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Team project descriptions
From 2013hs.igem.org
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AMERICAS EAST
Team BJHS Madison AL
We will insert the human insulin coding part and a glucagon-like coding part into the machine. We will use a two part system and insert two separate compatible plasmids into the plasmid backbone. The machine's promoters should respond to changes in environmental glucose levels and produce either a glucagon-like peptide (with hypoglycemic environmental levels) or a human insulin peptide (with hyperglycemic environmental levels).
Team Deerfield MA
Mercury poisoning is a serious problem, which can devastate fish populations and ecosystems. Humans who consume contaminated fish may experience negative affects as a result. The Deerfield, MA iGEM Team has proposed a remedy to this issue with the aid of a biosensor. Our goal is to manipulate the system found in part K346001 that uses the merR gene to detect mercury, and then either promote or suppress a reporter gene. Previously GFP has been used as the reporter, but our plan is to test a few different reporters including Lumazine (K216007) and LacZ (I0500). We will test for transform efficiency, reporter strength, and objective overall succes to find which reporter is most effective in this system. Once these transformed cells are produced, someone (i.e. a fisherman) would be able to take a water sample in the area he or she plans to fish, allow the cells to inoculate overnight in the water sample, and then discover whether mercury is present in the water source. Depending on the output, the cells may be able to detect the severity of the contamination.
Team Jefferson VA SciCOS
Domoic acid is an organic acid found in algal blooms and shellfish, and is produced by dinoflagellates. This organic acid is a neurotoxin that is both responsible for seafood poisoning and red tide fish kills. Its chemical structure includes kainic acid, a relatively harmless organic acid derivative of the amino acid proline. Currently, ELISAs for domoic acid test false positives when in contact with kainic acid; this causes safe seafood to be thrown away due to concerns of domoic acid tainting. Moreover, E.coli bacteria can degrade and live off of L-proline.
The purpose of this project is to bioengineer E.coli, using the codon for L-proline degradation, to degrade and detect domoic acid, as well as educating the general public about the risks of domoic acid poisoning and the positive and negative externalities of bioengineering.
Team Lambert GA
In 2010, Georgia Institute of Technology’s iGem team submitted the part K410000, a periplasmic heat generator made with HybB and OmpA. The following year several teams used HybB in their projects with mixed results. Our project is the continuation these projects and the characterization of HybB and OmpA. To do this we will put RFP under HybB promotion. In addition to we will put OmpA under three constituitive promoters.
The purpose is to determine whether the strength of constituitive promoters will change the amount of heat released by generator OmpA. With HybB we are hoping to get reliable results from cold shock treatment. Future applications of this project would allow us to control cell protein expression through temperature conditions.
Team MCIT Indianapolis
The number of melanoma cases has been increasing in populations worldwide. Nearly every hour one American dies from melanoma. The technology currently available for melanoma forces a person to get a biopsy in order to diagnose it, another less invasive tool for diagnosis would be very efficient. Places where health care is not as readily available, a skin detecting cream for melanoma would allow people to ‘self-check’ for cancerous skin spots. The test would be easy to read and would let a person know that they need to visit their doctor immediately for further action. The purpose of our experiment is to eventually produce a topical cream or salve that can be used to detect the early onset of melanoma. In order to do so, the project will start with triple antibiotic resistant E. coli and then insert a plasmid containing genes that glow in the presence of precancerous cells. The plasmid will consist of a biosensor for melanocytes specifically the mutated EGFR protein. After detection, our plasmid will code for the production of EPIC Firefly Luciferase and LRE, which will cause the E. coli to glow and show the patient where the melanocytes are located. The cream that will be created will act as a diagnostic tool for the early detection of melanoma, allowing for earlier and faster treatment to occur. In order for the system to be effective, a protein receptor on the surface membrane of the precancerous cell must be identified. The most applicable protein receptor would be the mutated version of the Epidermal Growth Factor Protein Receptor. We will look for a protein on the surface of the E. coli that will bind to the mutated EGFR. If this cannot be found we will find a suitable protein on the E. coli surface and alter the DNA to create a match. The protein receptor on the E. coli membrane will send a chemical signal from the binding site to promote the production of arabinose which will cause the firefly glow. The EPIC Firefly Luciferase and LRE biobrick is the most compatible part to use because it has a high luminescent output; it is highly efficient and reliable. In order to use this specific part, there will need to be the production of arabinose within the cell. A metabolic pathway for arabinose production will have to be determined or arabinose will need to be included in the cream itself.
