Filter projects 228 projects
Team Year Title Biosensor Category Abstract Track Inputs Outputs Application Results Awards Tags
AHUT China 2013 The Shinning Sanctifier Yes Environment Our goal is to design a wastewater treatment system which can absorb the pollutant efficiently while transform it into luminous energy. We plan to use E.coli to design a bacterium that can digest the nitrite and ammonium in its interior using the disposal system from the anammox. Through the introduction of luciferase, the energy can be transformed into bioluminescence. Therefore, we named it Shining Sanctifier. This new star in synthetic biology will overcome the traditional issues and be applied to the sewage treatment system on a large scale while it can also be made into illuminating system in the future. Environment Ammonium
Nitrate concentration
Luminous energy In vivo Bronze Medalist N/A N/A
Baskent Meds 2013 Transformation of Escherichia coli In Order To Develop Legionella pneumophila Sensing Bacteria Yes Health and Medicine Legionella pneumophila is the cause of the Legionnaires' disease which is a type of pneumonia. The bacterium is found in warm water environments, particularly in artificial water supply systems such as air conditioning systems and cooling towers. The enfection occures by inhalation by small droplets of contaminated water. Our aim, as the team “Baskent_Meds”, is developing bacteria which can recognize Legionella pneumophila specifically at species level by legionella quorum sensing, and respond by producing anti-Legionella peptide which is produced by some Staphylococcus strains. Quarum means “minimum”. Legionella pneumophila should sense the minimum amount of cells around to colonize in the environment and express its virulence. So our modified E. coli may sense the presence of Legionella pneumophila in any contaminated surface and kill it. Health and Medicine Legionella pneumophila Activation of degradation
Anti Legionella peptide
In vivo Bronze Medalist N/A N/A
BIOSINT Mexico 2013 Smartpro Yes Health and Medicine This year Biosint Mexico team will be developed a smart probiotic. Along the competition have been present several projects about probiotics, nevertheless the main disadvantage was that most of them were not being created in a lactobacillus strain. Because of this we constructed a Lactobacillus platform for others iGEM teams. Continuing with the idea of the smart probiotic system we include a sensor for xenobiotic substances that could detect and decrease intoxications by pesticides. Also the team implemented a kill switch for safety issues. This project contributes to resolve one of the Mexican food and health problems. Health and Medicine xenobiotic substances Not specified not specified Bronze Medalist N/A N/A
BIT 2013 Cr(Ⅵ)-biosensor to detect chromate in dairy products Yes Environment As we know, antibiotics are widely used in modern industry to prevent the infection of cow breasts. However, the residual of antibiotics and other components, such as Cr (VI) which is widely used in the recycle of proteins from leather, will endanger the health of customers. Therefore, it is necessary to find solution to identify these harmful chemicals, but the method of timely detection of harmful chemicals in products still remains unsolved. To solve this problem, our sensor has been divided into three, respectively, of hexavalent chromium, tetracycline and β-lactam there is a response, for each sensor, we are all assembled in a downstream of the amplification block (amplifier) and the control block (controller), the output signal to be amplified, by adjusting the concentration of IPTG to achieve the adjustment of magnification. Amplifier by the T7 RNA polymerase gene and T7 promoter composition control block is through the downstream of the T7 promoter plus lacO and the addition of regular expression lacI, by adjusting the concentration of IPTG, lacO then adjust the boot situation achieved, the final response module for the green fluorescent protein. In order to achieve real-time detection, we also made a biochip which provided a reaction room for both engineering bacteria and samples. Now we are able to detect all these three harmful chemicals with a hand-held electronic equipment made by ourselves. Food and energy B-lactam
Hexavalent Chromium
Tetracycline
Flourescence
GFP
In vivo Advance to Championship
Gold Medalist
N/A N/A
Buenos Aires 2013 No Title Yes Environment 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. Until now, there have been some experiences of pollutant biosensing in iGEM, but most of them rely on expensive and specific 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 also have designed it in a way that any user with minimal training (using an image-based instructions) could easily determine the presence and level of the contaminant on drinking water. 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, lead, hydrocarbons, etcetera. At the end of this project we expect to have a working prototype of the device plus a control field measurement. Environment arsenic Not specified In vivo Advance to Championship
Gold Medalist
Regional Finalist, Latin America
N/A N/A
Clemson 2013 No Title Yes Food safety Many regulatory agencies such as the Department of Agriculture and the Environmental Protection Agency have specific standards for pathogen concentrations in sample materials, including “zero-tolerance” for some foodborne pathogens. However, current detection methods for these disease-causing bacteria suffer from one or more of the following limitations: 1) requiring sample enrichment, 2) inability of low-level detection, 3) indiscrimination between viable and non-viable cells, 4) small sample volume capacity, 5) tedious procedures, and 6) high assay cost. Our Universal Self-Amplified (USA) Biosensor uses a genetically modified detection bacteria to solve many of the aforementioned issues. The engineered USA bacteria will recognize a target chemical produced by the pathogen of study, which will trigger a cascade of genes to both amplify the chemical signal and produce a visible alert to the pathogen’s presence. The USA pathogen detection mechanism strives for rapidity, economy, and simplicity. Environment E. coli O157:H7 Not specified In vivo Advance to Championship
Silver Medalist
N/A N/A
Colombia Uniandes 2013 Glucocorticoid sensor Yes Miscellaneous Glucocorticoids are hormones present in mammals that undergo changes in concentrations when the animal is under stressful stimuli. These hormones can be measured in blood plasma, urine, saliva and hair. Chemical methods are used to measure these hormones for veterinary and agricultural use, but these methods require expensive equipment and a capacitated technician which makes it uncomfortable and useless in the field. Our aim is to create a glucocorticoid sensor that is able to discern between basal levels and stress levels of glucocorticoid hormones in a sample with an easily recognizable signal, such as color, to allow the sensor to be used in the field, household or the laboratory. Environment Glucocorticoid
Stress
Colour
mCherry
In vivo Silver Medalist Best Model, Latin America
Best Wiki, Latin America
N/A
Fudan Shanghai 2013 A Novel Aminoglycoside Detection Strategy Yes Health and Medicine This summer, we focus on the detection of a group of antibiotics called aminoglycosides (for example the Kanamycin we used as a selection marker). The problem of aminoglycosides are more serious compared with other kinds of antibiotics,because they are difficult to be break down and tested, and they are most commonly used in the research, medical treatment, industry and agriculture. Even under the high temperature they are not easy to be inactivated. Moreover, they will maintain in the blood for weeks, much more than other kinds of antibiotics such as penicillin. The accumulation of aminoglycoside will also lead to ototoxicity and nephrotoxicity. By studying the regulation of resistance, we have found the natural parts which are sensitive to the antibiotics. With the quantitative methods, we are measuring the response curve of them. Then the optimized devices will be constructed for aminoglycosides detection. Meanwhile, we are also studying on the molecular dynamics and mechanisms of regulation of resistance. By modifying and estimating one riboswitch conserved in plenty of aminoglycoside acetyl transferases and aminoglycoside adenyl transferases, we are trying to find a novel principle to design and develop the bicistron-based translation initiation elements which can function more precisely and reliably. Foundational Advance aminoglycosides Not specified In vivo Advance to Championship
Gold Medalist
N/A N/A
Gaston Day School 2013 Fluorescent Detection of Cadmium in Water Supplies Yes Environment Heavy metal contaminants pose a serious health threat around the world, especially in locations with poor irrigation. Cadmium, in particular, is a known carcinogen that affects the cardiovascular, gastrointestinal, and respiratory systems. The Agency for Toxic Substances and Disease Registry compiled a Priority List of toxic substances, on which Cadmium was seventh. We combined the Green Fluorescent Protein coding region with a Cadmium Sensitive Promoter to create our detector, which provides a simple and inexpensive test for the presence of Cadmium in water supplies. We will incorporate sensitivity tuners to decrease the detection threshold, and we will use mutagenic PCR on both the promoter and the entire detector to increase its sensitivity. Proper use of this BioBrick could result in early detection of cadmium polluted water and potentially prevent deaths worldwide. Environment Cadmium
Heavy metals
Flourescence
GFP
In vivo Bronze Medalist N/A N/A
IIT Delhi 2013 pH. Coli Yes Miscellaneous pH based bacterial systems, wherein response is dependent on the pH of the medium have been explored rarely in iGEM (NYMU-Taipei(2008), Wisconsin-Madison(2010) others). pH based sensor systems have potential use in bio-remediation, gut-microbiota engineering, fermentation et cetera. pH based systems present various other challenges with respect to biobrick usability, pH dependence of reporters and lack of characterization.Our aim is to create a simple pH "bacterial" meter, not unlike a pH strip used in chemistry. We hope for this to be a template for future projects and applications Environment pH Not specified not specified Bronze Medalist N/A N/A
ITB Indonesia 2013 Aflatoxin Biosensor Yes Food safety High levels of aflatoxin contamination of foods are found in many developing countries around the world. Aflatoxins are known to be mutagenic and carcinogenic, therefore human exposure to aflatoxin would lead to an increased risk of hepatocellular carcinoma (liver cancer). One in every four liver cancers in Indonesia are induced by aflatoxin B1 exposure. Nowadays, aflatoxin exposure is not only a serious problem for human health, but it could also become a serious threat in terms of food security issue of a country. ITB-Indonesia team for iGEM 2013 focuses on designing a whole cell biosensor for aflatoxin B1 detection in foods. The biosensor uses Escherichia coli as the chassis to build a genetic circuit using SOS response system to detect DNA damage caused by aflatoxin B1-oxide attack. The SOS response promoter is followed by a reporter gene coding a chromoprotein, therefore the concentration of aflatoxin B1 in food samples could be easily detected by the color change of the bacteria. For the ease of usage, we will design a syringe shaped device with our whole cell biosensor in it. This device would allow aflatoxin B1 to enter the device, but would not permit the cells to leave the device. Food and energy Aflatoxin
DNA damage caused by aflatoxin B1-oxide attack
chromoprotein
Colour
In vivo Silver Medalist N/A SOS
response
Ivy Tech Southbend 2013 Design of a Fast-Acting Coliphage Biosensor Device Yes Health and Medicine Most E. coli are harmless and actually are an important part of a healthy human intestinal tract. However, some E. coli are pathogenic and can cause illness. The types of E. coli that can cause illness can be transmitted through contaminated water or food, or through contact with animals or persons. The Center for Disease Control (CDC) estimates about 73,000 cases of E. coli infection occur yearly in the United States and about 61 people die from the illness, most often children under the age of 5 and the elderly. We are developing a Coliophage Biosensor to detect E. coli in public waterways and lake water. Currently it takes three days to detect E.coli using the water testing method that is currently in place. A new method that has been developed by Stanek and Falkinham has improved this by detecting bacteriophage as a surrogate for E. coli. This method involves exposure of contaminated water to host bacterium expressing Bgal. Lysis of bacteria and release of the enzyme was correlated with extensive contamination. This procedure, however, takes three hours and involves filtration. We are designing a coliphage biosensor capable of detecting dangerous levels of E. coli within less than three hours without filtration. N/A Coliphage Not specified In vivo/in vitro N/A N/A not
listed
anymore
Leeds 2013 Micro-beagle Yes Miscellaneous Like the Beagle hunting dog chasing hares, our Micro-beagle is a biosensor designed to hunt down pathogens. Micro-beagle utilises the Cpx pathway and GFP, which, when it fluoresces can be seen with the naked eye. In order to achieve this we will have designed our biosensor to physically bind to antigens or particles. This binding will induce membrane stress activating the Cpx pathway. By placing the GFP gene downstream of the Cpx promoter, GFP protein will be produced following membrane stress consequently causing the cells tol fluoresce when the pathogen is present in the solution. As a proof of concept, we will be using silica beads as target analogue for pathogens. In order to bind to the beads will be expressing a silica binding peptide on the surface of the cells using Ice Nucleation Protein (INP). INP allows expression of any gene placed at its C terminus on the cell surface. The theory is that the silica binding peptide sequence can be easily swapped for a sequence of any antigen binding moiety and therefore enable us to detect any pathogen simply, quickly and cheaply. Upon completion of our project our suggested initial use for the Micro-Beagle will be a low cost easy to use test used to assess the efficacy of water treatment systems. However as stated earlier the detection system can easily be modified to allow any other large particles whose identification could be of value Health and Medicine Silica
Stress (at surface)
Flourescence
GFP
In vivo Bronze Medalist N/A Cpx pathway
Ice Nucleation Protein
NTU Taida 2013 QS array Yes Health and Medicine Bacterial infection is the invasion of the body by pathogenic bacteria, which causes pneumonia, urethral infection, bacteremia and other symptoms in hospital and community. The efficiency of traditional detection and diagnostic approaches is impeded by the time-consuming laboratory procedures, yet many of which grow poorly in bacterial cultures. All these limitations call for a new rapid and direct bacterial identification method to improve patient management and antimicrobial therapy. Quorum sensing is a type of bacterial cell-cell communication correlates with the population size. Many bacteria have one or several species-specific quorum sensing molecules released in different growth state and environment. Quorum sensing signals are shown to be involved in many physiological functions, including virulence, biofilm formation and drug-resistance. We aim to establish a novel bacterial identification method in clinical samples based on the quorum sensing profiles. Health and Medicine Not specified Not specified In vivo Gold Medalist N/A N/A
NU Kazakhstan 2013 Detection of Carcinoembryonic antigen with sandwich-biosensor Yes Health and Medicine Diagnosis of certain types of cancer at early stages is still challenging issue. Therefore, many biomarkers for early cancer detection have been investigated. Carcinoembryonic antigen (CEA) is one of the examples of the biomarker which appears at early stages of such types of cancer as colorectal, gastric, pancreatic, lung, and breast carcinoma. In this study, it is planned to develop a biosensor which will be used to detect the presence of CEA. The first part of the study is about selection of ssDNA aptamers, which have strong affinity for CEA, during 12 cycles of SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure, followed by characterization of them using dot-blot analysis, ELONA (Enzyme Linked Oligonucleotide Assay) and SPR (Surface Plasmon Resonance) methods. In the last part, it is planned to clone the genes that will assist in expression of streptavidin on the surface of membrane of the model organisms. The model organisms for creating the biosensor are Escherichia coli and Saccharomyces cerevisiae. E. coli will express the streptavidin through Lpp-Omp expression system, while S. cerevisiae will express this protein through Aga1 – Aga2 system. Since streptavidin has strong affinity to biotin, biotinylated aptamers will be used to make a sandwich biosensor for CEA detection. Twelve cycles of SELEX for CEA have been already finished. Health and Medicine Cancer
Carcinoembryonic antigen (CEA)
CEA
Not specified In vivo N/A N/A SELEX (Systematic Evolution of Ligands by Exponential Enrichment)
ELONA (Enzyme Linked Oligonucleotide Assay)
SPR (Surface Plasmon Resonance)
biosensor
ssDNA aptamers
streptavidin through Lpp-Omp expression system
carcinoembryonic antigen
Aga1 – Aga2 system
