Revision as of 21:33, 27 March 2014

iGEM 2013 Bioremediation Projects

In the iGEM competition, we encourage teams to be creative, work hard and build cool things. While most teams choose to build biological systems that meet requirements for our part and project evaluations, some teams take that further and build hardware. This can be anything from simple, low cost lab equipment to new sensors, bioreactors and microfluidics systems.

This page will show some of the teams who worked on hardware projects in 2013.

Cornell 2013: Organofoam: Genetically Engineering Fungal Mycelium for Biomaterials Development

Manufacturing Track

Best Human Practices Advance Winner, World Championship Jamboree, Overgraduate Section

Abstract: The goal of Organofoam is to develop a fundamental toolkit of genetic parts for engineering complex fungi, particularly plant-pathogenic basidiomycetes. We were inspired to do so by a local company, Ecovative Design, that uses lignin-degrading fungi and plant matter to produce a biodegradable Styrofoam substitute. The existing product that we are seeking to improve, known as “mushroom packaging,” is a sustainable and necessary alternative to Styrofoam. Polystyrene can take hundreds of years to degrade in landfills, produces dozens of identified chemical toxins upon combustion, and is tremendously inefficient to recycle, thus posing difficulties for disposal and polluting the environment. However, the production efficiency of Ecovative’s substitute suffers due to contamination from pathogenic molds, a problem that we seek to solve using synthetic biology. Using the complex, plant-pathogenic basidiomycete, Ganoderma lucidum, as a chassis, we are expanding the accessibility of fungal genetic engineering and demonstrating its utility for commercial purposes.

TU-Munich 2013: PhyscoFilter – Clean different

Environment Track

1st Runner UP, World Championship Jamboree, Undergraduate section

Best Environment Project Winner, World Championship Jamboree, Undergraduate section

Abstract: The contamination of aquatic ecosystems with multiple anthropogenic pollutants has become a problem since the industrial revolution. Antibiotics, hormones and various noxious substances threaten environmental health and are not effectively removed by conventional waste water treatment. We propose to employ transgenic plants which produce effectors for enzymatic degradation (BioDegradation) or specific binding (BioAccumulation) of pollutants. The autotrophic, sedentary, aquatic nature of the moss Physcomitrella patens makes it an ideal chassis for a self-renewing, low-maintenance and cheap water filter. A light-triggered kill switch prevents unintended environmental spreading by limiting viability to places where the spectrum of sun light is appropriately filtered. Furthermore, we have developed a device to implement this biological filter in an aquatic environment, investigated the application of this new technology and examined its economic feasibility. Based on our results, PhyscoFilter may become a game-changing approach to improve global water quality in an affordable and sustainable fashion.

Buenos_Aires 2013: To drink or not to drink

Environment Track

Best Model Winner, World Championship Jamboree, Overgraduate Section

Abstract: Our project is focused on developing a biosensor specific for certain water pollutants, with a modular and scalable approach. This approach would make it easy to adapt the response for the detection of different substances. In contrast to other iGEM biosensors, it does not rely on expensive equipment or qualified people to interpret the results. Being aware that most of the populations affected by consumption of contaminated groundwater don’t have scientific or technical training, we intend the device to be cheap and easily distributed. We have designed it in a way that any user could easily determine the presence and level of the contaminant on drinking water, using image-based instructions. The project will focus on measuring a primary pollutant: arsenic. However, its modular and scalable design provides an easy way to measure various contaminants such as nitrate/nitrite among others.

Dundee 2013: ToxiMop

Environment Track

Winner, Best Presentation, World Championship Jamboree

Abstract: The ToxiMop project attempts to tackle the problem of freshwater algal blooms by detecting, reducing, and reporting the levels of the algal toxin microcystin. This toxin causes liver damage and is also speculated to be a carcinogen. Microcystin’s toxic action lies in its ability to bind to the human Protein Phosphatase 1 (PP1), which is a major regulator of cell division, protein synthesis and other essential processes. Using synthetic biology techniques, we engineered bacterial chassis (E. coli and B. subtilis) to express PP1, which covalently binds to microcystin. The engineered bacteria can then be used as a molecular mop, the ToxiMop, to remove microcystin from contaminated water. Applying mathematical modelling to our experiments, we optimised our prototype ToxiMop. Additionally, we attempted to develop a biological detector for microcystin, which was combined with our electronic device, the Moptopus. This device has the potential for real-time monitoring and analysis of water bodies.

