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From 2012hs.igem.org

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AMERICAS

Team BioscienceDragons_AZ

Exploring new alternative energy sources in modern society has become a high priority in scientific research. The recent increases in energy costs have inspired and pushed scientists and engineers to continue to search for more efficient ways of powering our future. We plan to explore the field of synthetic biology to search for new sustainable methods of renewable energy production. Our approach involves using the protein Proterohodospin to test whether or not light can be a viable method for fuel production. Proterohodopsin(PR), used by cells when deprived of oxygen, exhibits the process, similar to photosynthesis, that converts ultraviolet light to an alternative energy source for the production of ATP to power the cell. One application of the PR protein is to use it on cells that produce ethanol/butanol and change their original food source to light to produce biofuel that can be used. Our approach is to alter the genetic structure of E.coli, using our understanding of synthetic biology, to mimic the cells that produces the ethanol/butanol and express the PR protein by using Azide to stop the cells from consuming oxygen, thereby forcing the cell to use light as a food source. The goal of our research is to create a "BioPanel" that will use the PR induced cells to produce ethanol/butanol that can be tested later for feasibility and future commercial applications. The success of this research will suggest whether or not using light to create fuel is a viable alternative energy source for the future.

Team BioToga_NY

Team BioToga is going to design a biobrick "Multimeter." Our multimeter will combine various biobricks into one design. We want to develop a biobrick that can test for the presence of water contaminants such as lead, cadmium, mercury, and arsenic. Each contaminant will express a different fluorescent protein, such as BFP, GFP, RFP, and OFP. Our goal is to develop a multimeter that can test for 3 contaminants, with a stretch goal to test 4 contaminants. Note: Two days after coming up with our idea, we did find that University of Seoul already did a similar project [1], but as best we can tell this project wasn't done using biobricks, so our hope is to build off of U Seoul's work, but make our project by combining mostly existing biobricks.

Team BVCAPS_Kansas

Current the Bioscience class is still debating what our project should be about. We have done research on other iGem projects from the past to help us get an idea of what other iGem projects are about and what other teams have done. In class we have been working on increasing our knowlege of biology especially dealing with DNA and the processes invloved with DNA. Corn syrup is metabolized into high-fructose corn syrup by means of members of the bacteria genus bacilius. Since corn syrup is obviously of considerable commercial value, we are considering using promoters to either decrease the metabolizing time or to add desirable traits (maybe vitamins) to the high-fructose corn syrup.

Team BVCAPS_Research_KS

Our project, in essence, designs the perfect alarm clock. The presence of a strong wintergreen smell is used to help the user wake up, heightening their senses. At night, when no light is present, a banana odor produced will assist in calming down the user, helping them go to bed. This all occurs in the absence of electricity through pure biological systems.

This system is the combination of the MIT and University of Texas teams' projects from years past. We are making a combined genetic circuit with the smell of the bacteria (banana or mint) depending on the time of day (presence of light). The light receptor protein, obtained from photosynthetic algae, turns the banana smell on in the absence of light, and the mint smell on in the presence of light.

Team CIDEB-UANL_Mexico

The detection of various components in a safe and rapid way has been a challenge in modern science. Biosensors using genetic circuits in bacteria have been made, which allow knowing whether the sensed component is present or not. Nowadays it is known that certain levels of heavy metals on water can be dangerous for living organisms. For that reason it is important to know the concentration of these metals, but the techniques for detection and quantification are complex and require expensive equipment.

The aim of this project is to make a study model for quantifying heavy metals with fluorescent colors depending on their levels of concentration. In order to do so, a biosensor based on three different fluorescent reporters will be built. Additionally, this design could be improved in order to achieve higher sensitivity by adding more modules to the circuit.

This genetic circuit could be applied for building biosensors to detect the presence of heavy metals and semi-quantify them. This design will recognize the component that it is meant to be analyzed and give an approximation of the quantity. According to that, it can be useful to know if the concentration is toxic for living organisms.

Team Evansville_Central

Our project is focusing on the incomplete metabolism of casein and gluten in the human digestive tract. Individuals with dairy intolerance are unable to consume foods containing milk or any milk product that contains casein. Individuals with gluten intolerance are unable to consume foods containing gluten such as wheat/flour products. Our goal is to research the isolation of the dipeptidyl peptidase 4 gene and create a BioBrick which will eventually produce a protein that will aid in the digestion of gluten and casein invitro.