Paris Bettencourt 2013 Fight Tuberculosis with Modern Weapons! Yes Health and Medicine We are testing new weapons for the global war against Mycobacterium tuberculosis (MTb), a pathogen that infects nearly 2 billion people. Our 4 synergistic projects aim to help in the prevention, diagnosis, and treatment of tuberculosis. 1) We are reproducing an essential MTb metabolic pathway in E. coli, where it can be easily and safely targeted in a drug screen. 2) We are building a phage-based biosensor to allow the rapid diagnosis specifically drug-resistant MTb strains. 3) We are constructing a mycobacteriophage to detect and counterselect drug-resistant Mtb in the environment. 4) We are programming E. coli to follow MTb into human macrophages and saturate it with bacteriolytic enzymes. We want to vanquish tuberculosis and build a TB-free world. Health and Medicine Antibiotic resistance gene
DNA
Colour
LacZ
In vivo Advance to Championship
Gold Medalist
Regional Finalist, Europe
Best Health & Medicine
Finalist
Grand Prize Winner, Overgrad
drug resistance
tuberculosis
RecA promoter
SOS response
CRISPR
Paris Saclay 2013 PCB Busters Yes Environment PCBs (Polychlorobiphenyls) are synthetic chemicals that were widely used in electrical equipments during the late 20th century. These hazardous organic compounds are extraordinary stable and not readily biodegradable. Thus they remain for many years in nature and belong to family of persistent pollutants. PCBs accumulate in animal fatty tissues due to their lipophilicity, starting from aquatic organisms and going further into the higher level of food chain. Indeed, they can be found in high concentrations in human adipose tissues. As most PCBs are probably carcinogenic (class 2A) and some are recognized endocrine disruptors, they lead to a series of important health issues. especially in France where a study revealed that higher levels of PCB in French people adipose tissues were observed than people from other parts of the world. Although PCBs are man-made and have no natural equivalents, some bacterial communities have evolved and developed the capacity to degrade PCBs. Degradation of highly chlorinated PCBs begins with an anaerobic reductive dechlorination that lowers the number of chlorine atoms carried by the PCB molecules. PCBs with few chlorine atoms can then be degraded via the biphenyl degradation pathway. Our project aims at constructing an Escherichia coli strain capable of degrading highly chlorinated PCBs. This will be achieved by introducing in an E. coli strains genes involved in the degradation of PCBs from the three most efficient PCB degrading strains described so far: Pseudomonas pseudoalcaligenes, Burkholderia Xenovorans and Rhodoccocus jostii. Because the first degradation steps are anaerobic and later steps are aerobic, we want to introduce an oxygen based regulation of the expression of the different genes implicated in both aerobic and anaerobic degradation steps. Finally, we are also developing a sensor system to detect PCBs in the environment. Environment Polychlorobiphenyls Activation of degradation
Colour
LacZ
In vivo Gold Medalist N/A N/A
Peking 2013 Aromatics Scouts Yes Environment Monitoring aromatic compounds in the environment remains a substantial challenge today. Noting the power of biosensors for quick and convenient testing, Peking iGEM has developed a functionally comprehensive biosensor toolkit to profile aromatics in the environment. Transcriptional regulators that each senses a specific class of aromatics were first bioinformatically determined; they were then utilized to build a comprehensive set of biosensor circuits. Characterization on the detection profiles of individual biosensors and their orthogonality/crosstalk prove that these biosensors are really high-performance to profile aromatics in water. Moreover, for the ease of practical applications, two types of genetic devices were also developed as plug-ins for biosensors: "Adaptors", a set of conceptually novel devices to convert undetectable chemicals into detectable aromatics, and "Band-pass Filter", a "concentration filter" that allows the detection of analyte concentration within a specific range. We expect that these novel biosensors, together with the plug-in devices, will serve as intriguing synthetic biological tools for diverse practical applications. Environment DmpR
HcaR
HpaR
NahR
PaaX
toxic aromatic molecules
XylR
XylS
sfGFP In vivo Advance to Championship
Gold Medalist
Best New Biobrick Part, Natural, Asia
Best Parts Collection, Asia
N/A
SCAU China 2013 No Title Yes Environment Synthetic organophosphorus (OP) compounds have been used as pesticides, petroleum additive and warfare agents, which is a highly toxic contaminant to agro-environment and food security. Parathion is a typical representative of organophosphorus pesticides. This year, our goal is to construct a p-Nitrophenol sensor in E coli., which is the degradation product of parathion, in order to reflect the existence of parathion. Considering the biosafety problem after its release, we designed a suicide system in which the lethal genes are only triggered by declining p-Nitrophenol concentration. This will enable the bacteria to commit suicide when p-Nitrophnol is sufficiently degraded Environment p-Nitrophenol Not specified In vitro Gold Medalist N/A parathion
SCU China 2013 No Title Yes Environment Synthetic multicellular system has always been one of the most interesting parts of syn-bio.In the fundamental researches, especially the imitations of the whole developing procedure from a single cell to a self-organized multicellular system, many pervious iGEM teams have made plenty of explorations. However, there haven’t been comprehensive study into the imitations of sex differentiation, gametogenesis, and sexual reproduction. In our project,we intend to construct two groups of differentiated E.coli,one imitates the male multicellular organism ,the other for the female(called G+ cells and G- cells respectively).When cultured separately, the male/female multicellular system gets bigger and matures, and cells will differentiate into gametes,which cannot divide any more but are capable of gene transfer. After that, you mix this two liquid cultures,the male gametes will recognize the female cells and begin to transfer modified F plasmids into female gametes through sex pili. The conjugation makes female gametes return to the state of un-differentiation(called G cells),which means they can divide again but are not sexually determined.Then,after several cell divisions,one G cell will differentiate into a G+ or G-,which, like zygote , can grow into next generation of the multicellular system maybe containing genes from both male and female gametes. We also have another minor project aimed at detecting different concentrations of nitrate & nitrite in water,especially in drinking water. Generally,we take the advantage of natural or mutanted promoters with different sensitivities, make use of sensitivity tuners to optimize the results,and exploit different enzymes from the same pathway to generate different visible colors. N/A Nitrate concentration Colour In vitro Silver Medalist N/A N/A
SydneyUni Australia 2013 Keeping DCA at Bay - Assembly of synthetic constructs and cassettes for degradation of dichloroethan No Environment The picturesque city of Sydney is marred by industrial efflux of chlorinated hydrocarbons into the aquifers around Botany Bay. 1,2-dichloroethane (DCA) is toxic and a suspected carcinogenic agent, and one of the more soluble and mobile contaminants. Conventional DCA treatment is both costly and time-consuming, involving pumping and heat-stripping groundwater. We propose a biological alternative which may be cheaper and more effective. There are strains of bacteria able to degrade low levels of organochlorine compounds in selective conditions. Polaromonas JS666 and Xanthobacter autotrophicus GJ10 contain two pathways of particular interest. Our goal is to construct our own versions of two metabolic pathways of DCA biodegradation for comparison in a BioBrick-compatible vector, and characterise their effectiveness in utilising DCA as a sole carbon source for growth. We hope to create friendly strains of bacteria capable of removing DCA at greatly reduced cost and effort, and reduce the environmental impact of industry. Environment organochlorine compounds Activation of degradation In vivo Advance to Championship
Bronze Medalist
Best BioBrick Measurement Approach, Asia
Best Human Practices Advance, Asia
N/A
Tianjin 2013 Alk-Sensor Yes Energy Biosynthesized alkanes are promising candidates for drop-in replacement of petroleum. We constructed and characterized a device named Alk-Sensor, which can sensitively detect a wide range of alkanes and generate certain response. Alk-Sensor is composed of ALKR protein——a transcriptional regulatory protein, and promoter alkM. ALKR recognizes alkanes and their interaction triggered a conformation change of ALKR dimers which isomerizes the promoter-RNAP complex and led to activate the downstream genes of PalkM. Based on Alk-Sensor, we built a relationship between productivity of alkanes with strain’s growth rate under certain environmental stress. Starting from this relationship we further designed a novel selection method to select out the engineered strains with highest productivity of alkanes. We demonstrated that this novel selection method could enable us to select out the optimized strains effectively and efficiently. Food and energy alkanes Not specified In vivo Advance to Championship
Gold Medalist
Best Poster, Asia N/A
TU Darmstadt 2013 No Title Yes Environment Mycotoxins produced by mould fungus are present in our daily life and are harmful for humans as well as for animals. The danger of contamination of gain and other natural products has fatal consequences for the economy and the supply of whole nations. The mycotoxins which are permanently formed by the fungus, can be used as biomarkers to detect contamination. We want to develop a handy device which allows an easy and reliable detection of mycotoxins. To achieve this goal our team uses various methods from the fields of synthetic biology, electrical engineering and information processing. The detection system relies on E.coli with modified aspartate receptors (TAR) which interact with specific mycotoxins. If these are present in the reviewed sample they will bind to the receptor and induce a conformational change and thereby generates a measurable FRET-beacon by bringing two flourophores in close distance to each other. The modified E.coli will be embedded in interchangeable capsules. Together with a handheld-device they will guarantee that measurements can be done quickly, easy to operate and secure. The data will be transferred from the handheld system to an Android smartphone app which will be able to analyze, illustrate and store the test results for the user. Food and energy Mycotoxin FRET-beacon In vivo/in vitro Silver Medalist N/A (TAR)
aspartate
receptors
UFMG Brazil 2013 Cardbio Yes Health and Medicine Death by heart diseases is very common worldwide, being Acute Coronary Syndrome (ACS) its main cause. This fact is deeply related to late diagnosis, which is usually made after the cardiac event had already occurred. We, from UFMG team, decided to explore this problem building a system capable of providing a precocious diagnosis for ACS based in 3 biomarkers: Brain Natriuretic Peptide (BNP), Trimethylamine-N-Oxide (TMAO) and Ischemia Modified Albumin (IMA). The main goal is to detect each of these biomarkers using our engineered E. coli by integrating the signals CFP, YFP and RFP produced when BNP, IMA and TMAO, respectively, are present in a sample of patient serum. This diagnosis is based on color intensity of the fluorescent proteins. So, we can establish the presence or absence and severity of ACS disease and predict earlier a myocardial event, thus providing information for fast treatment." Health and Medicine BNP, IMA and TMAO CFP
Flourescence
RFP
YFP
In vivo Advance to Championship
Regional Finalist, Latin America
Silver Medalist
N/A Brain Natriuretic Peptide (BNP)
Trimethylamine-N-Oxide (TMAO)
Ischemia Modified Albumin (IMA)
UniSalento Lecce 2013 NickBusters Yes Environment Nickel is one of the most widespread heavy metals in the ecosystem, and it is essential for many organisms, from bacteria to higher forms of life. However, as all the heavy metals, even a small amount of Nickel higher than the essential dose could be toxic, leading to various noxious effects [1-2]: then the need to remove its excess from many substrates. Nowadays bacteria-mediated bioremediation from inorganic substances seems to be a considerably relevant frontier in microbic biotechnologies [3]. Our project aims to develop a living system, in an easy monitorable bacterial platform, who would work as a Nickel detector and a Nickel remediation system. The whole system is based on genetic parts from the pathogen Helicobacter pylori, whose evolution led to a stronger reliance on Nickel ions for host interaction and pathogenesis. Sensing relies on nickel regulator NikR from H. pylori (HpNikR): though homolog of E.coli NikR, it has a stronger dependance on Nickel ions and a wider range of regulated elements, being a rare case of pleiotropic regulator in bacteria. As HpNikR could contemporaneously activate and repress gene expression [4-5-6], we thought of developing a synthetic gene cluster under HpNikR - regulated promoters. With a double regulation, one of the promoters being activated while the other being repressed, the system allows to follow up Nickel sensing as a fluorescence signal from fluorescent proteins. Thus, adding bacteria to a nickel containing medium results in switching off a basal occuring green fluorescence and in switching on a red fluorescence signal. Environment Nickel Flourescence
RFP
Turn off fluorescence
In vivo Silver Medalist N/A N/A
University of Calgary 2013 FerriTALEs Yes Food safety Outbreaks of foodborne illnesses are a growing problem for food safety and public health. Whether in your water, salad or steak, pathogenic E. coli causes upwards of 250,000 illnesses every year. To solve this problem, iGEM Calgary is developing the FerriTALE to detect harmful E. coli. It uses engineered proteins that detect and report the presence of dangerous E. coli in a sample. The detector, TALE, binds to genomic markers specific to dangerous E. coli. Next, our TALEs are attached to the scaffold and reporter, Ferritin, that rapidly alerts the user to the presence of E. coli through a visible color change. We have integrated these proteins into a handheld device, similar to a home pregnancy test, that tells the user if dangerous E. coli is present. Moving forward, the FerriTALE can be tailored to detect other pathogens as the basis of a powerful new detection platform. Food and energy DNA
Shiga Toxin II
Beta-Lactamase
Colour
Prussian Blue Ferritin
In vitro Advance to Championship
Gold Medalist
Regional Finalist, North America
1st Runner Up
Best Food or Energy Project
Best Wiki, Americas
E coli
lateral flow strip
EHEC
ferritin
TALEs
cattle
nanoparticles
USP Brazil 2013 Detecthol Yes Miscellaneous Our product is a bioengineered sensor, which will be able to detect levels of methanol above 2% in common alcoholic drinks. This will allow government to make high-throughput screening of ethanol drinks tainted will methanol. The device will be used as an initial low cost and portable test. The construction is based on the pAOX promoter, which is activated by methanol and repressed by ethanol. Several parts of the device must be tuned for proper function in Pichia pastoris; pAOX promoter, red fluorescent protein (RFP), Mxr1p transcriptional factor and FLD promoter. Since we aim to develop a product ready for the consumer to use, we plan to develop a plastic container for the lyophilized yeast, printed by 3D printer, that will help perform the test and will also contain the yeast. After use, the container will be able to apply bleach to eliminate the yeast. Manufacturing Methanol Flourescence
RFP
In vivo Silver Medalist N/A N/A
UTK Knoxville 2013 Modular design of Chemotaxis Biosensors Yes Miscellaneous The major limitation in synthetic biology today is the lack of numerous, well characterized sensors. Our project aims to provide a reliable scaffold to test potential sensing domains with unknown substrates. We have created a standard platform to test a range of intracellular and transmembrane domains. Positive results are reported with green fluorescent protein for easy identification which can be done with high throughput methods like 96 well plates. We test our platform on sensors with interesting known responses. The chimera proteins are also useful in creating signals orthogonal to the cell. Environment benzene
chlorotoluene
CO
CO2
Nitrate
NO
NO2
other aromatics
oxygen
redox state
ron
toluene
xylene
Flourescence In vivo N/A N/A TodS
chimeric biosensors
standard platform
characterize new biosensors
HemAT
NarX
RcoM
Aer
Warsaw 2013 FluoSafe Yes Food safety This year Warsaw iGEM team is presenting to you FluoSafe - a bacterial sensor for acrylamide detection. As many of you know acrylamide is usually present in laboratories. But what is the significance of this organic compound really? Well, it is a neurotoxin and its carcinogenic activity has been widely proven. We plan to implement bimolecular fluorescence complementation (BiFC) to our system. In order to do this we will make a fusion of α and β hemoglobin subunits with complementary parts of split sfGFP ( an improved superfolder green fluorescent protein derivative, which is often used as a marker in molecular biology). When there is no acrylamide in the environment both chains of hemoglobin can interact and bring within proximity the split parts of sfGFP, leading to reconstruction of three dimensional structure of sfGFP and resulting in green fluorescence. Food and energy acrylamide sfGFP
Turn off fluorescence
In vivo Gold Medalist N/A alternative: redox state reporter
bimolecular fluorescence complementation
Venus- and Cerulean-based systems
