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Project Overview

Toxins In Our Environment

During petroleum extraction and refinement processes, toxic byproducts are produced. These compounds have an enormous environmental impact, burdening our ecosystems with land, water, and air contamination. Common forms of air pollutants consist of NOx (nitrogen containing compounds) and SOx (sulfur containing compounds) which contribute to green house gas accumulation and acid rain (Schneider, 2006; Environmental protection agency, 1999). Similarly, land and water contaminants often consist of complex mixtures including highly toxic phenols and aromatic compounds, toxic and corrosive carboxylic acids (naphthenic acids) as well as sulfur and nitrogen-containing compounds. These often are recalcitrant, having complex structures that are difficult to break down, which causes them to persist in the ecosystem. Classical examples of water contamination include tailings ponds, which contain byproducts from the bitumen extraction process of oil sands. Although the water in tailings ponds is recycled to the extraction process, it is not treated to remove the toxins but kept contained in the ponds. This creates a susceptibility toward contamination of surrounding areas as a result of these toxic compounds leaching into ground water sources, through spills or through the accidental release of waste products into the environment.

Figure 1: Environmental toxins contaminate air, water, and land masses. These can consist of various compounds which could be divided into sulfur, nitrogen, carboxylic acid, and phenolic based compounds. What can we do to solve this problem?

Synthetic Biology As A Platform For Remediation

The removal of these compounds is becoming increasingly important, especially as government bodies start to become more proactive, implementing stricter regulation. Presently, there are a variety of solutions to remove these compounds from the environment by chemical means. These methods involve the use of chemical agents or the physical removal of contaminated soil or water samples and storing these products in contained areas (Scott et al. 2005). There is still however, no efficient, environmentally friendly mechanism for this to occur. The real question is,

What do we need to remediate these toxins from the environment?

We require a method to be able to easily and economically detect where these toxins are and then look to remediating them. Interestingly, microorganisms in the environment have evolved to be able to do both of these functions, responding to compounds in their environment and transforming them into food or other products. Harnessing these natural mechanisms through an engineered synthetic biology thus becomes a viable option.

What if we could detect toxins in our environment using a synthetically engineered organism? What if we could use a second organism to take these compounds and not only degrade them but convert them into useful compounds like hydrocarbons!


Figure 2: Introducing our dynamic duo FRED and OSCAR! This biosensor/bioreactor team is ready to detect and remediate toxins in the environment. Not only can OSCAR break down toxic carboxylic acid containing compounds such as naphthenic acids, but we also demonstrated that he can turn them into functional hydrocarbons!

We would like to introduce FRED and OSCAR! Our dynamic biosensor/bioreactor duo is designed to detect toxic compounds such as the ones illustrated above in liquid waste and contaminated waters and to convert these toxic components into usable hydrocarbons. FRED, the Functional Robust Electrochemical Detector, is capable of detecting various toxic components simultaneously through an electrochemical response. Building on the single output biosensor for NAs that we developed last year, we set out to design a multiple output biosensor. We illustrated how this sensor could work by showing that it has the potential to detect multiple toxins in contaminated water. Additionally, we developed a miniaturized circuit of the potentiostat for the prototype, validated this device in the wetlab, and designed our own software, which we have made available to everyone.

OSCAR, the Optimized System for Carboxylic Acid Remediation, is designed specifically to target toxins such as naphthenic acids (carboxylic acid-containing compounds), catechol, and nitrogen and sulfur containing heterocyclic compounds. Using the PetroBrick (BBa_K590025) we were able to convert various naphthenic acid based compounds into their hydrocarbon analogs. Additionally, we wanted to be able to degrade other toxic components of tailings so we used the xylE gene (BBa_J33204) in order to cleave catechol, an abundant intermediate in many toxic areas. Not only did we set out to break down catechol, but we attempted to see if we could further reduce the toxicity of the catechol breakdown product through use of the PetroBrick. When we co-culture these genetic circuits we can selectively produce new compounds from catechol compared to with xylE alone, suggesting that the Petrobrick may be used to create new hydrocarbon based compounds! Lastly we wanted to remove sulfur and nitrogen from heterocycles using the dsz and carA operons respectively. Not only would this improve the quality of fuel produced, but also prevent the production of NOx and SOx during combustion, reducing the amount of air pollution produced from burning fuel.

Taking A Step Back - Human Practices Inspired Our Project!

Before starting our project, the Calgary iGEM team felt it would be important to answer a few questions about how FRED and OSCAR could be applied in the oil and gas sector.

Would oilsands industry be interested in a biosensor and bioreactor for remediation purposes? Yes! Our meeting with the Oilsands Leadership Initiative (OSLI) has affirmed that industry is interested in potentially using synthetic biology for remediation of toxins.

What would people think about using synthetic biology in the oilsands? Do they have any concerns about its implementation? We consulted with two professionals working in biotechnology and ecological development in Alberta. Both of them made it clear that while the concept sounds great, it is important that we keep in mind the safety and ethics of our project.

How can OSCAR and FRED be designed with safety in mind? From our various conversations our team looked towards both physical and genetic design considerations to ensure that both FRED and OSCAR were designed form the beginning in a safe and functional way. This involved developing biosensor and bioreactor containment devices as well as kill switch.

How can we teach people more about FRED, OSCAR, and Synthetic Biology? From our interviews it was clear that not many people knew much about synthetic biology or its applications in the oil and gas sector. For this we partnered with the Telus Spark Centre, the local Science Centre in Calgary to help communicate synthetic biology to them. We also developed a video game that we took to the centre and better educated adults and kids on synthetic biology!

Learn More About FRED and OSCAR

To learn more about our team see the data page, or the FRED and OSCAR overview pages below.