Team GPHS_Snohomish_WA

The Puget Sound basin in Washington state is surrounded by many types of industry that introduce contaminants into the Sound. Of all of the chemicals introduced to the Sound, arsenic has been among the most prevalent and perhaps the most dangerous. Our team is designing an E. coli-based sensor to detect waterborne arsenic and provide a visual feedback. We plan to test our sensor using water from the Sound as well as controlled test samples with known arsenic concentrations.

Team GreenfieldCentral_IN

Our first project deals with Galactosemia. Galactosemia is a disease in which an afflicted person cannot break down galactose, a simple sugar found in many food items such as milk. Classic galactosemic individuals cannot effectively produce the enzyme GALT, which is needed to catalyze the breakdown of galactose. Galactose build-up can lead to many debilitating conditions, such as ataxia, liver failure, and learning disabilities. Our goal for this project is to create a blood-galactose monitor to help galactosemic patients monitor their condition. This is needed because current blood sugar monitors only detect both sugars together, which does not help galactosemic people. We are planning on creating a strain of yeast that can detect galatose and glucose separately in the bloodstream. We are planning on using the promoters Gal1/10 to detect galactose, and HXT1 to detect glucose. Then we are going to use the mCherry fluorescent protein and cyan fluorescent protein to indicate the concentration of both sugars. Once we assemble our plasmid and transform it into E. coli to amp up DNA concentration, we will then transform it into yeast. We are also going to characterize the promoters by testing the fluorescence when introduced with different sugar concentrations. This will help standardize the test and make it easier to use. This project will hopefully be a simple test for galactosemics to monitor the status of their condition.

Our second project focuses on the disease in fish called Mycobacterium Marinum. Mycobacterium is a strain of tuberculosis. Mycobacterium Marinum kills large masses of fish, mainly in aquariums, and is currently undetectable. This disease also affects humans; if a human has an open sore and comes in contact with the contaminated water, the human will then be a carrier of mycobacterium Marinum and could possibly infect other aquariums. Our project is to find the structure of Mycobacterium Marinum and have E. coli target mycolic acid, mycobacterium's defense mechanism to current vaccines and antibiotics. When our engineered E. coli detects the mycolic acid on the cell wall of the mycobacterium, the green fluorescent protein gene we will insert into the plasmid will indicate that disease is present in the aquarium. If this step is successful, then we will take the project one step further. We will attempt to engineer E. coli to target an enzyme on the cell wall of Mycobacterium and have it release the mycolic acid so the mycobacterium will become defenseless to current treatments. In the broad view, if we are able to detect Mycobacterium through the use of fluorescent proteins, then the actual test for tuberculosis today could be simplified and made cheaper compared to the current process. A blood sample would be taken from the patient, and exposed to our E. coli. A spectrophotometer would then calculate the fluorescent levels of the sample, and determine if the patient has tuberculosis.

Team Hewitt-Trussville

The United States Environmental Protection Agency and Alabama Department of Environmental Management (ADEM) has declared numerous companies to be in violation of runoff waste laws. Alabama Rivers are affected by high levels of phosphate, which influence the diverse ecosystems inhabited on the rivers, which include 118 species of snails in the Cahaba. There are four that are endangered or threatened. They include the Cylindrical Lioplax, Flat Pebble Snail, Rock Snail, and the Round Rock Snail. (Nijhuis, 2011) Our group is constructing a biobrick that will transform into yeast for ready use. An inverter, Pho5 promoter, and red flourescent protein will be combined and then inserted into the plasmid backbone. We are utilizing the natural pathway that yeast has to perform for survival. Just as the biological function of the Pho5 pathway secretes different levels of phosphate into the cell based on environmental levels, the RFP works within that pathway to visually show the different levels of phosphate by glowing red. Throughout the production of the Pho5 Plasmid lab procedures including: Biobrick assembly, Gibson assembly, Polymerase Chain Reaction, electrophoresis, and transformation were used.

Team Lethbridge_Canada

The purpose of our project is to create bacteria that will detect blood sugar levels and respond accordingly by producing insulin. Type one diabetes is caused by the degeneration of islet cells in the pancreas. Conventional methods of treatment for type one diabetes include direct injection of insulin intravenously, the transplantation of islet cells or even the introduction of an entirely new pancreas. Our engineered bacteria would provide a long-term solution compared to the standard injections, which need to be administered at least twice per day. In essence, our project has the potential to change the way that diabetes is treated.