Team Mt Lebanon PA
Currently, there is an escalating global epidemic of obesity. Diets with high contents of long-chain saturated fatty acid in Western nations contributes significantly to this pandemic of “globesity”. Our idea is to use genetically modified E.coli cells in the gut to take up the long-chain fatty acid molecules and convert them into polyunsaturated fatty acid molecules (such as Omega -3 or -6). If successful, such a probiotic approach will not only decrease the amount of saturated fat in the gut for absorption, but also enrich the “good” fat in the diet to improve cardiovascular heath.
The proposed project will have three stages. First, we will develop a long-chain fatty acid sensor system which will monitor the amount of fat in the environment. Second, we will using genetic engineering methods to empower the E.coli to convert saturated fatty acid to polyunsaturated fat. Finally, we will develop a method to secrete the polyunsaturated fat out to the gut lumen for host intake. But due to time constraints, we will focus primarily on the first two stages this year.
Team NC School of Sci Math
The goal of this study, therefore, is to develop a multi-input logic gate in Escherichia Coli, which can detect the presence of a number of these environmentally degrading compounds, and for each, produce a unique colorimetric output. We hope to apply the principles of electrical engineering by using the Google ADK to sense this colorimetric output and send a notification through email. We envision that for an end-user, our elegant synthetic biology solution will allow a homeowner to easily and effectively be notified of the need for inspection of their septic system.
Team SharonBasicallyAcid
We are planning to create a pH sensor/expression device. This device would allow bacteria to sense the pH of their environment and then indicate that pH by producing a color change. We think this could be used in hydroponics to indicate that the growth medium is at a proper pH. Eventually we would like to insert a gene that can respond to pH changes by secreting Hydrogen ions or Hydroxyl ions.
Team WHHS Cincinnati OH
We started by brainstorming topics that we could do further research on, and came up with topics including toxic metals, environmental estrogens (detergents, plastics (BPA), fertilizers, pesticides), hormones, biofilters, and biofuels. Research of topics was divided among team members and was subsequently done on topics including recycling and composting, pesticides, hormones, bacteria communication, and radiation. Much of this research began by looking for wikis of previous teams who may have done their projects around these topics.
Currently we are in the process of deciding which path to pursue. The majority of our proposed topics fall under the Food and Energy and Environment tracks, so we most likely will not deviate from those tracks for our final project. Right now we are also looking at conducting our experiments with yeast as opposed to E. coli and the possibility of conducting the same set of experiments with both organisms to study the differences.
AMERICAS WEST
Team BioscienceDragons AZ
Our team is looking to create a bio-panel. A bio-panel is solar panel type device where us bacteria to harness solar energy to produce ethanol. What we want to focus on for the time of competition is developing and testing the bacteria that will be used to produce ethanol. The bacteria we will use is E. coli and we will transform it with two separate plasmids. One plasmid to produce a protein that is a light driven proton pump to allow the bacteria to produce ATP from sunlight. The second plasmid will allow the bacteria to ferment glucose into ethanol. This would essentially allow the bacteria to get energy from the sun and thus use the glucose to produce ethanol, virtually creating a bacteria that in a sense produces ethanol from sunlight. Eventually the plan is to get this into a solar panel type device for the efficient production of ethanol as a biofuel, but for time being we will focus on engineering the light driven ethanol producing bacteria.
Team BV CAPS Kansas
Biofuels
The oil industry drives the economy and life of the world; however, this resource is dwindling and has detrimental effects on our atmosphere. In order to reduce oil usage and dependence, we will improve the efficiency of biofuels by manipulating the microbes used to make it. By mimicking the features of extremophiles such as halobacteria, we will increase the survival of microbes in extreme temperatures and saline environments. Microbes can also be used to degrade plant waste, and, someday, even household waste.
Life on Mars
By adding various features of extremophiles such as halobacteria, we will make microbes able to survive the conditions on Mars. It should grow in low oxygen/high carbon dioxide atmosphere with little water. In addition to extreme temperatures, the microbe needs to withstand mild radiation. We could do this by using a photosynthetic chassis, expressing antifreeze proteins.
Team Lethbridge Canada
Oxytocin is a hormone produced in the pituitary gland that plays a major role in relationships, social bonding, pregnancy and childbirth. Chemically synthesized Oxytocin is available as a prescription to induce labour and treat post-partum hemorrhage. However, many properties of Oxytocin are still unknown. When released, Oxytocin has a half-life of 5-10 minutes, making it difficult to study. It is normally bound to a precursor protein, Neurophysin I, which stabilizes Oxytocin and prevents degradation. This precursor complex is cleaved by an enzyme known as Neuroendocrine convertase I. Our goal is to produce the Neurophysin-oxytocin complex and Neuroendocrine convertase I in Escherichia coli. We will create two separate constructs, one coding for the Neurophysin-oxytocin complex and the other coding for the cleavage enzyme. We will express these constructs in separate cultures and purify them. We will then test the efficiency of the cleaving enzyme and optimize the E. coli system to produce the minimal necessary amount of enzyme. Our “naturally” produced Oxytocin will then be compared to the synthetically made Oxytocin for chemical properties and cost effectiveness of production. The Neurophysin-oxytocin construct will be maximally expressed in order to acquire an effective amount of protein to test. The construct containing Neuroendocrine convertase I will be produced in constructs containing varying efficiency promoters.