Amsterdam 2012 Cellular LogBook Yes Miscellaneous Multi-sensing genetic devices offer great future perspectives for biotechnology, environmental monitoring and medical diagnostics. In light of this we have created an innovative DNA-methylation based reporter system in E. coli, named Cellular Logbook, that has the potential of simultaneously reporting on significantly more signals than current fluorescence-based systems (eg. GFP). The Cellular Logbook can be used to detect and store the presence of any compound linked to a transcriptional regulator. This system allows for offline monitoring by functioning as a memory module. Assessment of the memory status is performed by digesting with restriction endonucleases followed by gel electrophoresis. Furthermore, the Cellular Logbook is able to infer the time of signal-onset or signal-intensity using the natural dilution of the registered signal’s due to cell division. In short our exciting new memory module could potentially be utilized as a platform for many groundbreaking technologies. Foundational Advance Arabinose DNA Conjugation
Size of bands on a gel
In vitro Gold Medalist N/A N/A
Arizona State University 2012 Crisys Yes Health and Medicine Diarrhetic pathogens including E.coli O157:H7 serotype, Campylobacter, Shigella, and Salmonella often contaminate drinking water supplies in developing nations and are responsible for approximately 1.5 million worldwide annual deaths. Current technologies for detection of bacteria include DNA hybridization FRET signaling, electrical detection via immobilized antimicrobial peptides, and PCR amplification followed by gel visualization. Our method of bacterial detection fills a niche in biosensor technology. Our design implies lower costs, higher portability, and a more rapid signal output than most bacterial biosensors. Additionally, our interchangeable DNA probe confers modularity, allowing for a range of bacterial detection. Using a novel split beta-galactosidase complementation assay, we have designed three unique chimeric proteins that recognize and bind to specific pathogenic markers and create a functioning beta-galactosidase enzyme. This functioning enzyme unit then cleaves X-gal and produces a colorimetric output signal. Our research demonstrates success in initial stages of chimeric protein assembly. Health and Medicine DNA Colour In vivo N/A Finalist N/A
Bordeaux 2012 A bacterial eyespot Yes Miscellaneous This project aims at creating a regulatory system in the bacteria Escherichia coli. Our main goal is to engineer a single strain of bacteria able produce concentric patterns on the dishes. The challenge is to model a regulatory mechanism which mimics both cell differentiation and cell-to-cell communication observed in eukaryotes. We chose to create four operons (a total of 21 assemblies): three to allow the communication and expression of a visible phenotype, the fourth containing the genes needed for signal transduction. Each of the three first operons will respond to a specific quorum-sensing system (QSS) and trigger another QSS resulting in a chain reaction communicating a unique signal to all bacteria nearby. We also developed our model in silico to run simulation and test parameters that influence pattern propagation on a petri dish. Foundational Advance Quorum sensing Flourescence In vivo Bronze Medalist N/A N/A
BYU-Provo 2012 Generating a Cre-Lox System for Stable Thermosensor Output Yes Health and Medicine In the initial stages of colon cancer, malignant cells give off excess heat, reactive oxygen species (ROS), and lactate. Last year, the BYU iGEM team genetically engineered E. coli to detect heat or ROS. This year we developed E. coli capable of simultaneously sensing lactate, heat and ROS, implemented a novel Cre-Lox system, and constructed a library of thermosensors. Our project uses two circuits, each with a unique reporter. The first circuit contains a RNA thermosensor driven by a ROS-inducible promoter, allowing expression of Cre recombinase when both heat and ROS are present. Although heat is transient, Cre ensures continued expression of the first reporter gene. The second circuit contains a periplasmic lactate sensor coupled to a second reporter. Finally, we have evolved a library of thermosensors that work in a narrow physiological range. Together, this two-circuit system may allow accurate and specific detection of early colon cancer cells. Health and Medicine Temperature Flourescence In vivo N/A N/A N/A
Cambridge 2012 Parts for a Reliable and Filed-Ready Biosensing Platform Yes Miscellaneous Implementation of biosensors in real world situations has been made difficult by the unpredictable and non-quantified outputs of existing solutions, as well as a lack of appropriate storage, distribution and utilization systems. This leaves a large gap between a simple, functional sensing mechanism and a fully realised product that can be used in the field. We aim to bridge this gap at all points by developing a standardised ratiometric luciferase output in a Bacillus chassis. This output can be linked up with prototyped instrumentation and software for obtaining reliable quantified results. Additionally, we have reduced the specialized requirements for the storage and distribution of our bacteria by using Bacillus' sporulation system. To improve the performance of our biosensing platform we have genetically modified Bacillus’ germination speed. Lastly, we demonstrated the robustness of our system by testing it with a new fluoride riboswitch, providing the opportunity to tackle real life problems. Foundational Advance Flouride
Magnesium
Flourescence In vivo Advance to Championship
Best experimental measurement approach, regional
Regional Finalist, Europe
N/A N/A
Carnegie-Mellon 2012 Real-time quantitative measurement of RNA and protein levels using fluorogen-activated biosensors Yes Miscellaneous We seek to develop a system that will allow researchers in the field of synthetic biology to accurately measure a variety of metrics in gene expression networks including translational efficiency and transcriptional strength.We hypothesize that we can use Spinach (a fluorogen-activating RNA sequence) and a FAP (fluorogen activating protein) as biosensors to measure these gene expression metrics in vivo (in living cells), rather than in vitro (in a test tube), which can be very costly and labor intensive.We aim to characterize the relationship between synthesis rates of Spinach and transcription rates and the relationship between synthesis rates of FAP and translation rates. Foundational Advance RNA Flourescence In vivo N/A N/A N/A
Chalmers-Gothenburg 2012 Biodetection of hCG hormone - Development of a biodegradable pregnancy test kit Yes Health and Medicine The goal of this project was to construct a biosensor for the hCG hormone consisting of S. cerevisiae. The human luteinizing hormone receptor (LH/CG), a GPCR with high affinity for hCG, was therefore expressed in yeast. The yeast strain used contains a yeast/human chimeric Gα-subunit, enabling coupling of the LH/CG-receptor with the pheromone pathway in yeast. Binding of hCG should consequently result in activation of the pathway. The genes tnaA and fmo, encoding tryptophanase and flavin-containing monooxygenase respectively, were introduced into the yeast strain. These enzymes catalyze the conversion of tryptophan to indigo. tnaA was set under the control of the pheromone induced FIG1 promoter and fmo was expressed constitutively. Hence, detection of hCG should result in the production of bio-indigo, the output signal of the biosensor. In order to ensure hCG to pass the cell wall, the gene CWP2, encoding a cell wall mannoprotein, was deleted. N/A hCG (Human chorionic gonadotropin hormone) Bio-Indigo Production In vivo Bronze Medalist N/A N/A
Cornell 2012 SAFE BET Yes Environment Canadian oil sands are a vast oil reserve that, given rising prices of petroleum, are an attractive alternative to traditional sources of crude oil. However, there are numerous public health and environmental concerns regarding the oil sands extraction process. One environmental concern is the contamination of Canadian watersheds by seepage from tailings ponds. To better monitor this issue, we have engineered a novel biosensing platform with the electroactive bacterial species Shewanella oneidensis MR-1, which has the unique capability to directly transfer electrons to solid-state electrodes. We exploit this feature by genetically manipulating S. oneidensis MR-1 to upregulate its metal-reduction capacity in the presence of analyte to generate direct current output in a whole-cell biosensor. Our goal is to develop a fully autonomous electrochemical biosensor that complements the current oil sands monitoring system by providing real-time data over extended periods of time. Furthermore, our device will circumvent the costs and complications of producing and maintaining photodiode circuits used for data acquisition in bioluminescent reporter systems by instead producing a direct electrical output. While our platform is adaptable to sensing a wide range of analytes, we will initially focus on arsenic-containing compounds and naphthalene,a polycyclic aromatic hydrocarbon (PAH) – known contaminants of oil sands tailings ponds. We believe that our biosensor will be a valuable tool for remote,continuous, and long-term monitoring of pollutants in rivers and key watersheds. Environment Poly aromatic hydrocarbons (PAH) Electrochemical In vivo N/A N/A N/A
Dundee 2012 Six, Lyse and Obliterate: a synthetic silver bullet against healthcare acquired infection. Yes Health and Medicine Hospital acquired infections are a global problem. One example is Clostridium difficile, a bacterial pathogen that infects patients undergoing prolonged antibiotic treatment and results in pseudomembranous colitis, a potentially fatal gut infection. This project aimed to design a synthetic bacterium that would respond to C. difficile infection and kill the pathogen in situ. Escherichia coli was engineered to secrete an endolysin from a bacteriophage that would specifically attack the C. difficile cell wall. The endolysin was fused to the extracellular components of an engineered Type VI Secretion System from Salmonella, which itself comprised 13 different proteins. In addition, a synthetic ‘inflammation biosensor’ was developed, based on a two-component system from Salmonella, with the aim of restricting endolysin secretion to the diseased colon only. Mathematical modelling was used to assist in the development of the laboratory work and to investigate potential therapeutic strategies beyond the scope of the experimental programme. Health and Medicine Tetrathionate- TtrRS signal pathway Flourescence In vivo Gold Medalist N/A N/A
Edinburgh 2012 Tools that make synthetic biology easier and safer - questioning legacy and friendliness Yes Miscellaneous Edinburgh’s 2012 iGEM project focuses on developing tools that expand the range of synthetic biology applications. We are characterizing Citrobacter freundii as a chassis in order to investigate the potential of a new host organism as an alternative to Escherichia coli in synthetic biology. The team is also looking at novel selectable and counter-selectable markers as a substitute for antibiotic based systems which facilitate the spread of antibiotic resistance in the environment. We seek to implement the MtrCAB electron transfer system from Shewanella oneidensis into E. coli, and test the resulting electron output from the organisms using microbial fuel cells. We are constructing computer models of the electron transfer chain and of cell survival with non-antibiotic markers. This tools-based project responds directly to legislation and safety. We considered how iGEM gives us the freedom to pursue blue-sky research and whether our work is driven by preconceptions of public opinion. Foundational Advance arsenic
IPTG
Electrical Resistivity
Electron export
In vivo Advance to Championship
Gold Medalist
N/A N/A
EFP-Laussane 2012 SWITCH: Direct, Light-induced Gene Expression for Optimal Drug Production in Mammalian Cells Yes Manufacturing The fusion protein our team aims to characterize is a version of the LovTAP construct (submitted as a BioBrick by the 2009 EPFL iGEM team) adapted to mammalian gene regulation. It allows for tight regulation of conditional gene expression (started upon illumination with a blue light) through a photo-sensitive domain coupled to DNA-binding and activating domains. We are also developing and building a custom bioreactor setup to create the appropriate conditions for the LovTAP switch to work, and modeling the behavior of our system. Development of optogenetics has mainly been focused on bacteria but we are also comparing our project to another mammalian system, developed by Fussenegger et al. (Science Vol. 23, 2011), that uses a melanopsin switch to trigger endogenous calcium-driven promoters. Light-induced gene expression eliminates the need for activating molecules in sensitive applications such as the production of therapeutic proteins in the pharmaceutical industry. Manufacturing light Flourescence In vivo Gold Medalist N/A N/A
ETH Zurich 2012 E.colipse – Who’s your pABA: intelligent sun protection Yes Health and Medicine E.colipse is an intelligent and adaptive sun radiation protection system which responds to UV exposure with the production of the protective agent pABA. To detect hazardous levels of sun radiation our system is based on UVR-8, a UV sensing protein from plants. In its dark state, this protein forms a homodimer that dissociates upon UV radiation. We fused UVR-8 with the DNA binding domain from TetR, which is unable to dimerize and to bind DNA in monomeric form. UV-exposure might force the TetR-UVR8 fusion dimer to split, release the DNA and enable transcription. Thus, TetR-UVR8 might act as a light-activated on-switch in bacteria. We plan to use this novel switch to start the production of para-aminobenzoic acid (pABA), a common ingredient of sunscreen, and - dependent on the intensity and duration of exposure as determined by our detailed in silico model - a colored pigment as a visible warning signal. Health and Medicine UV irradiation Colour In vivo Advance to Championship
Gold Medalist
N/A N/A
Evry 2012 A synthetic hormonal system for the vertebrate chassis Xenopus tropicalis Yes Miscellaneous Building on a long-standing French fascination for frogs, we wanted to spread this enthusiasm to the world of synthetic biology by introducing a new, vertebrate chassis to the community: Xenopus tropicalis. This leap towards multicellular biological engineering required new tools, so we first developed a new set of frog compatible vectors, biobricked tissue specific promoters and a new technique to assemble them in a single shot. To benefit from tissue compartmentalisation, we created a synthetic, orthogonal hormonal system using the plant molecule auxin. We also investigated E. coli/Xenopus interfacing, effectively creating a synthetic ecosystem. We modelled our system at the organism scale, using a multi-level and multi-technique approach. Finally, working with whole animals during iGEM brought a load of difficult ethical questions regarding animal biotechnologies and experimentation. This led us to wonder: Are we a chassis? Foundational Advance Pancreas-specific Tissue Flourescence In vivo Advance to Championship
Gold Medalist
Best Human Practices Advance
Best Model
N/A
Fatih Medical 2012 Cancel the Cancer Yes Health and Medicine Our project is mainly based on the early diagnosis of cancer. EpCAM (Epithelial cell adhesion molecule) is a pan-epithelial differentiation antigen overexpressed on the basolateral surface of most carcinomas and Circulating Tumor Cells(CTC); the cells which are released into blood in early phases of cancer. Our objective is to fix appropriate antibodies for EpCAM antigens to the E.coli cell wall so that we will be able to detect CTCs before the cancer precipitates its way to metastasis. For the next step, we plan to enhance the detection signal in our bacteria by the means of quorum sensing mechanism. Finally, to prevent the production of possible undesirable and detrimental genetically modified organisms (GMOs), we aim to induce self-destruction device in our E.coli via emission of light. Health and Medicine Ethanol Flourescence In vivo Bronze Medalist N/A N/A
Gaston Day School 2012 Detection of Heavy Metal Contaminants in Water Yes Environment Despite improvements in water quality, contaminants still interfere with farming in many of the world’s biomes. For 2012 the Gaston Day School iGEM team’s project is to help solve this problem by using the existing registry of parts to create new heavy metal detectors. We have shifted our project from last year’s nitrate detector in order to focus on cadmium, arsenic, and lead contaminants in water. These metals are known to be used in insecticides, fungicides, and fertilizers and are also byproducts of industrial processes such as smelting. If ingested they can cause numerous health problems (more information can be found at the bottom of the page). To detect each metal, we constructed sensors by using multiple promoters to narrow the range of the heavy metals down to one or two contaminants. Then we combined it with GFP reporters to create the new part. GFP was used because our spectrophotometer can accurately measure it. Once the parts were created, they were tested for accuracy and sensitivity. Many farmers need a way to measure the amount of heavy metals in water to determine whether the levels are dangerous; therefore, each heavy metal detector must be as sensitive as their respective federal limits in water. As the project continues, we plan to test the safety of the engineered bacteria and create survivorship curves as they are released into different environments, similar to last year’s testing. When the final kit is constructed we plan to include the heavy metal detectors and all components necessary to run, accurately measure, and safely dispose of the tests. This kit will help agricultural and environmental fields make improvements in safety. Environment Heavy metals Flourescence In vivo N/A N/A N/A