Team NewLondonFarquizzles

We are planning on creating an intervention which will enable a yeast cell to detect and alert consumers to high levels of carbon monoxide. Carbon monoxide is produced by the incomplete combustion of fossil fuels and can come from an oven or furnace that is working improperly. This gas can be deadly due to the ability of carbon monoxide to bind to red blood cells more readily than oxygen therefore results in cell death due to oxygen deprivation. The yeast carbon monoxide detector would be preferred over the traditional carbon monoxide detector as it will operate without the use of electricity. The materials will provide a green opportunity to protect your loved ones from carbon monoxide death.

The intervention will cause the yeast to glow red and release a strong odor to alert the consumer of danger.

Team PrepaTec_GarzaSadaMx

What we want to do is to insert a specific enzyme in the E. Coli for it to be able to create a textile dye, which is known as tyrian purple. Tyrian purple is known to be the world’s most expensive color, about $3,500 U.S. dollars per gram. This dye is known by the ancient cultures as: royal purple, imperial purple or imperial dye, the colors of the royalty, because it did not fade out, but became more intense with weathering and sunlight. It’s obtained by a specific mollusk, the Bolinus Brandaris, but due to its small size, the Byzantine Empire, which controlled the production of this coveted dye, needed to kill a large number of sea snails to obtain relatively small amounts of dye. Nowadays industries are not allowed to use this dye, even thought its color has been imitated with chemicals, but since it’s nothing more than an imitation it’s not as purely bright and long-lasting colored as the real natural tyrian purple. With our enzyme applied to the E. coli, the natural tyrian purple dye made by mollusks will be re-created by our E. Coli and therefore no more mollusks would be unnecessarily killed and a bright, long-lasting and really cheaper tyrian purple dye would be available for textile industries.

Team Sharon_BasicallyAcid

This semester, we are working on engineering bacteria with a pH sensor that will activate a gene in the presence of gastric acid (pH of 1.5 to 3.5). The gene will then allow the bacteria to excrete a base or stomach mucus to help neutralize the gastric acid in the esophagus, which is the leading cause of Gastroesophageal Reflux Disease (GERD).

Our updated project has been scaled down to utilize a pH sensing and modifying bacteria to monitor the environment of planting soil for tomato plants. The goal is to chain a pH sensor to turn on a hydrogen pump, effectively acidifying any area deemed too basic.

Team Sharon_MA_Aquila

The purpose of our project is to insert antifreeze protein (AFP) into yogurt cultures. Milk is converted to yogurt using Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus salivarius subsp. thermophilus bacteria. These cultures ferment the lactose sugar present in the milk and convert it to lactic acid, which gives yogurt its distinctive taste and texture. AFP is a protein produced by plants, fungi, bacteria, and some vertebrates to prevent the formation of dangerous ice crystals at subzero temperatures. AFP is about 300 times more effective than industrially produced antifreezes at the same concentration, so they have many possible commercial applications, including cryosurgery, hypothermia treatment, and farm fish production. Some companies have also started isolating AFPs from fish and introducing them into milk and yogurt products. The protein could help prevent freezer burn and improve the texture of the yogurt (frozen or otherwise). Our project will instead introduce the AFP-producing gene directly into the Lactobacillus bulgaricus bacteria, so that it is constantly produced as the bacteria metabolize lactose. Hooking up production of the protein to the lactose sensor already present in the bacteria would allow continuous production of the protein. Since transplantation of a small quantity of yogurt cultures can be used to produce another batch of yogurt, our altered bacteria would easily be able to replicate and produce AFP in new batches.

Team Sharon_MA_ArborVitae

Our project is based on the idea of detecting glyphosate, a dangerous pesticide, by triggering a gene that would cause a color change or a red fluorescent glow. The glyphosate is commonly found in pesticides used by agriculture-based corporations. This pesticide is found in water runoff and can have long-lasting negative effects, such as liver damage and mutations in amphibians. Glyphosate is similar to the amino acid glycine, so we will research bacteria that may recognize glycine, causing a series of reactions, aided by receptors and sensors, so that a viewer might recognize the presence of glyphosate. Ideally, this process would be done without the use of expensive, complicated equipment and materials, so that anyone with a basic set of tools could test a water supply to see if it is safe. While glyphosate can be found in air, water, and soil, we decided that the easiest test would be a water test, since that is easily added to incubating plates.

Team Tyngsboro_MA_Tigers

According to the National Conference of State Legislatures [1], 25 states have statutes requiring residential carbon monoxide detectors. Currently, the common household CO detectors sold on the market are only sound-based. However, as people age, their senses become less acute. We are investigating the development of a genetic circuit for an indole-free E. coli chassis that converts the odorless carbon monoxide into an indole output - the naturally produced smell of bacteria. Coupled with the common household detector, we might be able to greatly reduce the number of CO-related deaths. Our cell could help save even more lives with another sensory warning of the hidden danger.