Team The Agency Escondido
Our project seeks to create a triad of similar bacteria strains with complementary antibiotic production and antibiotic resistance to emulate the game of "rock, paper, scissors". Each type of bacteria will produce a single antibiotic while remaining resistant to both its own antibiotic and that of one other bacteria type. Each type will additionally resist an antibiotic included in an agar "playing field".
When two of the three types of bacteria are combined and exposed to an environmental stimulus, one type will resist the antibiotic produced by the other, while the other will be vulnerable to the antibiotic produced by the first. The first type will therefore spread freely through the media while the growth of the second will be inhibited. To identify the "victorious" strain, each will include a different fluorescent reporter gene.
Team TPHS SanDiego
Our project focuses on promoter engineering. Our goal is to characterize a set of promoters (of our design) by moving the repressor and/or activator binding sites with respect to the -10 and -35 regions of the promoter. Ideally, we would like to show that by moving an activator binding site it can become a repressor and that by moving a repressor binding site it may become either irrelevant to transcription rate or even boost it. We also want to see if there is a steep decline in repressor/activator function as the binding site move along the promoter or if it is a gradual/linear change. We believe this project could have application to genetic circuits by allowing a single protein to either activate or repress a promoter depending on where the binding sites are placed on the promoter.
ASIA
Team Beijing BHSF
The aim of our project is to design genetically modified bacteria which can efficiently degrade formaldehyde in certain environment through formaldehyde dehydrogenase displayed on cell surface.
Background 1. Autotransporter is a protein family that can display heterologous protein on cell surface. 2. Formaldehyde is widely used in many products, causing harmful health effects; Formaldehyde dehydrogenase synthesized in some microorganisms can facilitate the degradation of formaldehyde.
Approaches In our experiment, we are going to 1. Clone a series of genes necessary for cell surface display; 2. Construct Signal peptide-Passenger protein-Linker-Translocator fusion expression vectors; 3. Check the availability of this system by Green Fluorescent Protein presentation analysis and formaldehyde dehydrogenase activity analysis.
Team Beijing HDFLS High
Organ phosphorus pesticide (organ phosphorus, pesticides, Ops) is a kind of very important highly efficient pesticides. Its wide use with large amount has caused the serious environmental pollution, and it can adhere to the surface of some fruits and vegetables. Organic phosphorus belongs to the nerve poison, mainly the inhibition of acetylcholinesterase activity in blood and tissue of human, leading to accumulation of neurotransmitter, acetylcholine, thereby blocking nerve conduction, cause central nervous system poisoning. Organic phosphorus degrading enzyme can break the phosphate ester bond. If the phosphate ester bond of organic phosphorus is hydrolyzed, its toxicity will greatly reduce. Gene engineering bacteria degradation is new technology to treat organ phosphorous pesticides pollution. Our project aims to build a kind of E. coli with the organic phosphorus degrading enzyme gene, which can transfer the harmful organ phosphorus pesticide into nearly unharmful phosphorus compounds.
Team CSIA SouthKorea
In 2010 Collegiate iGEM, Team Cambridge conducted “E. glowi” project, in which the team used bioluminescence-related genes of firefly and Vibrio fischeri to engineer E. coli strains that emit a variety of wavelengths of light. Furthermore, Team Cambridge applied various techniques, such as mutagenesis and codon optimization, in order to improve the naturally-existing parts.
The goal of our team is to further improve the system of the parts of Team Cambridge into parts that can produce even greater amount of fluorescent protein. The main mechanism that we will utilize in order to achieve our goal is increasing the ATP concentration inside the cell. It is known from previous researches that higher concentration of ATP inside the cell leads to a greater rate of recombinant protein expression; it is also known that overexpression of PCK, which is an enzyme that synthesizes ATP under glycolytic condition, results in higher amount of ATP synthesis, which causes higher concentration of ATP inside the cell. Therefore, in order to enhance fluorescent protein expression in E. coli by increasing the ATP concentration inside E. coli, our team will improve the part engineered by Team Cambridge by incorporating PCK-expressing gene inside the part. Team Cambridge’s project comprises two sub-projects: Project Firefly and Project Vibrio; our team will specifically focus on the part with Vibrio fischeri genes.