Georgia Tech 2012 An intragenic complementation approach to engineer a faster fluorescence biosensor Yes Miscellaneous Our goal is to engineer a novel biosensor with a faster readout than is currently available. Many bacteria produce, secrete, and respond to chemicals called autoinducers to monitor population density and to synchronize gene expression, a process called quorum sensing. In quorum sensing based biosensors, detection of autoinducer activates transcription of a reporter gene, which must then be translated and accumulate to detectable levels, which can take two to four hours. In our system, we will use TraR, a protein used in the quorum sensing response of Agrobacterium tumefaciens, which dimerizes only in the presence of its autoinducer. We have successfully fused traR to sequence for two separate complementary fragments of GFP. Upon addition of autoinducer, we predict that already accumulated TraR-GFP fragment monomers will dimerize, allowing the GFP fragments to interact and fluoresce. This new approach may drastically reduce the time necessary for future biosensors to produce detectable output. Information Processing protein Flourescence In vivo N/A N/A N/A
Grenobie 2012 sEnsiColi: A tunable and reliable ultra-sensitive detector Yes Health and Medicine Multi-resistant bacteria are a worldwide issue which in a very near future will have huge impacts on our societies and ways diagnosis and prevention will be performed. In this optic, the Grenoble iGEM team has built an ultra-sensitive pathogen detector. It consists of three interconnected modules: 1- Detection, 2- Amplification/ Communication and 3- Output. The detection module consists of a recombinant membrane receptor that, once activated, actuates an amplification loop. The amplification system contains a genetic feed forward loop, which filters out false positive outputs. Once amplified and filtered, the signal is transmitted to neighboring bacteria via a diffusible molecule. In turn, the amplification loop is triggered which leads to the production of a measurable fluorescence output. The design of our network is easily adaptable to different input signals by using other receptor domains. Information Processing Pathogen Flourescence In vivo Gold Medalist Safety Commendation, Europe N/A
Groningen 2012 The Food Warden. It’s rotten and you know it! Yes Food safety Every year, one third of global food production -1.3 billion tons of food- is thrown away, partially due to the “best before” dating system. iGEM Groningen 2012 seeks to provide an alternative method of assessing edibility: The Food Warden. It uses an engineered strain of Bacillus subtilis to detect and report volatiles in spoiling meat. The introduced genetic construct uses a promoter to trigger a pigment coding gene. This promoter, identified by microarray analysis, is significantly up-regulated in the presence of volatiles from spoiled meat. The activity of the promoter regulates the expression of the pigment reporter and will be visible to the naked eye. For safe usage of the system, spores of our engineered strain are placed into one half of a semi-permeable capsule, the second containing a calibrated amount of nutrients. Breaking the barrier between the two compartments allows germination and growth, thereby activating the spoiling meat sensor. Food and energy Magnesium
Rotten meat volatiles
Colour In vivo Advance to Championship
Gold Medalist
Regional Finalist, Europe
Top 16
Best Food or Energy Project
Best Poster
Best Presentation
Finalist
Grand Prize Winner
N/A
HIT-Harbin 2012 Staphylococcus aureus Monitor Yes Health and Medicine Staphylococcus aureus infections are major causes of morbidity and mortality in community and hospital settings. Since bacterial sensors are attracting more and more biologists' attention owing to its' specific, fast and accurate detecting, we plan to construct a E.coli biofilm consisting of two different engineered populations, which are designed to detect and eradicate S.aureus, respectively. The two engineered populations communicate with each other by AHL signal transduction. We hope that compartmentalization of functions can lessen metabolism load and cross-reactions interfere, and achieve the assembly of different functions in bacterial level. The whole system comprises sensing, killing and biofilm formation devices. Detecting device: to detect the existence of S.aureus through sensing the AIPs secreted only from S.aureus. Killing device: to eradicate S.aureus through the production and release of lysostaphin. Biofilm formation device: to enhance biofilm formation by over-expression of yddV, a di-guanylate cyclase, which catalyzes GTP into c-di-GMP. Health and Medicine Staphylococcus Aureus Not specified In vivo Silver Medalist N/A N/A
HKUST-Hong_Kong 2012 B. hercules ------The Terminator of Colon Cancer Yes Health and Medicine The dispersal of toxic anti-tumor chemicals in the circulatory system during conventional cancer treatment prompts us to consider the need of alternative cancer therapies. In an effort to combat with colorectal carcinoma, we aim to use genetically modified Bacillus subtilis to execute targeted drug delivery to cancer cells in the digestive tract, offering an advantage of generating minimal adverse effect on normal colon epithelial cells. Targeting is achieved by expressing RPMrel, a colon tumor specific binding peptide, on the cell wall using a LytC cell wall binding system. The anti-tumor cytokine, bone morphogenetic protein 2 (BMP-2), is synthesized and secreted out from the bacteria with the help of a signaling peptide fused to the protein. To control the timing and amount of BMP2 release, two regulatory systems, xylose-inducible system and ydcE/ydcD toxin-antitoxin system are introduced to minimize the harmful effect from BMP2 overdose. Health and Medicine Cancer
DNA
Anti-tumor excretions In vivo Advance to Championship
Gold Medalist
N/A N/A
Hong_Kong-CUHK 2012 Light of No Return Yes Miscellaneous Although the sensory technology has been deeply explored and implemented in various means, most of the developed sensors are chemically-dependent promoters which regulate downstream gene expression. We exploited the use of halobacterial sensors, the sensory rhodopsins which are sensitive to a wide spectrum of readily available light source and build a series of sensing systems to control cellular movement and gene regulation. This system can be executed as a fundamental part for further applications, such as cell targeting and refining. Furthermore, to counter the safety issues caused by the leakage of bioengineered cells, this sensing method altogether with the CRISPR/Cas sytem can targart and achieve the cleavage of the transformed plasmid under the stimulation of natural light sources. Foundational Advance light Motility In vivo Advance to Championship
Gold Medalist
N/A N/A
Ivy Tech Southbend 2012 The Arsenator: A Tuneable Biosensor for Arsenic Yes Environment Millions of people worldwide are exposed to toxic levels of arsenic in drinking water. Bacteria have an efflux operon regulated by an arsenic sensitive inducible promoter. It is possible through recombinant DNA technology to isolate this promoter and combine it to a reporter system and transform bacteria to create a biosensor for arsenic. Induction of the arsenic-sensitive promoter occurs by the binding of arsenite to an inhibitory protein, de-repressing transcription. We have observed the arsenic responsive promoter from E. coli to have a consistent, low level of background induction. We have tested the hypothesis that by increasing the quantity of the inhibitory protein in the cell, we can quantifiably raise the threshold of the response. Our intention is to create a tunable biosensor to form the basis of a low-tech device that can reliably detect dangerous levels of arsenic in water for use in the developing world. Environment Heavy metals Flourescence In vivo N/A N/A N/A
KAIT Japan 2012 E.coli which has ability to kill the cancer cell. Yes Health and Medicine We try to make E.coli which has ability to kill the cancer cell. Regulatory T cells move toward to cancer cells by which produced CCL22. Killer T cells and helper T cells are inactivated by reguratory T cells, so, the cancer cells elude from the immune system. We think to make use of this mecanism underhand. We will give E.coli three functions. First,we give E.coli the function to have the chemotaxis to cancer cells by recognision of CCL22 which is a chemokine produced from cancer cells. Second, we give E.coli the function that they combine with cancer cells. Cancer cells express the MICA on their cell membranes. NKG2D recepter from NK cells combine MICA. Third,We give E.coli function that they release the azurin to cancer cells. The azurin induced apoptosis in cancer cells by binding with p53. We would like to be help the treatment of cancer . Health and Medicine Chemotaxis to CCL22 Azurin In vivo Bronze Medalist N/A N/A
Korea_U_Seoul 2012 Rice Guardian Yes Food "Bacterial leaf blight disease (BLB) is one of the preeminent vascular diseases inirrigated rice. Bacterial leaf blight in rice is caused by infection of bacteria known as X. oryzae pv. oryzae. Based on previous researches, it was proven that bacterial rax gene complex (rax A, B, C, P, Q, R, H) and their protein products(Ax21) are responsible for BLB. Since Ax 21 is a major pathogen that causes BLB and ever present molecule that signifies presence of X. oryzae pv. oryzae, we decided to make synthetic bacteria that detect Ax21 and furthermore, kill them. We will use rax R and H gene promoters to detect Ax21. As a result of transcription activation, gene will synthesize bacteriocin to kill X. oryzae species." Food and energy Pathogen Bacteriocin In vivo Silver Medalist N/A N/A
Macquarie_Australia 2012 Flick of the Switch: Employing Light-Sensitive Bacteriophytochromes to Control Gene Expression Yes Miscellaneous Phytochromes, or photoreceptors with the ability to control the expression of genes, exist in bacteria as bacteriophytochromes. This project creates a light-dependent biological switch using the bacteriophytochromes from Deinococcus radiodurans and Agrobacterium tumefaciens. When coupled with heme oxygenase, these bacteriophytochromes are supplied with biliverdin, a pigment which allows for the self-assembly of a switch within the host system. In the presence of red light, the conformation of the bacteriophytochrome is modified. This reaction produces a visible colour change in the presence of red light, and can be used to control expression of a targeted gene when coupled with the appropriate response regulator. Exposure to far-red light will cause the bacteriophytochrome to revert to its original conformation, thus repressing the gene and reversing the colour change. New Application light Colour In vivo Advance to Championship
Silver Medalist
N/A N/A
NRP_UEA_Norwich 2012 A future using quantitative computing and its applications using a dual promoter. Yes Environment Imagine a world in which all sectors of industry use synthetic biology to meet specific needs. The NRP-UEA team have developed novel biobricks, which provide a foundation for a system with this level of complexity. The project began with a simple idea with widespread applications: the detection of exogenous nitric oxide (NO). However it soon became clear the detection of highly reactive NO was challenging, and this was addressed in two main ways. A bacterial promoter, PyeaR, was fused to its mammalian counterpart, CArG. The functionality of this flexible dual promoter was determined in both mammalian and bacterial chassis. Yet it was determined that further specificity was still needed, leading to the comparator circuit, that subtracts the expression of one promoter from that of another, allowing for signal integration and quantitative computing. This system thus allows for the detection of any chemical, providing the promoters have overlapping specificity. New Application nitric oxide (NO) Flourescence In vivo Gold Medalist N/A N/A
NTU_Taida 2012 epdEx: Smart Peptide-based Therapies Yes Health and Medicine We seek to bridge the fields of synthetic biology and pharmacology to provide a revolutionary way of drug delivery called PEPDEX, the ultimate delivery system of peptides. Peptides bind to specific receptors and regulate many physiological processes. For instance, peptide-based hormones such as insulin, growth hormone, and ACTH coordinate many physiological functions, including energy metabolism and stress responses. Peptides have long been widely used in pharmacology to treat certain diseases. With a better understanding of diseases, peptide-based drugs can now be applied in many disease modalities (except for hormonal supply), such as neurology, and immunology. Structurally, peptide-based drugs have many benefits. First, they can be processed and modified to bind seamlessly to specific receptors with complex 3D structures, which may not be accessible to small molecule drugs. Second, when applied in immunology, synthetic peptides can be used to mimic epitopes presented to antigen-presenting cells. Modified synthetic peptides show great efficacy in the induction of cognate CD4 T-cells, which is required for therapeutic activity against infectious diseases, and, in particular, cancer. In our project this year, we demonstrate the PEPDEX system as a mind-altering bacterium which can deliver neuropeptide GLP-1 directly into circulation and act on the central nervous systems, modulating the eating behavior and protecting the cognitive function of brians as well. Based on the connection and interaction between complex adaptive biosystems, we extend the essence of brain-gut-microbiota axis and tailor a living, communicable bacterium that mooderate and dance with human health. Health and Medicine fatty acids
Flouride
gene expression In vivo Advance to Championship
Gold Medalist
N/A N/A
Osaka 2012 Bio-Dosimeter Yes Environment It is still sharp in our memory that, on March 11, 2011, the Great East Japan Earthquake struck off the coast of Eastern Japan and triggered a series of equipment failures, nuclear meltdowns, and releases of radioactive materials at the Fukushima 1 Nuclear Power Plant, leading to the nationwide nuclear crisis. While ‘Grays’, ‘Sieverts’, ‘exposure’, ‘equivalent dosage’ and other related terms and units became referred daily in the media, much of the general populace remained ignorant of their meanings and significance. The need for low-cost, portable and easy-to-use dosimeters was apparent as measurements of radiation exposure could only be conducted at dedicated installations spaced far apart and the numbers reported only infrequently.Moved by that accident in iGEM 2011, we have built a synthetic biological dosimeter to detect the radiation. In this year we further develop that "Bio-dosimeter". Our "Bio-dosimeter" consists of two points: damage tolerance and radiation detection. To introduce the tolerance to E. coli, we are trying to put in some radiation resistance genes from Deinococcus radiodurans. For the detection of the radiation, we are trying to connect the native DNA damage response system of E. coli to production of pigment lycopene as a reporter.Last year, we cloned selected genes from radiodurans genomic DNA and BioBricked them. We then conferred additional UV-induced DNA damage tolerance by transforming certain genes into E.coli. Now, we are attempting to assess its tolerance to various types of DNA damage and to evaluate DNA damage detection more clearly. Environment radiation Colour In vivo Bronze Medalist N/A N/A
OUC_China 2012 Oceanfloat and Oceanfeel Yes Environment Sensor:Our phosphate- and nitrate-sensitive devices are responsible for detection of environmental phosphate and nitrate. Besides that they transform the input signals into "readable information" for decision-making devices. much work has been done for characterization and modification of nitrate- and phosphate-sensitive promoters. A whole set of design ideas for TCS modifications are also presented for other igemers. Additionally an actuator that can remove the phosphate is recommended. Decision-making Device: Our decision-making device aims at processing the concentration change of nitrate or phosphate into visible buoyancy increase. Comparator recognizes the difference of two inputs quantitatively ,while ratio sensor could senses a particular ratio between two inputs.Both comparator and ratio sensor facilitate a ternary system consisted of two small RNA and GFP mRNA. The concentration change of external two inducers leads to the transcription rate change of small RNA(alpha s)in this ternary system, the interactions between three RNAs will lead to interesting behaviors of our system like sensing the difference between two inputs quantitatively(Comparator) or the ratio of two inputs(Ratio senor). Floating Device: In our project, by transforming the buoyancy device BBa_K737010(designed by ourselves), the gas vesicle cluster from the genome of Planktothrix rubescens into E.Coli, we succeed in making Escherichia.Coli floating on the surface of the water. It can help the cells produce the gas vesicle inside, which could make densities significant stratification in the culture. Not only the gene cluster but the two parts BBa_K737006 and BBa_K737007, which produce the gas vesicle structure protein, can also make the Escherichia.Coli floating. We use the shorter length of the part achieve a better effect than BBa_K190033 and the gas vesicle application prospect. Environment Phosphate gene expression In vivo Advance to Championship
Best Model, Asia
Gold Medalist
Best Model N/A
