Ready, Set, Go for OSLI 2012 iGEM Teams
The green flag has been dropped for eight OSLI-sponsored university teams competing in the 2012 International Genetically Engineered Machine (iGEM) competition to find synthetic biology solutions to oil sands challenges.
"We're really excited about the work being undertaken as part of the competition this year because a number of teams are building on and advancing work completed last year," says Jill Lang, of ConocoPhillips who co-ordinates OSLI's iGEM projects. "This is the type of collaborative effort that OSLI supports and believes will more quickly advance our knowledge of synthetic biology and its application in the oil sands."
She explains that OSLI representatives and subject matter experts evaluated proposals from iGEM teams all over the world using the following criteria:
- overall fit with OSLI's objectives;
- demonstration of a real need or desirable outcome for the oil sands;
- sound methodologies;
- creativity/uniqueness of the project;
- organizational credibility of the host institution;
- staffing and collaboration;
- evaluation plan and dissemination;
- financial or in-kind contributions from other organizations; and
- overall proposal clarity, organization and completeness.
The teams were ranked by their results, with the top eight receiving sponsorship, which has been divided into three tiers with three teams receiving $20,000 each, three teams receiving $10,000 each and two at $5,000 each.
"Again this year we have teams represented from a broad range of universities, from Mexico, to Canada, the USA and France," says Lang. "Four of the teams we sponsored last year, the universities of Calgary, Alberta, Lethbridge and Queen's, are building on or adjusting their work from previous years. There are a lot of connections between the teams which is what we like to see."
The 2012 teams include: University of Alberta, University of British Columbia, University of Calgary, Centre for Research and Advanced Studies of National Polytechnic Institute (Mexico), Cornell University, Institut National De Sciences Appliquees de Lyon (France), and Queen's University.
iGEM, in association with MIT, is the world's foremost synthetic biology competition in which students alter biological parts and systems to address real-world challenges and are judged in an international competition held in November of each year. OSLI sponsored eight university teams from around the world in the 2011 iGEM competition and five teams in the 2010 competition.
In the iGEM competition, student teams are given biological parts from MIT's Registry of Standard Biological Parts, a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems.
The following is a brief description of the projects being carried out in 2012 by the OSLI-sponsored teams.
Advances in DNA sequencing and synthesis are enabling landmark changes in our ability to engineer organisms to sense, report and process chemicals in the environment. The UofA team is proposing the development of new sensors and readouts for monitoring chemicals present in oil sands process-affected water (OSPW), specifically the naphthenic acids (NAs) present in tailings ponds.
Simple and accurate biosensing systems will be useful for environmental monitoring. Further, they have the potential to be used in conjunction with bioengineered degradation systems, signaling where and when to start and stop bioremediation. The readout system is designed to allow a multi-dimensional, sensitive, and graded response, thus bringing biosensing out of the domain of all-or-none and yes-or-no responses.
The tools and techniques developed by UofA will be useful in designed environmental monitoring for OSPW, as well as being broadly useful in bioengineering.
Industrial-scale methods have been developed to remove inorganic sulphur compounds from heavy oil or bitumen during the refining process. However, these methods are not effective in removing another type of sulphur known as organosulphur. Due to the difficult nature of organosulphur, the UBC team is proposing to develop communities of microorganisms (consortia) — rather than single strains — that will use a distributed pathway to more effectively remove organosulfur during the refining process.
To do this, the UBC team will use synthetic biology and environmental genomic approaches to engineer groups of consortia capable of desulphurization. This research will establish tunable microbial consortia that will remove organosulphur, resulting in more efficient heavy oil refining with reduced environmental impacts and improved operating costs. The resulting data products and cellular BioBricks will set a precedent for the use of engineered consortia in other industrial processes such as hydrofracking and nitrogen removal, which will inform future policy development on the release of engineered consortia into the environment.
The UofC team is developing a biosensor-bioreactor system that will provide the ability to sense and degrade naphthenic acids (NAs), a group of waste compounds that result following the bitumen recovery and extraction process. These wastes are deposited along with sand, clay and water into large holding
areas called tailings ponds, which are an environmental and disposal concern.
The team's major objective is to develop procedures for the conversion of NAs into useful clean hydrocarbons suitable for industrial use. This will require the removal of a variety of chemical groups (carboxyl, sulphur, and nitrogen) from NAs using known biological pathways from a variety of microorganisms. The team also aims to develop biological and structural solutions to safety problems found in the scale-up process of synthetic biology industrial applications.
This work builds on efforts of the UofC 2011 iGEM team to develop a NA-sensing organism.
