. These pathways were implemented in ''E.coli'' using the BioBrick principle and [[Team:TU_Delft/Project/alkane-degradation/characterization|characterized]] in detail with respect to single enzyme activities and affinity. Using these measurements the efficiency of different enzymes can easily be compared. '''The characterization showed that ... '''
Read more about [[Team:TU_Delft/Project/alkane-degradation|Alkane Degradation]]
Read more about [[Team:TU_Delft/Project/alkane-degradation|Alkane Degradation]]
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===Survival===
===Survival===
In order to be able to use our alkane degrading biological system in the intended environments some though must go into the survivability of the system. These environments include those with high levels of hydrocarbons as well as high salt levels, aspects which would cause an inhabitable environment for our system. It was found that organisms which are naturally hydrocarbon tolerant and salt tolerant produce chaperons and other proteins, which maintain the cellular activity - these genes were the basis of the [[Team:TU_Delft/Project/tolerance/parts| survival parts]]. [[Team:TU_Delft/Project/tolerance/characterization| Characterization]] of these parts showed an increased survivability for both salt and hydrocarbon environments of up to [[Team:TU_Delft/Project/tolerance/results|33% and 50%]] respectively.  
In order to be able to use our alkane degrading biological system in the intended environments some though must go into the survivability of the system. These environments include those with high levels of hydrocarbons as well as high salt levels, aspects which would cause an inhabitable environment for our system. It was found that organisms which are naturally hydrocarbon tolerant and salt tolerant produce chaperons and other proteins, which maintain the cellular activity - these genes were the basis of the [[Team:TU_Delft/Project/tolerance/parts| survival parts]]. [[Team:TU_Delft/Project/tolerance/characterization| Characterization]] of these parts showed an increased survivability for both salt and hydrocarbon environments of up to [[Team:TU_Delft/Project/tolerance/results|33% and 50%]] respectively.  

Revision as of 10:06, 20 October 2010

Project Abstract

Alkanivore: Enabling hydrocarbon degradation in aqueous environments

Pollution of soil and water environments by crude oil has been, and is still today, an important environmental issue. This was once more confirmed with the oil-spill in the Gulf of Mexico, but is also an issue that has to be faced continuously during the process of oil extraction from oil sands. Cleaning has proven to be challenging, but synthetic biology may hold the key to sustainable bio-remedial solutions for the future. What if we could design a small, autonomous, self-replicating, inexpensive method to remove oil from aqueous environments? The TU Delft iGEM 2010 team spent their summer designing a system that can tolerate, sense, dissolve & degrade hydrocarbons in aqueous environments, which could open new doors for the oil-industry.

Read our full introduction

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 (C5-C13) and long chain (C15-C36) alkanes from Gordonia sp. TF6 and Geobacillus thermodenitrificans were the basis for the alkane degradation parts. These pathways were implemented in E.coli 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. The characterization showed that ...

Read more about Alkane Degradation


Survival

In order to be able to use our alkane degrading biological system in the intended environments some though must go into the survivability of the system. These environments include those with high levels of hydrocarbons as well as high salt levels, aspects which would cause an inhabitable environment for our system. It was found that organisms which are naturally hydrocarbon tolerant and salt tolerant produce chaperons and other proteins, which maintain the cellular activity - these genes were the basis of the survival parts. Characterization of these parts showed an increased survivability for both salt and hydrocarbon environments of up to 33% and 50% respectively.

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.

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 Characterization

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.