From their wiki:The Moptopus is an electronic environmental sensor, developed to collect and relay real-time data from water reservoirs. The device could be placed in a water body to measure:

• Light Levels
• Temperature
• Humidity
• pH level of the water
• Dissolved oxygen level
• An on-board camera

The Moptopus device could be used in conjunction with the biological microcystin detection system that we attempted to develop. Presence of microcystin in water would trigger the production of Green Fluorescence Protein (GFP) by the E. coli detector. The Moptopus has been designed to quantify the amount of GFP produced by the excitation of GFP via a blue light and the capture of fluorescence emitted via a highly green light sensitive photodiode.

Abstract: The ToxiMop project attempts to tackle the problem of freshwater algal blooms by detecting, reducing, and reporting the levels of the algal toxin microcystin. This toxin causes liver damage and is also speculated to be a carcinogen. Microcystin’s toxic action lies in its ability to bind to the human Protein Phosphatase 1 (PP1), which is a major regulator of cell division, protein synthesis and other essential processes. Using synthetic biology techniques, we engineered bacterial chassis (E. coli and B. subtilis) to express PP1, which covalently binds to microcystin. The engineered bacteria can then be used as a molecular mop, the ToxiMop, to remove microcystin from contaminated water. Applying mathematical modelling to our experiments, we optimised our prototype ToxiMop. Additionally, we attempted to develop a biological detector for microcystin, which was combined with our electronic device, the Moptopus. This device has the potential for real-time monitoring and analysis of water bodies.

TU-Delft 2013: Peptidor: Detection and killing of resistant S. aureus using antimicrobial peptides

Health & Medicine Track

Abstract: Methicillin-Resistant Staphylococcus aureus causes major problems, especially in hospitals, leading to over half a million infections annually in the US alone. Of the alternative treatments currently under investigation one of the more promising is through antimicrobial peptides (AMPs). These small, highly-specific peptides attack the membrane of target organisms. Thousands of AMPs are known to exist and little resistance against them has been developed. The Peptidor project consists of an E. coli that can detect S. aureus, using S. aureus’ native quorum sensing system, in order to locally produce and deliver AMPs. Upon detection, peptides inactivated by a SUMO-tag fusion, are overexpressed. After a delay period, introduced through a negative transcriptional cascade, a SUMO protease is expressed cleaving off the inactivating tag. Using this mechanism, high concentrations of peptide are delivered at the infection to efficiently kill S. aureus. As a safety mechanism, the timer also activates an E. coli kill-switch.

BIT 2013: A New Strategy to Detect Antibiotics in Milk: Based on Sensors with Controllable Bio-enhanced Blocks

Food & Energy Track

Abstract: Bio-amplification, especially controllable bio-amplification is significant for biological detection. In a synthetic biological way, 2013 BIT iGEM assembled the T7 RNA polymerase gene and T7 promoter as an amplification block (amplifier), which is based on the high activity of T7 promoter to amplify the signal. To make the magnification controllable, a lacO operator regulated by lacI was assembled in downstream as a control block (controller), by adjusting the concentration of IPTG. With this block, several sensors of materials including but not limited to antibiotics are able to be enhanced controllable. This year, a sensor of beta-lactam newly designed and one of tetracycline are applied to detect the residual of antibiotics in milk which endangers human health. To make the detection faster and more convenient, milk samples and engineered E.coli are mixed in a tailor-made bio-chip and the green fluorescence will be detected and shown on a tailor-made electronic equipment.

Valencia_Biocampus 2013: Wormboys

New Application Track

Abstract: Bacteria are essential in biotechnology, but they can hardly move. Nematodes, such a C. elegans, are fast crawling organisms, but they have limited biotechnological applications. By combining the best from both organisms, we present the first artificial synthetic symbiosis with bacteria engineered to ride on worms, which concentrate in hotspots where bacteria perform a desired biotechnological process, such as bioplastic (PHA) production. We have engineered Pseudomas putida with a whole operon that allows the formation of a biofilm on the worm. Biofilm formation is swhitched on and off depending on the media, and thus bacteria get on and off the worm like travellers on a bus. We have also engineered a third partner, E. coli, to express an interference RNA that promotes clumping. Taken together, our artificial symbiosis allows biotechnologically interesting bacteria to travel on nematodes, reach nutrient-rich biomass spots and maximize the efficiency of biotechnological fermentations in heterogenous substrates.