A colorless, odorless, and soundless killer takes the lives of nearly 2,100 unsuspecting United States citizens every year; that translates to an average of three people every day. Carbon monoxide poisoning is the leading cause of unintentional poisoning deaths in the United States, and one in every 2,400 people falls victim to CO poisoning, unaware of the invisible attacker. People over the age of 65 have the highest risk of falling victim to this silent killer [2]. Only by being aware of the grave danger, and understanding the structure and function of this gas, we can create a circuit that produces a scent to CO and a warning before it's too late.

The mechanism for CO detection in our system is derived from the bacterium Rhodospirillum rubrum that naturally metabolizes CO as an energy source. This photosynthetic bacterium accomplishes this task in the following chemical reaction: CO + H2O --> CO2 + H2

The enzyme carbon monoxide dehydrogenase (CODH) is a peripheral membrane protein that carries out the primary oxidation of CO to CO2 and then passes the products through a ferredoxin-like sub-unit. R. rubrum also has a carbon monoxide-sensing protein called CooA that activates the gene expression of oxidation enzymes. In our research of R. rubrum, we found that a Turkey iGEM team in the 2010 college division developed CooA and CooA-responsive promoter BioBricks they wanted to make to transform into E. coli. They were able to successfully build these parts, and now our goal is to try and put them into our own genetic circuit that, in the presence of carbon monoxide, will output an unpleasant warning smell.

Team WarrenCentral_WCC_IN

Exposure to mercury is a widespread problem that affects many people all over the world. Most people ingest mercury through water sources. Mercury in water can arise from runoff from farms, chemical and industrial plants, household products in the trash, and sewage. Three types of mercury can adversely affect humans. Elemental, inorganic, and methyl mercury can all harm humans if ingested. Inorganic mercury is the most common form in drinking water and can cause kidney damage if enough is taken in. Methyl mercury is found in fish and humans can be exposed if they eat too much mercury-containing fish. Mercury ingestion can cause both acute and chronic symptoms.

We are using Saccharomyces cerevisiae yeast as a tool to detect mercury. In yeast, there are a number of transcription factors and genes that respond to oxidative stress and toxic metals. The yes associated protein (YAP) family is a family of transcription factors that is involved with oxidative stress regulation and redox homeostasis. They affect a number of genes, but we are focusing on GSH1 and GSH2. These genes are involved in the glutathione pathway. Glutathione is an antioxidant that protects the cell from oxidative stress.

In order to detect mercury, we are using several biological parts included in the BioBrick. The Kozak + mCherry translational unit is being used to give off a red fluorescent glow when the mercury is detected. In the plasmid, we will include the GSH2 promoter and the ADH1 terminator.

Team Yachachiq_Peru

Currently different theories describe the presence of gravitational fields which has apparently been crucial during the biological evolution and development of the living beings when they emerged from the sea towards the continental land. Our work describes the design and development of a set of possible biomolecular sensors which could detect changes in the gravitational forces. These molecules are expressed by specific genes and have homologous in the most animal species including humans. This group of genes was detected by microarrays techniques comparing RNA sequences under real and simulated microgravity. Additionally, the development of a correlation algorithm such as a function between the MAS 5.0 and Affymetrix RMA allowed demonstrating that these group of genes meet with all the mathematical and physical conditions of a sensor. Future applications of these sensors in biotechnology, astrobiology, and medicine are highly encouraging.

ASIA

Team CSIA_SouthKorea

The main mechanism that we are planning to use is the repressilator mechanism. Repressilator is a synthetic genetic regulatory network. It was reported by Michael Elowitz and Stanislas Leibler in 2000. This network is composed of 3 genes connected in a feedback loop, and each of the genes is repressed by the previous gene. This system is designed to exhibit a stable oscillation in the expression of each gene with fixed time period. In each of the wells in the 96 well plate, a colony of Escherichia Coli that expresses fluorescent protein with repressilator system will be put in. Then, by putting in different inducers in each of the wells, we are planning to control the time period and the gene expression of the E. Coli colonies and therefore express the specific shape that we are trying to express withe E. Coli display.

Using this mechanism of repressilator to make time difference in expressing GFP, we would be able to make a certain figure on a 96 well plate. However, the periods of GFP expression in each cell will be slightly different, so we thought of applying quorum sensing to synchronize the periods of bacterias.

