Team:UTDallas/Project

Project Description

The University of Texas, Dallas iGEM team will develop a new generation of biosensors for contaminants. These sensors will be engineered in bacteria and will be able to combine heterogeneous inputs, process the incoming information dynamically, and release accordingly a reporter.

We are mainly interested in producing biosensors for use in disasters such as the recent Deepwater Horizon Spill. Even though the rig was recently closed, the World Water Assessment Program (WWAP) warns of health risks associated with the presence and circulation of such pollutants. Therefore, there is an urgent need for cheap and reliable contaminant sensors. Chemical sensors can have wide-ranging environmental applications, but can be very expensive depending on the technology. On the other hand, bacterial biosensors offer a cheaper alternative to existing systems. We will use Synthetic biology to implement gene circuits responsible for combinatorial logic, feedback and noise-reduction functions in a similar manner to electronic devices.We will employ molecular biology techniques to develop new and modify existing BioBricks that respond to the following contaminants:

Crude oil: Commercial oil spills release millions of gallons of toxic chemicals into the ocean, which severely implicate wildlife and their habitats. These chemicals comprise several oil fractions including light ends, naphtha, kerosene, fuel oil, PGO and residual oil fractions. Crude oil is a complex mixture of hydrocarbons consisting primarily of alkanes, cycloalkanes and aromatic hydrocarbons. The alkane series are saturated hydrocarbons with linear or branched chains. The cycloalkane series are saturated hydrocarbons that include non-aromatic rings. The aromatic series are unsaturated hydrocarbons that include six-carbon benzene rings. We will engineer novel BioBricks to convert straight-chain alkanes into aldehydes. Existing parts sensitive to aldehydes would then indicate the presence of alkanes. We will also modify parts submitted by the Glasgow 2007 team, which are inducible by aromatic compounds benzene, toluene, ethylbenzene and xylene.

Nitrates: Nitrates are a common ingredient in fertilizers, whose use is widespread and often excessive. Nutrient-rich runoff enriches water sources such as lakes, rivers and aquifers with the nitrates in a process called eutrophication, which facilitates the onset of algal blooms that deprive the water of oxygen and essential nutrients. Afflicted water sources are difficult and expensive to cleanse and the process would severely implicate the native wildlife.

We have several options for the sensor’s output. One possibility is for each contaminant sensor to activate the transcription of a pigment protein. For example, aromatics could produce red, nitrates purple, and alkanes green. When used in conditions with multiple contaminants, this would produce a specific color. A second possibility is using logic functions in a gene network implementation. For example, the presence of aromatics OR nitrates OR alkanes produces green. We will explore both options.

Introduction

Petroleum, a nonrenewable resource valuable as a fuel source, plays a pivotal role in the economies and environments of countries. The United States as one of the top oil-producing nations in the world participates in the production and refining of crude oil. However, over one quarter of the United States’ crude oil is produced offshore in the Gulf of Mexico bringing up hazards to the marine environment. With the recent news of the Deepwater Horizon Oil Spill occurring in the Gulf of Mexico, the issue of safe and effective cleanup of the oil comes into greater concern. Oil spills, usually resulting from tanker spills, penetrate the surface of sea water as well as decreasing fauna populations affecting the food chain of marine ecosystems. [1]

Crude oil consists of many different types of hydrocarbons including alkanes, cycloalkanes, and aromatic compounds. The alkanes (C_nH_2n+2), either straight or branched, consist of a chain of carbons and hydrogen molecules, while cycloalkanes (C_nH_2n) are composed of carbon rings and hydrogen molecules, and aromatic compounds are hydrocarbons consisting of benzene rings. [2] Crude oil is immiscible with water and is lighter than water, causing it to float on top of the water surface. Based on the crude oil’s specific gravity, the ratio of the weight of equal volumes of oil and pure water, it is categorized into types such as tar sands, heavy oils, and light oils. [1]

Past oil spills such as the Gulf War Oil Spill occurring in the Persian Gulf reveal the truly detrimental and potentially long-term impacts of oil spills in aquatic environments. The oil spill which began in January of 1991 has been found to contain truly significant long term effects on the environment. The lack of shoreline cleanup caused a large amount of oil sediment remaining even 12 years after the spill, and the oil penetrated so deeply that it cannot be retrieved now. A method to detect the presence of oil even after visible oil is removed from an area is necessary to aid the recovery of oil-affected ecosystems.

The Exxon Valdez spill occurring near Prince William Sound, Alaska resulted in unprecedented damage to the fragile Arctic ecosystem and a large portion of the oil from the massive oil spill of the Exxon Valdez in 1989 remained retained in the land. However, the oil spill occurring in Prince William Sound revealed not only the potentially deleterious effects of a large oil spill on the aquatic environment, but the harmful effects of large, cleanup machinery. [3] When oil reaches the shoreline, some components of the oil evaporate leaving behind the heavier components of oil. In rocky shores, the heavier components will convert into tar and will eventually be washed away through wave action; in marsh areas, however, the oil can sink down below the surface and remain for years. Low energy environments such as marshes are the highest risk areas because the marsh areas are the most vulnerable to the effects of oil. [4]

Research

Any articles that are relevant to our project and project goals

1. Paper entitled [http://www.jbioleng.org/content/pdf/1754-1611-2-5.pdf Engineering BioBrick vectors from BioBrick parts] describing how to make BioBricks using existing parts in the registry - useful for constructing parts necessary for alkane and nitrate sensors.

Project Details

Details of the project

Components

Project Components

Experiments

Experiments Conducted

Results

Results obtained

References

[1] [http://www.britannica.com/EBchecked/topic/454269/petroleum Petroleum; Encyclopedia Britannica; 2010]

[2] Idem, R.; Simanzhenkov, V. Nature and Classification of Crude Oil. In Crude Oil Chemistry; 1st Ed. Marcel Dekker: New York, 2003; pp 5-13.

[3] [http://www.eoearth.org/article/Deepwater_Horizon_oil_spill Cleveland, C. Deepwater Horizon oil spill; Encyclopedia of Earth. 23 June 2010.]

[4] [http://www.eoearth.org/article/Oil_spill Patin, S. Oil Spill. Encyclopedia of Earth. 23 June 2010.]