Panama-INDICASAT 2012 Genetically Modified E. coli as an Alternative Biosensor of Cyanide and Cyanide Compounds Yes Environment Cyanide is considered an extremely harmful toxic for the environment and living organism’s compound, since it inhibits the cellular respiration at the level of electron transport chain. In the industrial sector, cyanide is used to produce paper, paints, textiles, plastics and in the mining industry as a way to recover metals. In this project, we will incorporate genes that will allow the bacteria to become a biosensor with the capacity to detect the presence of cyanide and cyanide compounds by adding the expression of cyanide resistant genes (cioAB) and a reporter gene under the control of an inducible promoter. This new technique will also become a platform so that in the future we could incorporate a gene that allows the bacteria, not only detect, but also to degrade these compounds using a method that is accessible and environmentally friendly through bioremediation. Environment Cyanide Colour In vivo Bronze Medalist N/A N/A
Paris_Saclay 2012 GEMOTE: a new tool to control gene expression by temperature Yes Miscellaneous We designed a system that allows controlling the expression of a gene or an operon over a specific temperature interval (between 32 and 42 degrees Celsius). This system consists of an RNA thermometer controlling the translation of a thermosensitive transcriptional repressor, which itself controls the expression of the targeted gene or operon. In our current construction, the crtEBI operon directing lycopene biosynthesis is used as a reporter, allowing us to check our system's performance. However, the possible applications of this system are extremely numerous. For example, controlling the expression of a toxin would allow creating a “suicidal bacterium” that would bring on its own death outside the specified temperature range. This will help preventing its spread in the environment. And this is just one example... The only limit is our imagination ! New Application Temperature Colour In vivo N/A N/A N/A
Peking 2012 Programming Cells Through Light Yes Miscellaneous Light has created innumerable wonders in nature. Equipped with tools and methods in optogenetic research, scientists have also achieved some truly fascinating goals in a synthetic way. This year, 2012 Peking-ECUST iGEM utilized an ultra-sensitive engineered sensor of luminescence -- the Luminesensor. Amazingly, the Luminesensor was proven to be so sensitive as to be able to detect natural light and even bioluminescence. With this sensor, spatiotemporal control of cellular behavior, such as high-resolution 2D and 3D bio-printing using dim light and even the luminescence of iPad were shown to be very easy. What’s more, we successfully implemented cell-cell signaling using light for the very first time in synthetic biology, which will be of great importance for biotechnological use. Foundational Advance light gene expression In vivo Advance to Championship
Gold Medalist
Best presentation-Asia
Best Presentation, Finale
Best Wiki, Asia
N/A
Rose-Human institute of technology 2012 Checkmate Yes Miscellaneous Easily manipulated genetics make the yeast Saccharomyces cerevisiae a versatile and widely used model eukaryote. To progress, researchers must often determine the mating type of haploid strains, which typically takes days. The goal of our project is to reduce that time to hours. So we designed a novel promoter harboring Ste12 and LexA binding sequences and placed it upstream of an ORF encoding a red fluorescent reporter fused to LexA binding and VP64 activator domains. Others have shown that this fusion protein induces its own expression from a LexA promoter. We propose that Ste12, activated in the pheromone response pathway, will bind the hybrid promoter and induce expression of the fusion protein, which will amplify and maintain its own expression. Therefore, when mating pheromone receptors on a haploid harboring this latch-type circuit are bound and activated, the cell will fluoresce and function as a rapid mating type detector. New Application protein Flourescence In vivo N/A N/A N/A
SEU-A 2012 Don’t hide from me, bacteria Yes Health and Medicine As we all know, since the discovery of penicillin, people gradually rely on various antibiotics to kill bacteria. However, the adaptation ability of bacteria that of responding to these medicines is out of our imagination , the speed of production of resistance to drugs is faster than creating a new effective drug as well. We come across a big dilemma in drug resistance when fight with the bacteria. Consequently, a new and effective method of killing bacteria is in urgent need.Based on this consideration, we come up with two innovative ways which have great advantage over the traditional one.The idea is from the bacteria's own selection system and we try to take advantage of it. We intend to construct a system through which bacteria will transfer the death gene by themselves. The question is bacteria won’t keep the gene that play negative role to their survival and will drop the system someday. In order to maintain or even widely spread the suicide system we endow it with the sweet gene that will has positive affection to the multiplication of bacteria. Regularly, the sweet gene expresses to make bacteria glad to accept it, promoting the spread of plasmid from one bacteria to another through conjugative transfer (a process bacteria inherently own) in some degree. Once its account reaches a certain threshold, the dead gene switch will turn on, resulting in the death of the host bacteria. So, function of the whole device can be abstractly described as the toxic apple in fairy tale. Health and Medicine Salt concentration
Temperature
Flourescence
Motility
In vivo Silver Medalist N/A N/A
SEU_O_China 2012 Breaking the symmetry Yes Miscellaneous Our team, SEU_Omega aims to execute a synthetic biology project based on colony of bacteria. An initial idea concerns the control of the pattern of colony, which would be in the shape of a pentagram. Light sensing would be used as a switch to manipulate the differentiation of cells and the quorum sensing system of AHL would govern the holistic pattern with antisense RNA effecting the division rate. Further cellular differentiation would automatically lead aggregating cells with separated division rates and similar phenotype into specific patterns. Available applications may include bacterial quantitive biosensor,logical gates, and so on. Information Processing light
Quorum sensing
gene expression In vivo Gold Medalist N/A N/A
Shenzhen 2012 Project: Yeast Artificial Organelle Yes Miscellaneous This year, our team focuses on one of the major problems we faced in synthetic biology. When a synthetic pathway is introduced into the cell, it may somehow disturb the original system. On the other hand, the original system may prevent the synthetic pathway from working as expected. People are trying many different ways to solve this problem. One of them is to learn from eukaryotic organelles, using membrane structures to separate synthetic pathways to reduce interferences. However we think that a simple membrane is not enough for a cell factory. Foundational Advance NAD/NADH Flourescence In vivo Gold Medalist N/A N/A
Tec-Monterrey 2012 Development of a freeze resistant E.coli strain and an allergy detection kit produced by P.pastoris. Yes Health and Medicine The development of synthetic biology has eased the production of innovative materials, two scenarios have come to our attention: the medical/clinical field and the improvement of laboratory protocols. Our team, Tec-Monterrey, decided to develop two projects including a freeze resistant cloning Escherichia coli strain and the harnessing of bioproducts from Pichia pastoris followed by their assembly into a novel standardized allergy detection kit. The aim of our first project is to develop a new strain of E.coli capable of expressing an antifreeze protein from the Rhagium inquisitor (RiAFP), resulting in a cloning strain capable of sustaining its viability over the cryopreservation cycle. The goal of our second project is to develop an affordable, standardized allergy detection kit, integrating components that are both easily manufactured and purified. Moreover, the kit’s components can be produced either in P. pastoris or E. coli thanks to the design of our engineered shuttle-expression sequence. New Application Bee venom
Dust mites
Maize
Flourescence In vitro Silver Medalist N/A N/A
TMU-Tokyo 2012 Chef Ant E.coli Yes Food safety Formaldehyde is a common harmful chemical, and it has a bad effect in relatively low concentration. (For example, in agricultural chemicals, in disinfectant at hospitals and in paint of building materials) Also, since formaldehyde is mass-produced in factories, it is highly possible to exceed over the permissible amount in the environment. This year, in Japan, the detection of formaldehyde in Tone river became an issue. (1) We planned to create E.coli with an ability to detect and detoxify formaldehyde named Chef Ant E.coli. About detection, we try to visualize formaldehyde by ligating regulated promoter, frmR and GFP. Moreover we plan to overexpress two enzymes in Chef Ant E.coli. First, formaldehyde dehydrogenase decomposes formaldehyde to formic acid. The gene of formaldehyde dehydrogenase is from Pseudomonas Putida. Second, formic acid dehydrogenase converts formic acid to CO2 and H2O. The gene of formic acid dehydrogenase is from Methylbacterium extorquens. Environment Formaldehyde Flourescence
gene expression
In vivo Bronze Medalist N/A N/A
Tokyo-NoKoGen 2012 Coli express for long distance communication Yes Environment We created an E. coli for long distance communication. This “Communicheria coli” was inspired by the Pony Express, a rapid mail delivery service in the American Wild West, where mail was relayed by horseback riders. Communicheria coli sends a message, in the form of light, to distant cells, which then relay the message to other distant cells. Communicheria coli has light sensors constructed using the light receptor domain of bacterial sensory rhodopsin or the cyanobacterial green light sensor CcaS. In response to light signals, cells will induce their own lux operon to send the message to other distant cells, for example in a separate flask, which will in turn relay the message to other distant cells. To improve the effectiveness of our new signal delivery system, we set out to enhance the light intensity, change the light color, and shorten the response time. New Application light quorum sensing In vivo Silver Medalist N/A N/A
Tokyo_Tech 2012 "Romeo and Juliet" by E.coli cell-cell communication Yes Miscellaneous A love story contains several processes. Two people fall in love and their love burning wildly. However, no forever exists in the world, in most occasions, love will eventually burn to only a pile of ashes of the last remaining wind drift away. In our project, we have recreated the story of "Romeo & Juliet" by Shakespeare vividly by two kinds of Escherichia coli. We aim to generate a circuit involving regulatory mechanism of positive feedback rather than commonly-used negative feedback to control the fate of E.coli by signaling between two types of E.coli. Besides, Rose represents love. We will challenge to be the first iGEM group ever to synthesize PHA (a kind of bio-plastics) from glucose using the whole PHA gene sequence to represent rose. Information Processing Quorum sensing gene expression In vivo Gold Medalist Best Food or Energy Project
Best Information Processing Project-Asia
N/A
Tsinghua 2012 Domino Ecoli Community Yes Environment The domino effect, a chain reaction that occurs when a small change causes similar changes nearby and leading to a set of changes in linear sequence, can be viewed as a form of information processing and signal amplification. In prokaryotes, information transmission through slow diffusion of chemical compounds is limited either in width or rate. In our project, we constructed a bio-film like Domino E.coli community, aimed at achieving an expansive and rapid biological signal processing system. Domino E.coli community, as its name suggests, is capable of amplifying a weak starting signal via geometrical progression, taking advantage of quorum sensing effect. Meanwhile, our system undergoes multi-signal integration, logical computation and transformation of chemical inputs to visual outputs, suggesting the approach of constructing multi-cellular biocomputing. Information Processing Quorum sensing Flourescence In vivo Silver Medalist N/A N/A
Tsinghua-D 2012 Designable Thermoswitch Yes Miscellaneous By creating the term ‘Designable thermoswitch”, we are trying to deliver an idea that metabolic controllers responded to given temperatures can be designed. Besides explanation and prediction, the ultimate goal of science is creation. Here, we create several regulatory RNAs as thermal metabolic controller. Pre-set a ‘switch-on’ temperature and a ‘switch-off’ temperature, in silico simulation will give the sequence of the regulatory RNA that meet the requirement. A step further, we apply our ‘Designable Thermoswitches’ to the field of fermentation industry. For a long time, engineers are trying to find a more economic and more automatic way to extract fermentation product inside the engineered microorganism. We align our ‘Designable Thermoswitches’ and gene of lysozyme together and put them into E.Coli to solve this problem. The reconstructed E.Coli will switch on the procedure of self-lysate at the given temperature. Thus, the fermentation product inside the engineered microorganism can be released. Foundational Advance Temperature cell death In vivo Silver Medalist N/A N/A
TU-Delft 2012 Snifferomyces Yes Miscellaneous The aim of this year’s iGEM project will be the synthesis of an olfactory device for the purpose of characterization of volatile compound. Here, the aim is to introduce olfactory receptor gene fusions into Saccharomyces cerevisiae and linking these receptors to a transcription response. Aims: The diagnostics of the presence of tuberculosis bacteria in the lungs by sensing chemical compound methyl nicotinate by S. cerevisiae. For diagnostics, the response to these molecules is light, generated by the Lux proteins (visible blue light) or GFP (fluorescent green). Introducing receptors for sensing the presence of banana-smell (iso-amyl acetate). This is done to see whether communication between S. cerevisiae and E. coli is possible by this volatile intermediate. Supplying a toolkit which allows scientists to introduce olfactory receptors in yeast with minimal effort. Further we want to characterize the receptor parts submitted by the 2009 Hongkong university. Information Processing PHB
Volatile
Flourescence In vivo Advance to Championship
Gold Medalist
N/A N/A
Tuebingen 2012 Yeast based measurement system for endocrine disruptors in aquatic environments Yes Environment Lacking a genetically strict sex determination system, fish are very sensitive to hormonally active agents in water. The extensive use of fertilizers and the inability of sewage treatment plants to break down drug waste lead to increasingly high concentrations of so-called endocrine disruptors in rivers. As a result, male fish have been found to be less fertile and even develop female sex tissue, so called ovotesties. Since fish spawn is constantly exposed to river waters, fish development is easily disturbed, and while the ratio of female fish increases, population numbers decrease. For sensing we use a membrane-bound receptor of Danio rerio. Activation will lead to bioluminescence which can be read out by photometric measurement. Environment Endocrine disruptor Luminous energy In vivo Bronze Medalist N/A N/A
TU-Eindhoven 2012 SOMY – LCD, the Super Optimized Modified Yeast – Light-emitting Cell Display Yes Manufacturing Eindhoven, the city famous for its light bulbs, is the place where the roots of Dutch television lie. The iGEM team of the Eindhoven University of Technology developed an innovative electro-biological equipment which will be the replacement of your old television screen in the future! They proudly present to you the SOMY – LCD, the Super Optimized Modified Yeast – Light-emitting Cell Display. It’s a multicolor display, in which genetically engineered yeast cells are electrically stimulated to induce a fluorescent light response and consequently function as pixels. Since calcium takes the leading part in this process, the yeast cells are engineered with fluorescent calcium sensors and extra voltage-gated calcium channels. New Application Electricity Colour In vivo Silver Medalist N/A N/A
University of Calgary 2012 Detect and Destroy: Building FRED and OSCAR Yes Environment Tailings ponds are large bodies of water containing toxic compounds that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms to detect and destroy (bioremediate) the toxins, turning them into useable hydrocarbons. Environment Napthenic acids Change in voltage In vivo Advance to Championship
Regional Finalist, Americas West
Top 16
Best Human Practices Advance, Americas West
Best Human Practices Advance, Finals
Best Model, Americas West
Best Poster, Americas West
Best Wiki, Americas West
Safety Commendation, Americas West
oilsands
Athabasca
napthenic acids
electrochemistry
oil sands
prototype
University of Southern California 2012 E. musici Yes Environment Our project aims to create a new system to quantify how environmental conditions effect the bacterium E. coli by engineering a system that produces a predictable response in a controlled environment. Many strains of E. coli possess flagella, a whip-like appendage that can be found protruding from both eukaryotic and prokaryotic single-celled organisms. The assembly and motor control of E. coli flagella is under the control of a key group of genetic factors primarily for flagella assembly and chemotactic control. Expression of these genes can be regulated by creating various combinations of genetic promoters, which modulate the activity of individual components of the flagella apparatus. By promoting the E. coli flagella genes under varying conditions, such as salt concentration, nitrate concentration, pH and temperature, we can identify a significant change in flagella rotation and frequency. Ultimately, this frequency can be translated into an audible range which can act as an indicator of the bacteria’s distress based on the varied environmental condition (see below). Thus, by specifying the bacteria’s response to an environmental change on a genetic level, the resulting frequency can be used as a convenient assay to determine the real time status of the culture. New Application Nitrate concentration