Team HAFS_Bioholics

Without doubt, our current society is suffering from a lack of natural resources and environmental degradation. It is imperative that we seek for a method, or work towards a model that would sufficiently address these problems to establish a green earth-which would in turn secure more developed models and methods to effectively tackle environmental problems of the future.

In nature, there is an amazing diversity of organisms that emit light through enchanting processes in which living organisms convert energy into light. Yet a working method to utilize such wonders for the benefit of earth has never been found. It is the goal of our team to discover this method so that we can move one step further towards a green earth.

So now we have the overall idea- how is our team going to make it really happen using synthetic energy? We are going to put luciferase DNA part (possibly BBa_I712019) behind the promotor of photosynthesis mechanism.

Since photosynthesis cannot happen without light, to make the light glow in the dark,we must make the light reaction to make enough ATPs.

EUROPE

Team AUC_Turkey

We breathe 10,000 to 20,000 liters of air a day, mostly through our noses. The olfactory system comes in contact with a different variety and concentration of odors every day. Certain groups of chemicals that produce odors are potentially harmful and can cause health problems. There are some odor syndromes affecting people social life like Trimethylaminuria also called fish odor syndrome, and also some odors in body are unpleasant and need to be masked with deodorants. In our project, we aim to eliminate the nasty odor by degrading the chemical compunds existing in the media. To do this, we plan to modify E. Coli with chemoreceptors to sense the presence of chemicals and link this sensing pathway to the transcription of the degrading enzymes. After catabolism of chemicals, we also aim to produce some mediators causing fresh perfumes. Thus, we can full a room with perfume just by using bacteria. This would change the belief of bacteria which are blamed for the disgusting smell in the environment.

Team Heidelberg_LSL

UV radiation and radioactivity are two main natural radiation types we get in contact with each and every day. In low doses, UV and radioactive radiation are mostly harmless to cells and can even be beneficial for the survival of an organism, i.e. UV-B, which is mandatory for Vitamin D3 production in the human body. Still, exceeding the healthy range, radiation can cause severe cellular damage, which- in the worst case- leads to diseases like radiation-sickness and finally cancer in humans.

Although many people in our modern society generally know about the potential danger of sunlight (UV radiation), the true public awareness of the “invisible danger” of harmful radiation is insufficient. This is reflected by an increasing number of melanoma patients in western countries every year, promoted- besides other factors- by an overall increase of extensive sun bathing or usage of tanning beds.

The iGEM Team Life-Science Lab Heidelberg will develop a multicolor measurement toolkit consisting of standardized measurement parts for the precise quantification of both UV and radioactive radiation, applicable in a wide variety of everyday life settings- from checking the exposure of your body to UV-light during a sun bath to detecting dangerous sources of radioactivity in high-risk-areas, such as atomic power plants. Our multicolor measurement toolkit will offer a cheap, robust and easy-to-use approach for the detection of radiation and its application will not require any special equipment. Thus, it has a great potential to become a synthetic biology product widely used in our daily lives. With our project, we will offer the synthetic biology community a valuable collection of new, widely-applicable and well-characterized measurement parts and thereby contribute to the future development of the whole synthetic biology field.

Team Saloniki_Greece_12

In the recent months many people throughout Greece have been returning to agriculture as their main source of income. This makes agricultural developments extremely important for Greece’s economic future. For this reason we have selected an agricultural project for the focus of this year’s iGEM team. Furthermore, the American Farm School in Thessaloniki was founded to educate young men and women in agriculture and life science, thus the students from this school have practical training in this area.

The key factor to having healthy soil is the presence of a plethora of different bacterial species. There are millions of different types of bacteria in nutritious soil. These bacteria do everything from decomposing dead matter to simple carbons or degrading pollutants to forming nitrogen-fixing, mutualistic relationships with plants.

We can take advantage of the roots that exists at the American Farm School by working with the different soils and their equipment. We first plan to take soil samples from different areas at the farm. We will analyze the different bacterial and chemical composition of the soils in relation to the crops that are being grown in the area. Then we will identify the beneficial properties of the existing types of bacteria to see which would be most beneficial to express on a large-scale.

We plan to focus on nitrogen-fixing bacteria. These microorganisms are called diazotrophs and are extremely important to the environment. They convert nitrogen (N2) in the atmosphere to ammonia (NH3). This allows the nitrogen to be easily used as a biological building block. Many of these bacteria form relationships with plants where the plant supply carbons and the bacteria supply the nitrogen for plants to use in growth. We are hoping to increase the ammonia supplied from the bacteria or work on protocols to make these bacteria easier to work with in synthetic biology.