Team:MIT/Safety

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The iGEM Competition

The International Genetically Engineered Machines (iGEM) competition is annually held at the Massachusetts Institute of Technology (MIT) in the field of Synthetic Biology. Since 2004, this competition encourages undergraduate teams from all over the world to develop a project that intertwines the principles of Biology and Engineering. The competition not only determines the worth of projects solely based on biological merit, but also requires teams to examine their project as a whole. This includes aspects such as modelling of genetic circuits, marketing the project and educating the public about iGEM and Synthetic Biology.

Randy Rettberg, the director of iGEM, once described the main question as follows: "Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology just too complicated to be engineered in this way?" The iGEM-approach to answer that question is to actually try to engineer biological systems with a proper function. To this end, more than 100 interdisciplinary student teams from all over the world, mainly consisting of undergraduate students in biology, biochemistry, engineering, informatics and mathematics, carry out different projects during the summer.

These projects reach from medical applications, i.e. genetically modified bacteria used in cancer-treatment to environmental and manufacturing projects, i.e. the construction of a watch-like counter consisting of living cells.

BioBricks

Biological parts can be well defined and characterized in the same way as electric or mechanical components (standardization). These basic biological building blocks, the “bio-brick”, can then be used to design devices and systems that are more and more complex (hierarchy). The designer of a bio-system does not need to worry about all the details of the individual devices, and the designer of a bio-device does not need to know all the details of the single parts (decoupling): all that is required is to fish out into a repository the most suitable building blocks (parts or devices) required for the design at hand.

A database of bio-bricks has been actually initiated few years ago, and is currently maintained by the Massachusetts Institute of Technology (Registry of Standard Biological Parts). The existence of such a repository has fostered, over the last few years, the development of an incredible variety of different bio-devices ranging from sensors, logical circuits, computational devices, oscillators, supply chains of bacterial colonies etc.

Previous Achievements

TU Delft iGEM Team 2009 - BACTERIAL RELAY RACE

The teams aim was to build an improved cell to cell communication system. They were attempting to construct an E.coli strain which is capable of passing a GFP (Green Fluorescent Protein) signal through conjugation. This mechanism provides the ability of transferring genetic material between bacteria through direct cell to cell contact. A delayed self destructing mechanism caused the destruction of the genetic material of the donor cell after the transfer. The idea is comparable to a relay race.

Reward: Gold medal and award for ‘Best Information Processing Project’.

Read more on the TU Delft iGEM Team 2009 Wiki

TU Delft iGEM Team 2008 - ENGINEERING A BIOTHERMOMETER

The teams goal was to construct a temperature-sensing bacteria Escherichia coli that changes color at different temperatures. Such a thermometer can be applied e.g. as a temperature reporter system in large-scale fermentations, or as a temperature-inducible protein production system.

If the temperature exceeds a certain threshold, a sensitive RNA structure opens up and the ribosome (a molecular protein manufacturing machine) can bind to the RNA. This results in the production of a color compound - Farnesyl PyroPhosphate (FPP).

Reward: Golden medal and the trophy for the ‘Best Wiki’.

Read more on the TU Delft iGEM Team 2008 Wiki

Background

Dissolved oil molecules in (waste) water are a serious threat to our ecosystem. One liter of oil pollutes 1,000,000 liters of drinking water. Chemicals are usually used to deal with this problem, however they often contribute to the problem instead of the solution. The iGEM team of this year builds on this global problem and seeks solutions from nature. Some organisms possess genetic properties that enable them to process oil in salty environments. The team will develop biobricks containing these attributes and implement them into E.coli. In this way we can contribute to the development of new bioremediation technologies by creating a bacterium that can purify water contaminated with oil.

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, 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.

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:

• Conversion of hydrocarbons

The aerobic alkane conversion pathways of medium and long chain (<C36) alkanes from Gordonia sp. 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 single enzyme activities and affinity. Using these measurements 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 chaperons and other proteins, which maintain the cellular activity. We will implement this type of hydrocarbon by generating the respective BioBricks.

• 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.

• Halotolerance

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

• 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 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.

• 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.

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.

We also presented our project in more detail for a number of faculty members, you can find this presentation here.

All registered BioBricks will be published here:

<groupparts>iGEM010 TU_Delft</groupparts>

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.

Press

For more information about our project, feel free to contact us!

TU Delft iGEM Team

Phone: +31 15 278 1625

Email: info@igemtudelft.nl

Address

KLUYVERLABORATORIUM VOOR BIOTECHNOLOGIE

Julianalaan 67

2628 BC Delft

THE NETHERLANDS

Press Contact

Nadine Bongaerts - nadine@igemtudelft.nl +31 (0) 6 22 87 92 83

Sponsor Contact

Pieter van Boheemen - pieter@igemtudelft.nl +31 (0) 6 14 15 32 98

Media Coverage

• [http://www.delta.tudelft.nl/nl/archief/artikel/green-solution-for-oil-spills/21312 Green Solution for Oil Spills] - TU Delta - 2010-05-27
• [http://headlines.nos.nl/forum.php/list_messages/20585 TU heeft groene oplossing] - NOS Headlines Radio 3FM - 2010-06-16