Furthermore, considering that proteorhodopsin, under conditions in which normal cellular respiration is impossible, works to convert light energy into chemical energy of ATP, our team is considering adding gene that expresses proteorhodopsin so that we can construct E. coli that can consistently produce fluorescent protein, even when put under harsh conditions.
One plausible application of this project is constructing a BioPrinter with the bioluminescent E. coli strains. If time permits, we will try to devise a way with which we can use the E. coli strains as BioPrinter material.
Reference:
[1] Kwon, Y. D., Lee, S. Y., and Kim, P., A Physiology Study of Escherichia coli Overexpressing Phosphoenolpyruvate Carboxykinase. Biosci. Biotechnol. Biochem., 72(4), 1138-1141 (2008).
[2] Kim, H. J., Kwon, Y. D., and Lee, S. Y., An Engineered Escherichia coli Having a High Intracellular Level of ATP and Enhanced Recombinant Protein Production. Appl. Microbiol. Biotechnol., 94, 1079-1086 (2012).
[3] Walter, J. M., Greenfield, D., Bustamente, C., and Liphardt, J., Light-powering Escherichia coli with Proteorhodopsin. PNAS, 104(7), 2408-2412 (2007).
Team Shenzhen SFLS
Too much phosphorus in the body can be just as harmful as having too little. Likewise, too much phosphorus in lakes and streams can have negative side effects on the surrounding environment. The process we have created of degrading phosphates in an aqueous solution uses two engineered sequences on the same construct. The first sequence contains a phosphate sensitive promoter (name of promoter), agfp gene (name of gene), and aLac gene (name of gene). The second sequence contains a Lac sensitive promoter (name of promoter), an rfp gene (name of gene), and a gene (name of gene) that codes for a polyphosphatase. In the presence of high concentrations of phosphate, the Lac sensitive promoter is turned on and the production of Lac is allowed. After a certain threshold of Lac is made, the Lac sensitive promoter is turned on and the production of polyphosphatase is allowed. The polyphosphatase then degrades phosphates present in the solution. The production of GFP is used as a visual marker for the production of Lac and the production of RFP is used as a visual marker for the production of polyphosphatase. In a timed experiment, GFP should be seen first. After enough Lac is made RFP should then be seen. Upon the degradation of phosphates, the termination of both of these proteins should follow.
Team Shenzhen SZMS
Nitrate (NO3-) and nitrite (NO2-) are chemical roots of nitric acid (HNO3) and nitrous acid (HNO2) respectively. They exist in the aquatic environment, the living organisms and artificial products, as pollutants, which can cause food poisoning, cancers or even death. It's important to detect and eliminate such chemicals with the efficient methods. Currently, several detection methods have already been in use but all are not entirely harmless. For example, granular Cd grains are recommended for the NO3- determination for fruits and vegetables because they are easy to make and recover, and can be used repeatedly. However, Cd cannot be recycled easily, and may cause additional pollution. So the goal of our project is to provide an efficient and a more environment friendly method of detecting nitrates/nitrites and we strive to design biosensors to avoid the disadvantages of traditional methods.
Our team is going to develop novel modular biosensors that enable cost-effective and on-site detection of nitrates/nitrites by using an Escherichia coli (E.coli) chassis. And our development toward the nitrates/nitrites sensor is based on the previous work of the UT Dallas 2010 and Cambridge 2009. Their aim was to enable E.coli to report the existence of nitrates/nitrites with green fluorescent protein (GFP), but we found several drawbacks of this biosensor. Firstly, the GFP reporter within the bacteria is not efficient enough to respond to the inducer so only dim green fluorescence can be detected. Also, this biosensor cannot be recycled for repeated usage because it does not have an efficient way to turn off the reporting process after the detection. Thus, our team aim to improve the biosensor.
We selected the PyeaR promoter as the initial part of biosensor, which is used to respond to nitrates and nitrites. In order to make a remarkable expression, we then plan to use a reporter gene, the CrtEBI, that, when synthesized, will lead the E. coli to release a specific pigment, lycopene, as the visible color to determine the existence of nitrates/nitrites. Simultaneously, we will incorporate another reporter, the banana odor enzyme (ATF1) generator, which enables our biosensor to produce an aroma of bananas with the existence of nitrates/nitrites. Therefore, our biosensor containing dual reporters may ensure a high accuracy in the detection of nitrates and nitrites. We also intend to build our biosensor to trigger the release of lipoxygenase to facilitate the degradation of the lycopene, which may enable the repeated usage of this biosensor.