To better monitor the integrity of oil sands tailings ponds, the team from Cornell University is working to develop a fully autonomous electrochemical biosensor that complements the current monitoring system by providing real-time data over extended periods of time. The team will use their biosensor to focus on detecting and transforming known contaminants of oil sands tailings ponds such as naphthalene.
By manipulating a unique electroactive bacterial species that is capable of directly transferring electrons to solid-state electrodes, the team will create a strain of bacteria whose metal-reduction capacity is increased in response to these environmental toxins, generating direct electric output in a whole-cell
biosensor. This unique reporter system is engineered to reduce the costs and challenges associated with producing and maintaining the necessary electric circuits for data collection in more traditional bioluminescent reporter systems.
To build and test the platform, the team will:
- synthesize novel reporter strains for the production of electrical output in response to known contaminants;
- characterize electrical output of reporter strains in response to the pollutants of interest;
- optimize the response for relevant concentrations of pollutant in water samples; and
- construct a functional prototype for an affordable, field deployable device.
Cinvestav is focused on constructing a biological system that will produce the biofuel butanol from carbon dioxide (CO2) using different light and oxygen conditions. This system would include capturing CO2 and finding alternative, sustainable uses for it, such as the creation of butanol.
Here's how it works. A metabolically diverse bacterium called rhodopseudomonas palustris can grow under different culture conditions, including anoxygenic photoautotrophic growth, which uses light energy and CO2 as a carbon source. The team proposes to construct a genetic circuit that allows the bacteria to produce butanol in two different ways. In the first method, carbon would be converted into biomass without the use of oxygen and with the use of light sources, in a process known as anaerobic photosynthetis. In the second method, the team will use enzymes to catalyse and create a chemical reaction. Organisms are then used to synthesize organic compounds from CO2, deriving energy from the chemical reactions. This system could provide a way to use the captured CO2 to obtain high yields of butanol.
The UofL team is working to reduce greenhouse gas (GHG) emissions such as CO2 from oil sands in situ operations using a modified microbial enhanced oil recovery (MEOR) system. MEOR is used throughout the world to increase the productivity of difficult resources including carbonate oil deposits, which make up 26 per cent of Alberta's bitumen resources.
Using a synthetic biology approach, the UofL team is designing an extraction method that demonstrates a modified MEOR method for extracting carbonate oil deposits. CAB (CO2, acetic acid and biosulfactant) extraction will use natural carbon fixation machinery to convert CO2 into sugars to fuel the production of acetic acid and biosurfactant. The pores of carbonate rock increase in size when acetic acid is applied, capturing CO2. Coupling carbon capture with acetic acid and biosurfactant production, will allow in situ oil sands deposits to be produced with fewer GHG emissions.
Microorganisms have a natural tendency to attach to wet surfaces, to multiply and to embed themselves in a slimy matrix composed of extracellular polymeric substances that they produce, forming what is known as a bioﬁlm. Since biofilms can cause serious operational problems both topside and in the reservoir of in situ operations, INSA de Lyon is working to engineer a bacterium capable of destroying biofilms, and form a resistant protective biofilm.
In the oil sands reservoir, biofilms can result in the production of hydrogen sulphide, causing what is known as reservoir souring. Sulphide is corrosive and negatively affects the reservoir fluids, reducing the quality of hydrocarbons being produced. The removal of sulphate and sulphide from the water is very costly. Thus, many operators have identified microbial activity as a key factor requiring control in oil production systems due to corrosion, product quality, and maintenance — including cleaning and replacement of parts.
The Queen's University team is investigating methods of bioremediation to remove unwanted byproducts of oil sands production to preserve delicate aquatic ecosystems in northeastern Alberta. The recent creation of a biofilm that binds heavy metals holds promise for further work on heavy metal bioremediation of tailings ponds.
Some bacterial species possess tail-like appendages called flagella, which can be genetically altered for novel functions. Using flagella to host heterologous proteins would result in thousands of useful enzymes organized in an extensive scaffold, with the benefits of extracellular synthesis/degradation and arrangement. By replacing the variable D3 domain of the flagellin protein with proteins for binding, degradation, adhesion, and synthesis, the team hopes to increase the efficiency of bioremediation and biosynthesis, and facilitate the collection of products in situ or ex situ. To accomplish this, three specific tasks are required:
- clone and modify the constant domains of the flagellin protein in order to efficiently insert the genes of interest and make them standard Biobrick parts;
- design a unique and flexible cloning method for making chimeric insertions using Biobricks and parts obtained from the wild; and
- build and characterize constructs by making chimeric flagellin proteins with fluorescent proteins, enzymes, metal binding proteins (MBPs) and adhesion.