pH
Salt concentration
Temperature
Sound In vivo N/A N/A N/A
USTC-China 2012 Anti-phage E.coli Yes Miscellaneous Bacteriophage is one of the most severe threats the fermentation factories have to face. To help solve the problem, we design a gene circuit which can both detect and defend against the phages. We use the modified promoter pRM to sense the phage’s infection and initiate the defence. The lysis gene which can make bacteria lyse is installed in our circuit. When it works, the phage won’t be able to take advantage of its host to replicate any longer. To win more time for lysis to function well, we design antisense RNA to prevent the phage from turning into lytic life cycle. Thus, when the lysis protein kills the host, the phage is still at lysogenic life cycle or the newly assembled phages are still immature. By using the quorum sensing system, the bacteria around the host will prepare to defend in advance. Attribute to these parts, our bacteria survive. Food and energy phage infection cell death In vivo Gold Medalist N/A N/A
Valencia 2012 Project Synechosunshine: photosynthetically powered biolamp Yes Food We present an artificial consortium between 2 specialized bacteria by the means of genetic engineering, in order to obtain a photosynthetically fed biolamp. It is a novel proposal of synthetic ecology, based on the use of an efficient photosynthesizer (the cyanobacterium Synechococcus elongatus) modified to become an exporter of sucrose and diel switch of the activity of Aliivibrio fischeri, a marine bacterium widely known for its bioluminescent properties in response to quorum sensing signals. Our modified cyanobacteria feed the population of A. fischeri through a transporter protein and produce AHL to induce bioluminescence in response to the activity of a photosensitive operator, which would activate only at night. We also have tried to transform different microalgae with bioluminescence genes to test their effectiveness. We look forward to develop an efficient and autosufficient environmentally friendly biolamp, with potential application to cover the illumination needs of many infrastructure sectors. Food and energy light Luminous energy In vivo Bronze Medalist N/A N/A
Virginia 2012 Genetically engineered bacteriophage for diagnosis of whooping cough Yes Health and Medicine Whooping cough, the infectious respiratory disease caused by Bordetella pertussis, is diagnosed in tens of millions of people and results in almost 300,000 deaths globally each year. Low-income and unvaccinated individuals as well as infants are especially susceptible. Current diagnostic procedures are complicated, costly, and can take up to a week, by which time the disease may have progressed or spread. The enormous impact of this disease urgently motivates the development of a faster, cheaper, and more reliable diagnostic test. Our epidemiology models suggest that earlier diagnosis could drastically reduce the incidence and impact of the disease. We propose an engineered bacteriophage diagnostic system for rapid clinical detection of pertussis. We first engineered T7 bacteriophage to demonstrate this approach in E. coli. Our modular diagnostic approach can be applied to the high-sensitivity detection of other bacteria.  Health and Medicine protein Colour In vivo N/A N/A N/A
Westminster 2012 iSTEM (Intelligent Synthetic Tumor Eliminating Machine) Yes Health and Medicine We have created a genetically engineered machine to identify, isolate and eliminate Cancer Stem Cells (CSCs). According to the latest Cancer Stem Cell Theory, not all the cancer cells have the same ability to generate new tumors. Tumor growth is mostly driven by a small proportion of cells, the CSCs. In addition to having high proliferation rates, CSCs are more resistant to chemotherapy. This indicates that while regular cancer cells are killed, CSCs may remain unaffected and give rise to new tumors once the treatment stops. CSCs produce increased levels of a particular enzyme, Aldehyde Dehydrogenase. We have identified its 3 most frequent isoforms (ALDH1A1, ALDH1A3 and ALDH3A1)in aggressive types of cancer, and used their gene promoters to build our CSC-targeting constructs: the iSTEM -Intelligent Synthetic Tumor Eliminating Machine. Health and Medicine Aldehyde dehydrogenase Flourescence In vivo Bronze Medalist N/A N/A
WHU-China 2012 E. coslim: Synthetic Probiotics Help Defy Obesity Yes Health and Medicine Utilizing human microbiota to tackle diseases has long been the keen desire of scientists. This year, we WHU-China team engineered a probiotics “E. coslim” from Escherichia coli, hoping to provide a new approach for treating obesity. Specifically, three genetic devices were designed. The first two devices were assembled to sense and response to fatty acids and glucose. To achieve these goals, promoters repressed by FadR and CRP were devised and synthesized respectively. When functional genes are placed downstream of these promoters appropriately, the two devices are supposed to degrade fatty acids and convert glucose into cellulose rapidly, thus preventing excessive calorie intake as well as producing prebiotics. Meanwhile, the third device was designed to control the densities of “E. coslim” and forestall horizontal gene transfer in future applications. As a whole, by simulating, we are developing “E. coslim” to regulate the microbiome composition in intestine to reduce risks of obesity. Health and Medicine Glucose concentration gene expression In vivo Advance to Championship
Silver Medalist
N/A N/A
Wisconsin Madison 2012 The Translational Coupling Cassette: a tool for evaluating the translation of heterologous proteins Yes Miscellaneous A powerful method for the production of novel metabolites is the expression of heterologous enzymes in a bacterial host. A common challenge when using non-native genes in metabolic engineering is determining if they are being properly expressed. To address this issue, we have constructed a BioFusion-compatible system for testing the translation of a gene of interest. This system couples the translation of the target gene to a fluorescent reporter gene; fluorescence will only be detected when the target gene is entirely translated. This construct enables synthetic biologists to quickly determine if a gene is being expressed without the need for costly antibodies or analytical instruments (e.g. mass spectrometry). Currently, we are utilizing this cassette to optimize the expression of limonene synthase, an enzyme that catalyzes the production of limonene, a monoterpene with potential as a renewable jet fuel. Food and energy protein Flourescence In vivo N/A N/A N/A
XMU-China 2012 E.Lumoli: a shining synthetic device for digit or time-course display Yes Energy We haved constructed a fluorescent digital display device with synthetic logic gates, which is able to respond to signals by displaying and switching numbers. We put GFP equipped with degradation tags in downstream to illuminate our numbers and change them quickly as well. Considering our engineering background, we accordingly employ cell immobilization to build our device. Engineering bacteria have been embedded in intra-hallow calcium alginate microcapsules and in PDMDAAC-NaCS microcapsules, respectively. In addition, 3D CAD design is performed for a perfect device. Our genetic circuits vary in length and RBS strength, leading to different durations of time delay for GFP expression. This inspired us to extend our work last year. By altering the strength of RBS at five grades, another five circuits have been built. After the induction by arabinose, the duration of response time for GFP expression increases as the strength of RBS declines, bringing about a time-course display. New Application Arabinose Flourescence In vivo Advance to Championship
Gold Medalist
N/A N/A
Berkeley 2011 Detectr Yes Miscellaneous Biosensors have widespread applications ranging from diagnostics to environmental monitoring. Vibrio cholerae's ToxR system can be used as a component in biological sensing devices. ToxS causes ToxR homodimerization, activating transcription of the ctx promoter. By replacing the periplasmic domain of ToxR with existing or engineered ligand-dependent homodimers, we hope to link ToxR dimerization (and gene expression) to the presence of specific ligands. Initially, ToxR constructs proved toxic to E. coli. We built a stress-regulated transcription system that drives relatively high expression of toxic proteins. This allowed us to further engineer ToxR chimeras. We fused an estrogen-dependent dimer with ToxR hoping to create an estrogen biosensor. We observed a range of constitutive phenotypes and plan more experiments to engineer a dose-dependent transcriptional response to estrogen. By fusing existing or engineered ligand dependent homodimers to ToxR, this modular system can be used to build new biosensors. New Application estrogen Flourescence
GFP
In vivo Advance to Championship
Gold Medalist
Best Poster, Americas West stress
library
ToxR
ILK
Bielefeld Germany 2011 The bisphenol A Yes Environment The development of sensitive and selective biosensors is an important topic in synthetic biology. Biosensors can be used in a wide range of applications - from the detection of toxic compounds in the environment up to clinical diagnostics. Because cells have to sense their surroundings, there are a lot of natural systems that can be used as biosensors. Unfortunately, cellular biosensors often have interfering properties that preclude any practical application. Common problems are the limited use outside the laboratory due to the use of genetically engineered cells, the low durability because of the usage of living cells and the appearance of undesired signals induced by endogenous metabolic pathways. To solve these problems, the iGEM-Team Bielefeld 2011 aims at developing a cell-free bisphenol A (BPA) biosensor based on a coupled enzyme reaction fused to S-layer proteins for everyday use. Bisphenol A is a harmful substance which is used in the production of polycarbonate. To detect BPA, it is degraded by a fusion protein under formation of NAD+ which is detected by an NAD+-dependent enzymatic reaction with a molecular beacon. Both enzymes are fused to S-layer proteins which build up well-defined nanosurfaces and are attached to the surface of beads. By providing these nanobiotechnological building blocks the system is expandable to other applications. N/A Bisphenol A fluorophore In vitro Advance to Championship
Gold Medalist
N/A cytochrome P450
ferredoxin
cell-free bisphenol A sensor
ferredoxin-NADP+ oxidoreductase
(BPA) biosensor
BYU-Provo 2011 E.colinoscopy Yes Health and Medicine The International Genetically Engineered Machine competition (iGEM) is the world's premier synthetic biology competition. Last year 130+ teams from all continents participated. As BYU's first iGEM team, we propose constructing a molecular AND gate in E. coli. An AND gate requires two positive inputs to generate a positive output. To detect our chosen inputs we are investigating the OxyR promoter and a thermo-sensitive riboswitch. The OxyR protein activates transcription in the presence of hydrogen peroxide, a reactive oxygen species (ROS). The riboswitch allows translation only above a specific temperature. Both inputs activate a Cre/Lox system to remove a terminator sequence and allow transcription of a molecular signal. We intend to express this system in E. coli where, in the presence of both inputs, the cells will produce green fluorescent protein. A similar system, in theory, could be used for early detection of colorectal cancer. Information Processing Arabinose
heat >37 degrees
alcohol acetyltransferase I (banana smell)
Colour
Flourescence
LacZ
sfGFP
In vivo Advance to Championship
Gold Medalist
N/A OxyR
AND gate
colon cancer
Thermosensor
Colombia 2011 No Title No Environment Our objective is to generate a genetically-modified bacteria "detect and alert" system, particularly as a defense aid for coffee plantations against fungi. Bacteria are built such that they can detect chitin, an organic compound found in fungal cell walls, amplify this initial signal, and finally alert the plant by stimulating an early hypersensitive response against infection, while controlling their own population density. We strongly believe this biocontrol method may prove to become a powerful tool for farmers and crop workers everywhere. In addition, our constructed "detect and alert" biobricks could be useful to plentyful synthetic biology experiments and future iGEM teams. Using the bacteria Escherichia coli DH5α, the system will use two differently-modified bacteria in the system. The first bacteria will detect the presence of chitin and will produce chitinase and a signal molecule to engage the response of the second bacteria. The second bacteria will react to the molecule and start to produce a signal (salicylic acid) to activate the hipersensitive response of the plant and control the bacterial populationg growth, since high salicylic acid concetrations are toxic to them. Environment chitin Production of salicylic acid In vivo Advance to Championship
Bronze Medalist
N/A N/A
ETH Zurich 2011 SmoColi Yes Miscellaneous We create a bacterio-quantifier of smoke. SmoColi cells are engineered to sense toxic substances found in cigarette smoke (for example acetaldehyde or xylene). They are immobilized in a microfluidic channel, in which a concentration gradient of the toxic substance is established. The sensor is linked to a band-pass filter that leads to input-concentration-dependent GFP expression. Continuous increase of the input concentration and its detection, therefore, establishes a moving fluorescent band in the channel. Finally, if the input concentration exceeds a certain threshold, cells produce RFP and the device turns red. Due to its modularity, our SmoColi system can be used in fact as a quantifier for a range of substances, as long as the sensor is adapted. To show that our system can be activated by different signals, as a proof of principle, we modified the circuit so that it can be induced by arabinose. Information Processing acetaldehyde
Arabinose
xylene
Flourescence
GFP
RFP
In vivo Advance to Championship
Gold Medalist
Best Information Processing Project, Finale quorum sensing
XylR
AlcR
Fudan Shanghai 2011 E.Tree - Neon Lights - Dinner service Yes Environment E.trunk bacteria detect nitrates in the medium and release either LasI or RhlI directed signals. It includes two circuits: the first pathway is controlled by a nitrate sensitive promoter (pYeaR), so that if the medium contains nitrates, the entire pathway will be on, RhlI (produces AHL C4-homoserine lactone), tetR and GFP will be produced. TetR then binds with pTet in the second pathway and blocks it. If the medium contains no nitrates, the first pathway is repressed while the second one is unblocked, so LasI (produces 3OC12-homoserine lactone) and RFP will be synthesized. E.leaf bacteria change color according to the signal molecules released by E.trunk. LasR and RhlR are constitutive synthesized in E.leaf; they bind to the LasI and RhlI directed signals, respectively. New Application Nitrate Flourescence
GFP
RFP
YFP
In vivo Gold Medalist N/A 3OC12-homoserine lactone
LasI
IsrR
AHL C4-homoserine lactone
pYeaR
nitrates
RhlI
LuxR
Gaston Day School 2011 No Title Yes Environment Increasing levels of fertilizer required for mechanized farming can result in elevated nitrate levels in soil and groundwater. Due to contaminated food and water, humans are at risk for methemoglobinemia caused by enterohepatic metabolism of nitrates into ammonia. This process also oxidizes the iron in hemoglobin, rendering it unable to carry oxygen. Infants in particular are susceptible to methemoglobinemia, also known as 'blue baby syndrome', when formula is reconstituted using water contaminated with nitrates. By combining the red fluorescent protein coding region with a nitrate sensitive promoter, we are developing an inexpensive, simple, visual test for nitrate contaminated water. Use of this detector in agricultural areas could alert families to the presence of nitrates in groundwater and prevent blue baby syndrome Environment Nitrate concentration Flourescence
RFP
In vivo Silver Medalist Safety Commendation America N/A
Grenoble 2011 Mercuro-coli Yes Environment Our project aims at constructing an easy to use, transportable sensor capable of quantifying the concentration of mercury, in an aqueous sample. Our system is based on a comparison between an unknown mercury concentration and a known IPTG concentration. A linear IPTG gradient is present on a test-strip containing the engineered bacteria. When the mercury solution is added, the regulatory network will switch to one of two states depending on the IPTG/mercury ratio. Bacteria become either “sender” or “receiver”. The bacteria sensing a predominance of mercury over IPTG, the “senders”, will release a quorum sensing molecule which is detected by the nearby “receivers”. The reception of quorum sensing molecules will induce the expression of a red dye in the “receivers”. In this way, a red line emerges at a position in the IPTG gradient from which the unknown mercury concentration can be deduced." Environment IPTG
Mercury
Lycopene In vivo Advance to Championship
Gold Medalist
N/A quorum sensing
comparative measurement system
sending and receiving bacteria
Post-transcriptional regulation
Gardner toggle switch