EUROPE
Team AnatoliaGreece
We are hoping to construct an E. coli bacterium that will recognize Mercury and produce red fluorescent protein in response. Mercury is considered to be toxic, but is still highly used in devices like thermometers, barometers and sphygmometers, and also in liquid wall paints. Therefore, we believe that it is essential to create this construct, that will emit a 'danger alarm' (the red colour) in response to presence of Mercury identified.
Team AUC Turkey
In Jamboree 2013, we look forward to present to you the bactocooler that we have started to design.
We shall add a part to our system which shall detect "thermal stimuli". This may be a system that will be activated at a certain temperature.
As a result of thermal stimuli, we want our cooler system to be activated. To decrease the temperature, we are thinking of breaking down an organic compound with an endothermic reaction.
Overall, we can state that we intend to make a synthetic cooler which will be activated after a specific temperature.
Team NGSS AEI Turkey
What can we do by changing the wavelenght of the light to which bacteria are exposed to? This was our initial idea and starting from this point we designed a new light switchable system in E. Coli. When we think of light one of the first things which come in our minds is Dracoli; why not? For Dracoli, we want to assemble the antibiotic resistance of E. Coli with photo sensitivity. In this way, we want to establish a system which allows bacteria to resist two antibiotics at night or day, while one of the antibiotic resistances will be abolished at the other time. We will analyze how the strength of the antibiotic resistances changes at different wavelengths. Thereby, we want to design a Superman bacteria for particular wavelengths and with it safety systems for diverse devices.
Team Salonica Schools
Our team will work on constructing an E.coli bacterium that will identify CO and emit red fluorescent protein in response. The complexity can increase by making the bacterium emit GFP and RFP for different CO concentrations but we will see if such thing is possible. The mechanism’s applications include: adding bacteria on power plant filters, thereby checking if they work (if they don't, red smoke will be produced), to households with boilers as a safety precaution etc.
Team St Pauls London
We plan to use red, yellow and green fluorescent proteins in a “traffic light” system, whereby the colour of the protein translated corresponds to the concentration of lactose, with red fluorescent protein denoting a high concentration of lactose, yellow fluorescent protein representing a low concentration of lactose and green fluorescent protein showing that there is no lactose present in the immediate environment the E.Coli is exposed to. It is our hope that this could potentially be used in allergy testing and in the analysis of food samples, and by individuals who are lactose intolerant; because we hope to design a semi-quantitative detector it will show a spectrum of lactose concentrations so mild intolerants and severe intolerants will be able to use the sensor in different ways.
Team UCL Academy
12.5 million tonnes of paper and cardboard are used annually in the UK. Collection costs undermine the benefit of paper recycling. The UCL Academy iGEM team propose an alternative solution, a home system that converts cellulose into glucose and allows the up-cycling of paper into a commercial product: biofuels + PHBs (bio plastics).
We decided to construct a two stage apparatus containing two reactors. The first reactor contains cellulolytic enzymes that output glucose and allows monitoring of the production levels. A filtered feed from the first reactor enters the second, which contains Cupriavidus metallidurans, a PHB producing organism. Ideally we would like both parts to be contained in one stage reactor where all organisms and enzymes would be placed in one compartment. This would be more challenging as intermediate product, glucose in this case, would be harder to monitor.
LATIN AMERICA
Team CIDEB-UANL Mexico
The agriculture is a very important activity and is the base of our alimentation and the production of raw materials that eventually will be transformed into products or more complicated materials. Different technologies have been applied to agriculture to reduce important problems and some obstacles that decrease the efficiency in the cultivation of certain plants. One problem that affects considerably some cultures is the presence of plagues. Some insects cause a significant damage to cultures and reduce the quality of the products. In order to avoid or reduce the impact of these organisms, the use of pesticides has increased and it is very common in the cultivation of almost all plants. Nevertheless, the use of these substances causes damage in the environment by the contamination of water and soil. Nowadays we can find Genetically-Modified plants adapted to avoid these problems such as the GM maize: “The GM maize planted in Europe produces a substance that enables it to defend itself against a persistent pest known as the European corn borer.”1
Our idea is about a genetically modified bacterium which produces a biological pesticide (Vip3ca3) against target organisms: earthworms Bacillus Turingensis. The bacterium would be regulated by temperature and aims to control pesticide production. As it is a biological pesticide it does not harm the environment and affects only target species reducing the impact this could have in such environment and its effects on other species.
1.GMO Compass. (2008, December 3). Genetically modified maize in the EU. Retrieved from http://www.gmo-compass.org/eng/grocery_shopping/crops/18.genetically_modified_maize_eu.htm