ITESM Mexico 2011 Dual light controlled arabinose biosensor Yes Health and Medicine Using previously developed mechanisms, this project will develop a new system capable of detecting a desired analyte, the system will report the concentration of such analyte at a given time lapse with the possibility of setting an instant concentration reading at will. Since most of the mechanisms used are based in detecting arabinose, this project will use arabinose as the measured analyte to avoid unnecessary difficulties. Our project is a biosensor for arabinose build in an E. coli chassis, it will measure the concentration levels of arabinose by reporting two different fluorescent proteins, GFP for a low concentration level and CFP for a high concentration level. N/A Analyte
Arabinose
Flourescence In vitro N/A N/A N/A
KAIST Korea 2011 E.Casso Yes Miscellaneous E. Casso is an E. coli system engineered into art. This system consists of two types of genetically modified E. coli: the random signal generating E. coli (the “Brush E. coli”) and the color generating E. coli (the “Paint E. coli”).The Brush E. coli possesses genes (lasI, luxI, rhlI, and cinI) that produce quorum in its chromosomal DNA. Each Brush E. coli will secrete quorum molecules randomly associated with one of four colors among red, cyan, yellow, and green by a modified Cre-loxP mechanism. The Paint E.coli possesses plasmid vectors that express one of four colors of fluorescent proteins in response to the type of quorum it receives from the Brush E.coli. The quorum sensing complex completed in the Brush will bind to the ribosome binding site (RBS) of the corresponding fluorescent gene. Using this system, we can create art on an LP plate with the cells' “random” contribution. New Application Not specified
quorum molecules
Colour
Flourescence
In vivo N/A N/A Paint E.coli
art
Brush E.coli
KIT Kyoto 2011 Mr.D -who will cure leukemia- No Health and Medicine Leukemia is a serious disease and its remedy has been never found yet. People are afraid of it not only because it is incurable but also it is unpredictable what will happen and when it will happen. Patients have to put up with both of them. Here we propose the convenient testing kit for leukemia which makes its symptom visible. To accomplish this we are developing leukemia disease models in Drosophila. The usefulness of this kit will be evaluated by characterizing the Drosophila model. This kit may provide a guideline to overcome fear and pain which have not been immeasurable and relieve the fear for leukemia. Our team, KIT-Kyoto challenges making a leukemia disease model in Drosophila melanogaster. Drosophila is being used as many hereditary disease model because over 70% of known human disease genes have similarities to Drosophila genes. This year, we focus on a leukemia in which the etiology and the therapy have not been established. We therefore decided to make a leukemia disease model in Drosophila. We insert human leukemia genes into Drosophila genome and also fuse a green fluorescent protein(GFP) with a leukemic protein to monitor its expression in E. coli or Drosophila. We expect that establishing a leukemia disease model in Drosophila will be a first step to determine the etiology and to establish the method of therapy in the future. Health and Medicine leukemic protein Flourescence In vivo Silver Medalist N/A N/A
LMU Munich 2011 No Title Yes Environment We develop a set of bacterial strains that are able to detect the different metals. Via our reporters we also measure their concentration. Our aim is a kit for fast and easy metal detection. We have the vision to develop a set of bacterial metal sensors for easy qualitative and quantitative measurement of toxic metals just by reading the output after adding the water test sample. We use two different kinds of metal sensors. The ones in the first category work with reporter genes that lay downstream of an inducible promoter. The respective promoter is activated or deactivated by a specific metal-sensitive protein which binds to DNA dependent on the presence of that metal. As a consequence of this statistical event, there is a concentration-dependent transcription of the reporter gene, which is either GFP, luxAB or lacZ´. The second kind of metal sensors directly uses the characteristics of special proteins to obtain a measurement of the metal, e.g. by analyzing the activity of an enzyme that needs a special metal ion as a cofactor. For easy handling and compatibility we use the E. coli strain DH5α and B. subtilis for our two promoters taken from this organsim. Environment Heavy metals Colour
Flourescence
GFP
LacZ
luxAB
In vivo Bronze Medalist N/A petE2
iron
pAseR
pnikA
pabA
pnorB
promoter and protein based sensor
cobalt
arsenic
copper
antinomy
nickel
prcnA
pCueR
pars
Macquarie Australia 2011 the switch-a-roo Yes Miscellaneous Phytochromes are ubiquitous proteins that allow an organism to sense light. These proteins have evolved in unique environments to sense light intensity in different colour ranges. This experiment focuses on constructing a biological switch that uses phytochromes from Deinococcus radiodurans and Agrobacterium tumefaciens. The coupling of heme oxygenase supplies our phytochrome proteins with biliverdin, allowing for the self-assembly of the switch within host systems. The switch is the first stage of a two component light sensor and when expressed at high level, there is a noticeable colour change of the cell when it is activated by light. New Application light Colour
phytochrome
In vivo Silver Medalist N/A light
Phytochromes
hemoxygenase
Missouri Miners 2011 Glucose sensor Yes Health and Medicine Our goal is to model a system that can measure glucose levels at different concentrations. In the future, this system could lead to cheaper blood glucose testing devices or an economic and efficient insulin pump. To achieve this goal we are utilizing the EnvZ-OmpR two-component regulatory system. If the OmpR binding region were to be mutated, theoretically, the system would be sensitive to glucose at different glucose concentrations. Each of these mutations could then be isolated and characterized. Once an adequate number of mutants are identified, the fluorescence reporter gene could be substituted with other reporter genes (e.g. a spectrum of color genes) to make an inexpensive glucose sensor. eYFP could also be replaced with an insulin gene so the system produces insulin at specific concentrations of glucose. In the future, this system could possibly be used as an insulin pump to replace insulin in the body when needed. Health and Medicine Glucose concentration eYFP
Flourescence
In vivo Advance to Championship
Silver Medalist
N/A EnvZ
OmpR
RNAP
Northwestern 2011 My N.U. P.A.L : Northwestern University's Pseudomonas aeruginosa Locator Yes Health and Medicine Pseudomonas aeruginosa is an opportunistic pathogen commonly found in immunocompromised patients. In addition to being the primary cause of lung infections in cystic fibrosis patients, many severe nosocomial infections can be attributed to P. aeruginosa. Currently, the standard detection method requires a potential sample to be grown overnight and then screened for the pathogen of interest. We have engineered an E. coli-based biosensor capable of detecting the presence of autoinducer molecules unique to P. aeruginosa. Thus, our system provides a faster detection method without sacrificing reliability or experimental resolution. Quorum sensing in P. aeruginosa is a complex hierarchy that governs the expression of numerous virulence genes. To realize our objective, we harnessed the native cell signaling and quorum sensing machinery of P. aeruginosa. We have thus created a novel, inexpensive biosensor capable of detecting the presence of P. aeruginosa both quickly and effectively. Health and Medicine P. aeruginosa autoinducers Flourescence
GFP
RFP
In vivo Advance to Championship
Gold Medalist
Best Model, Americas West LasR
autoinducers of quorum sesning
RhlP
Osaka 2011 Bio-Dosimeter Yes Environment The bacterium Deinococcus radiodurans shows remarkable resistance to a range of DNA damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. It is an aerobically-growing bacterium that is most famous for its extreme resistance to ionizing radiation; it not only can survive acute exposures to gamma radiation that exceed 15,000 Gy, but it can also grow continuously in the presence of chronic radiation (60 Gy/hour) without any effect on its growth rate or ability to express cloned genes. For comparison, E. coli can withstand up to 200 Gy, and an acute exposure of just 5-10 Gy is lethal to a human being. We explored various genes from D. radiodurans, implicated in its remarkable DNA damage resistance. By BioBricking selected genes and transforming them into E. coli, we hoped to confer additional DNA damage tolerance to the host cells. Our Bio-dosimeter must have some sort of visible output to alert users to radioactivity (detected as DNA damage). In a previous iGEM project, "colrcoli", we attempted to use E.coli as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage. Environment Ionizing radiation Colour
Lycopene
In vivo Advance to Championship
Silver Medalist
N/A RecA
PprM
PprA
PprI
Penn State 2011 Radicoli : bacterial dosimeter Yes Environment Ionizing radiation and radiation pollution is an important environmental problem that affects many. It affects those working around radiation facilities, as well as, those who are exposed to it due to widespread nuclear disasters such as those at the Fukushima Daiichi nuclear reactor or the Chernobyl reactor. Penn State’s team project will focus on using a genetic circuit introduced into E. coli bacterial cells, in order to rapidly detect and report the presence of harmful ionizing radiation. We are working to develop a robust and reliable biosensor which utilizes the lambda phage lytic-lysogenic switch coupled with a fast-acting reporter capable of producing an easily visible effect. We believe that the final construct may have the potential to rival current radiation detection methods, such as digital dosimeters. Our hope is that the basis of our biological dosimeter system will prove to be an effective genetic system capable of detecting harmful levels of radiation and relaying it to those working in the field or an affected area. We envision our system to not only be useful in such applications, but also be capable of further expansion and evolution through the expanding field of synthetic biology. Environment Ionizing radiation Flourescence
GFP
mCherry
In vivo Advance to Championship
Gold Medalist
N/A Pr promoter of Or
lambda phage bistable switch
RecA protein
Prm promoter of Or
University of Calgary 2011 Senseomonas NAstytoxins Yes Environment The University of Calgary’s iGEM team is working on developing an electrochemical biosensor for Naphthenic Acids (NAs). NAs are toxic surfactants released into tailings ponds as a by-product of the bitumen extraction process of oil sands. Microorganisms indigenous to tailings ponds that are uniquely capable of degrading NAs suggest that bioremediation may be a viable solution. To be successful, however, levels of NAs need to be monitored and existing methods for detection are costly and offsite. Using two NA-degrading organisms relatively new to iGEM: microalgae and pseudomonads, we used bioinformatics and a novel NA affinity-based screen in an attempt to identify a sensory element. In the process, we have characterized an electrochemical reporter system and built a working measurement device. We have also submitted new parts for future work in microalgae, as well as novel parts to move constructs between Pseudomonas and E. coli. Environment Napthenic acids Electrochemical
LacZ
Luciferase
Luminous energy
In vivo Advance to Championship
Gold Medalist
Best Experimental Measurement Approach, Americas
Best Wiki, Americas
naphthenic acids
Uppsala Sweden 2011 Setting the colour Yes Miscellaneous Regulation of gene expression by light is a milestone in synthetic biology. As a contribution of UT Austin in iGEM 2004, the concept of ""coliroids"" was coined and thereby widely recognized. Light regulation introduces noninvasive, direct and advanced spatio-temporal control of engineered biological systems. Ever since iGEM 2004, as more and more naturally occurring light-sensing microorganisms are being discovered and sequenced, synthetic biologists realize there is a whole range of natural light-sensing systems at their disposal. Other than using natural light-sensing proteins, engineered proteins have been designed from the natural templates. However, most of the light-sensing systems developed thus far focus on studying one light-sensing system at a time, characterizing the activation light spectra, active state, etc. Nobody has ever built systems capable of detecting multiple wavelengths until recently. In short, our project focuses on improving the existing multichromatic sensing systems by expanding the number of useful wavelengths. Our system can regulate the expression of three different genes independently from each other using three different wavelengths. These ""multichromatic coliroids"" upgrades the present coliroids, much like upgrading black-and-white movies to color TV. The proof of concept will be demonstrated by growing a colorful picture on bacteria culture, much like Andy Ellington's coliroids picture but with color. New Application light Colour In vivo Advance to Championship
Gold Medalist
N/A N/A
UTP Panama 2011 The RENBO : Thermogenic Response Nutrient Biosensor Yes Environment To develop flexible and better sensors for environmental, agricultural and engineering applications are the aims of the UTP-Panama Team “SynBio Engineering Tool Kit”. In this way we work with Nitrate Biosensor (PyeaR - GFP composite) developed by Team BCCS-Bristol 2010, which expresses fluorescent signals upon nutrient detection, producing a high-resolution map of arable land. To achieve this goal we use the collateral effect of the AOX enzyme (Alternative oxidase) mainly designed to generate heat in response to a cold-shock, using the hybB promoter. This effect increases the bacteria growth at temperatures below 20°C. Finally we design a prototype device with a better cold shock promoter (CspA promoter) developed by UNAM-CINVESTAV Team in 2010, in order to give our E. coli a “Intelligent Coat", which means that not to only survive a cold-shock but to also still been able to keep up with his duties due to improve their expression mechanism at low temperature. Food and energy Nitrate concentration Flourescence
GFP
In vivo Advance to Championship
Bronze Medalist
N/A HydB cold shock promoter
AOX periplasmatic heat generator
OmpA signal peptide
widening operating temperature
Wisconsin Madison 2011 Sensing Biofuel Yes Energy This summer, the UW-Madison iGEM team will be working on streamlining the biofuel discovery and production processes through the use of biosensors. The necessity for sustainable, economical sources of fuel is ever growing, and UW-Madison is a forefront institution in the hunt for such supplies. In association with the Great Lakes Bioenergy Research Center (GLBRC), we are creating new E. coli biosensors that can accelerate high throughput screening of potential fuel sources. We’re specifically interested in ethanol and alkane, derived from sources ranging from cellulose to metabolically engineered E. coli. We have found regulatory systems which respond to each of the biofuels of interest, and are using standard BioBricks assembly to create E. coli strains which can be used to perform fluorescence-based assays. By using fluorescent biosensors, we hope to lower costs (in both equipment and cost-per-sample) while maintaining a high degree of accuracy. In the interest of creating robust and accurate assays, we are also attempting to increase the magnitude and range of the linear fluorescence response through directed evolution. We hope to leverage multiple selections to both decrease basal fluorescence and increase the point where the response becomes saturated. As a more direct approach to increasing microbial biofuel yields, we also pursued the use of bacterial microcompartments (BMCs) as scaffolding for key enzymes in the ethanol producing and sensing processes. Through localizing crucial anabolic enzymes, as well as the beginning of our sensing cascades, to the BMC surfaces, we can increase fuel titers as well as our reliability in accurately sensing them. However, due to the complexity of this project and the time investment needed, we have stopped work on the BMC. Food and energy Ethanol Flourescence
RFP
In vivo Advance to Championship
Bronze Medalist
N/A exaD & exaE genes
AlkS
PalkB
PexaA promoter
Art Science Bangalore 2010 Synthetic and Post-Natural Ecologies Yes Miscellaneous In our second year as artists and designers at IGEM, we have decided to investigate the consequences of creating a Synthetic Ecology: an ecosystem in which organisms designed for a techno-scientific environment interact with organisms in the wild. C.elegans live on a diet of a variety of bacteria, E.coli being such strain. Genetically-modified E.coli can be fed to C.elegans which can then express any double stranded RNA of interest. The dsRNA can knock off specific genes in C.elegans. In our experiments, we are using C.Elegans as a marker to expres a range of external factors in two sets, temperature and IPTG. On a utilitarian level, our project investigates the use of C.elegans as a visual marker for changes in environmental conditions. On a more critical level, C.elegans is used to study the consequences of interactions between engineered organisms and the 'natural' world. New Application E. coli
IPTG
Temperature
C. elegans survival
dsRNA
In vivo N/A N/A ecosystems
C. elegans
natural
BCCs Bristol 2010 agrEcoli: Smarter farming through bacterial soil fertility sensors Yes Food Fertiliser production is a major contributor to global carbon emissions, and excess fertiliser can cause immense damage to local ecosystems. Our lab has developed and characterised a cheap, versatile soil fertility sensor based on an E.coli chassis. It expresses fluorescent signals upon nutrient detection, producing a high-resolution nutrient distribution map of arable land. The ratio of two fluorescent signals allows farmers to quantify soil nutrient content. agrEcoli bacteria, encapsulated within a gel container to improve visibility and prevent escape, have been shown to work on soil in lab conditions. We have explored the marketing of our device, considering public perceptions of synthetic biology. BSim, our prize-winning modelling framework, has been extended to analyse our new biobricks’ behaviour within gel capsules. In addition, a new interface for BSim has improved its accessibility to the wider synthetic biology community, facilitating collaboration. agrEcoli optimises fertiliser use, saving farmers' money and reducing environmental damage. Food and energy Nitrate
Nitrate concentration
GFP In vivo Gold Medalist 2nd Runner Up
Best Food or Energy Project
Finalist
nitrates
agriColi
agriculture
Bielefeld Germany 2010 MARSS - Modulated Acetosyringone Receptor Sensor System Defining Spiciness since 2010 Yes Food The iGEM-Team Bielefeld is going to modulate an Agrobacteria receptor in Escherichia coli in order to detect capsaicin which is responsible for the hot taste of chilies. The intention is to make the spiciness in fare visible using a gradient light signal. The original receptor is the acetosyringone detection system of Agrobacterium tumefaciens. By using directed evolution, we aim to modulate the receptor binding domain to enable the interaction with similar phenolic substances like capsaicin. Brought into E. coli, this modulated system will induce light effects of different intensities - depending on the concentration of capsaicin respectively the spiciness of the sample. The capsaicin detection is a proof of principle concept. We aim to establish a system, which is characterized by a high sensitivity and specifity and is capable to replace slow and high priced diagnostics or analytic methods. The targets of the system could be allergy-triggers, explosives and toxins. Food and energy capsaicin Luciferase In vivo Gold Medalist N/A spicy
pepers
chilli
Capsaicin
BIOTEC Dresden 2010 SensorBricks Yes Health and Medicine SensorBricks is a reliable and modular system for antigen recognition, signal amplification and quantification. Initial steps of SensorBricks will focus on the detection of CD33 and other leukemic markers to increase diagnostic stringency. There are three major components in SensorBricks: (i) monoclonal antibodies that bind to an antigen of interest, (ii) a LuxI-Protein A fusion construct which non-specifically binds antibodies and produces the autoinducer N- Acyl homoserine lactone (AHL), and (iii) a Escherichia coli based biosensor which strongly amplifies the production of a fluorescence protein in the presence of AHL. By coupling signal detection to a genetic circuit, we would be able to amplify the signal in a quantifiable manner, allowing the identification of cancer markers expressed in minute quantities. Health and Medicine AHL GFP
mCherry
RFP
YFP
In vivo Gold Medalist N/A blood
cancer
leukaemia
Brown University 2010 Light Pattern Control of Cell Circuits Yes Manufacturing Biological manufacturing of complex compounds often requires the synthesis of many intermediate products. Production of these intermediates is currently triggered by inefficient methods, such as chemical inputs (tetracycline, estrogen-analogs, arabinose, etc) or drastic changes to the cellular environment (pH, oxygen levels, temperature, etc). On an industrial scale, this chemical induction requires large quantities of reagents and extensive purification, while environmental induction requires conditions that can adversely affect cell vitality and yield. To this end, we have designed an E. coli genetic circuit that can pass through four stable states of protein production triggered solely by ON/OFF patterns of light. To efficiently test the components of our circuit, we have also created a system for the transient delivery of transcription factors through the cell and nuclear membranes. With this production method, we can link multiple synthesis steps to a single, clean and rapidly scalable input. Manufacturing light Flourescence
Transcriptional State of the Cell (On or Off)
In vivo Bronze Medalist N/A transcriptional state
light control
Cambridge 2010 E.glowli: a bioluminescent future Yes New Application Bioluminescence is one of the most striking spectacles in the natural world. Taking genes from fireflies and Vibrio fischeri, the Cambridge team have constructed BioBricks which allow light output at a wide range of wavelengths. Firefly luciferase is already used as a reporter, but requires continual addition of the expensive substrate luciferin. We have created codon-optimised operons combining luciferase with a luciferin regenerating enzyme (LRE). This allows recycling of luciferin for sustained light output. In addition, we have submitted the first lux operon to the registry, taking genes from bacteria which form symbiotic relationships with squid. This is the first BioBrick to emit light without addition of substrate and can be used as a reporter with any promoter. These two approaches will allow cheaper assays with brighter signals. We also hope they will lay the foundations for natural light sources that help to address the energy crisis facing our planet. New Application light Colour In vitro Advance to Championship Best Wiki firefly
vibrio
luciferase
Chiba 2010 Eliminating the False-Input ~Genetic Double-Click System~ Yes New Application We daily double-click the icons to open the files or to exert the program: this is clearly distinguished from the single click, which is often for selecting or highlighting the program. This year, iGEM CHIBA is constructing genetic double-click system whose output is released only when the input (inducing agent) is given twice within a limited time. To discriminate double-click from two separated single-clicks, the 1st input is to be memorized temporarily. If the 2nd input is added before the memory gets lost, output will be produced. If the 2nd input is not added within the given time, the system will be reset to the original state. This mechanism could work as a sort of safety device; by requiring the 2nd ‘confirmation’ input, one can drastically reduce, or even eliminate, the frequency of false-inputs. This system could be useful in operating the potent or potentially-hazardous biochemical processes. New Application AHL
Pulse
GFP not specified Gold Medalist N/A double-click
memory
Debrecen-Hungary 2010 The lipid sensor eukariotic toolkit Yes Food Eukaryotic synthetic biology has huge potential, yet it is still in need of more diverse molecular tools for defined gene regulation. Nuclear receptors are a conserved family of proteins responsible for sensing lipids; they may be viewed as lipid activated transcription factors. We have successfully developed a kit with a variety of lipid responsive domains (from H.sapines, D.melanogaster and C.elegans) for the rational construction of synthetic transcription factors. The domains respond only to predefined lipids and selectively activate predetermined gene expression. To characterize theses domains, we used standardized protocols for comparable measurements. In vivo gene expression was measured as a function of ligand concentration using luciferase activity. The potential for these tools is immense; e.g. from the ultra sensitive detection of lipid contaminants in the environment to the opportunity of titration specific gene expression canges in patients undergoing gene therapy. Food and energy Not specified Not specified not specified Gold Medalist N/A lipids
multispecies
DTU Denmark 2010 Bi[o]stable – Engineering a bistable switch Yes Miscellaneous The aim of this project is to engineer a genetic bi-stable switch that produces two different, mutually exclusive outputs when given two different inputs. The switch is based on the repressor-anti-repressor system of the salmonella phages Gifsy1 and Gifsy2 and the λ-phage anti-termination system. The latest induced output will remain stable through generations, even once the input ceases, due to the phage regulatory systems. We present the framework for this development and characterize the regulatory mechanisms by using fluorescent proteins as the reporter (outputs). The dynamics of the system have been modeled and we have also attempted to characterize and submit the promoters, repressors and anti-repressors from the salmonella phages, as well as the two anti-terminator proteins from the lambda phage, as BioBricks. We have hereby demonstrated the engineering of a multipurpose bi-stable switch sensor/reporter tool that can have numerous applications. Foundational Advance DNA GFP
RFP
In vitro Gold Medalist N/A bistable
mutually
switch
exclusive
ETHZ-Basel 2010 E. lemming – a remote controlled living robot No Energy We control the movement of a single E. coli cell by light. In wild type E. coli flagella movement is controlled by proteins of the chemotaxis pathway, so called Che proteins. In our engineered cells one of these Che proteins is fused to a synthetic light-sensitive localization system. Two external inputs – red light and far red light - induce the relocation of the fused proteins, thus reversibly changing flagella movement direction. Cells, imaged by bright field microscopy, are automatically detected and tracked while a closed loop controller guides the cell into a user defined direction by autonomously sending light inputs. This makes our engineered cell the smallest remote controllable living robot on earth. Information Processing light Lack of Taxis In vitro Gold Medalist Best Information Processing Project, Finale chemotaxis
Gaston Day School 2010 Construction of a Biological Iron Detector in a Secondary School Environment Yes Environment Our team’s project was to create a biological iron detector using techniques and procedures available to an ordinary high school laboratory that replicate methods used in university research laboratories. We constructed our reporter by combining an iron-sensitive promoter with a red fluorescent protein (RFP) coding sequence. We chose RFP because of its high visibility and easy detection. Although the assembly was successful, the resulting detector is leaky with measurable RFP even in conditions with no iron present. In our lab environment, we found that it was necessary to work with relatively high concentrations of bacteria and DNA. We developed simplified procedures for transformations, digests, and ligations, but we continue to face problems with DNA visualization and measuring the pigments from the bacteria. Environment iron RFP not specified N/A N/A iron
Georgia Tech 2010 Inducing a Thermogenic Response to Cold-shock in Bacteria Yes Manufacturing Alternative Oxidase (AOX) is a terminal oxidase protein found in the respiratory chain of various organisms ranging from aquatic prokaryotes to plants and animals. In the AOX pathway, electrons are transferred from ubiquonone to AOX, and then directly used to reduce oxygen. The drop in the electric potential energy of the electrons transferred from AOX to oxygen is dissipated as heat. Our project has focused on 1) cloning the AOX gene from a thermogenic plant (Sacred Lotus) into E. coli to induce a thermogenic response to a cold-shock, and 2) calculating a theoretical rate of heat production per bacterial colony to select for an appropriate calorimetric technique. Further, numerical methods in MATLAB will be employed to model the steady-state temperature profile of the synthetic bacterial colony, and to potentially corroborate later experimental findings. Engineering a controlled thermogenic response in bacteria could lead to improved bacterial functioning in cold shock environments. Manufacturing Cold Shock Heat In vivo Silver Medalist N/A plant
heat
bio-film
HKU-Hong Kong 2010 The Bio-Safety Net Yes Manufacturing Our team’s project is a “bio-safety net” that limits the survival of bacteria according to tailored conditions. Bacteria could be designed to perform promising tasks, such as the biodegradation of oil to clean up oil spills. Yet, there are risks associated with the possibility of living bacteria performing undesired activities. Our goal is to introduce a “bio-safety net” that will be applicable to virtually all genetically engineered bacteria as a vital termination step after their tasks have finished. We have made this possible by introducing a "suicide" mechanism, that will be triggered under specific conditions. By combining different promoters, the system can respond to changes in environmental factors and control expression specific to chosen factors. Such mechanism can be easily assembled and incorporated to bacteria through the use of biobricks. Manufacturing Crude Oil cell death In vivo N/A N/A killswitch
net
suicidemechanism
IIT Delhi 2010 Dr.coli Yes New Application The use of bacteria for sensing applications has been around for a while now, and they have been used to produce recombinant proteins as needed for even longer time. The current project focuses on integrating these two components to create a device capable of responding to external stimuli in the form of quantitative protein production. For this device to function, it needed to be capable of producing and secreting the protein extracellularly. Further the dynamics of elicitor interaction with the bacteria in a flow stream and concomitant product release have also been a part of the study. We believe that such a system can play a major role in drug delivery systems that treat as needed and further in creating artificial glands for diseases such as insulin. New Application AHL
IPTG
GFP In vivo N/A N/A drugs
Imperial College London 2010 Parasight – Parasite detection with a rapid response Yes Health and Medicine More than two billion people around the world live with unrelenting illness due to parasites” - WHO Director General Lee Jong-wook. Synthetic biology offers great opportunity for biosensors, however current designs require hours before useful output. To tackle this issue in the field, it's crucial that our project can respond in minutes, hence we have engineered a fast, modular sensor framework. This allows detection of a range of different parasites, and may also be used as an environmental tool for mapping their spread. We have developed two new technologies that enable our modular input/output - a novel cell surface biosensor, customisable for specific parasitic proteases, linked through quorum-sensing to a new 'fast-response' module capable of producing a detectable output in minutes. To demonstrate the concept, we've designed and fabricated B. subtilis to give a striking colour readout upon detecting the waterborne Schistosoma parasite which affects 200 million people worldwide. Health and Medicine Transcription Factor Colour In vitro Advance to Championship
Gold Medalist
Best Human Practices Advance
Best Wiki
B. subtilis
Schistosoma
waterborne
parasite
Ivy Tech Southbend 2010 To Swim or Not to Swim? Yes Environment Anyone who wants to enjoy bathing in natural bodies of water in or near areas populated by humans or livestock may encounter unsafe levels of enteric bacteria. Contemporary methods of assessing water quality have a slow turn-around time so we have taken steps to perfect a biosensor for rapidly indirectly quantifying the presence of enteric bacteria in natural water samples through the detection of quorum sensing factors. Previous IGEMS have exploited the LuxR/pLux system for the detection of a variety of N-acylhomoserine lactone autoinducers. We have taken steps to further perfect a biosensor based on this device by transforming a gram-positive bacteria host to eliminate any background autoinducer signal and to build-in an enzymatic “read-out” to obtain an analog output. We envision the development of a handheld monitor that uses this IGEM biosensor, immobilized on input paper strips, to rapidly detect unsafe levels of enteric bacteria in water samples. Environment Not specified Not specified not specified Bronze Medalist N/A water
bacteria
Johns Hopkins 2010 Synthetic Voltage Sensitivity at The Transcriptional Level in Saccharomyces cerevisiae Yes New Application If the goal of iGEM and the Parts Registry is to take the messy world of genetic engineering and transform it into something like the standardized world of electrical engineering, it may be useful if electronic systems could directly interface with biological systems. Past iGEM projects have used chemical or optical stimuli to actuate transcriptional responses. Our project, however, seeks to add voltage sensitivity to Saccharomyces cerevisiae. Baker’s yeast was chosen because in some sense yeast have a system that responds to voltage input. With a voltage stimulus one can open the voltage-gated calcium channels of yeast, causing calcium ions to rush into the cytoplasm. This causes calcineurin to dephosphorylate Crz1, which enters the nucleus and binds various promoters. Our group presents a library of characterized Crz1-sensitive promoters of both naturally-occurring and synthetic varieties. Genes downstream of these promoters are thus voltage-regulated in media containing calcium. New Application Calcium GFP
RFP
In vivo/in vitro Gold Medalist N/A cardiac
research
interface
computer
voltage
KAIST Korea 2010 DiscoverY: universal diagnostic yeast Yes Health and Medicine Large portion of the world is still suffering from diseases despite of the availability of treatment -tuberculosis in Africa for instance. Such trouble originates from unavailability of cheap and effective diagnostic method. Team KAIST will present DiscoverY that is capable of diagnosing multiple diseases. S.Pombe chassis holds FGFR1-STAT1 pathway with modification in FGFR1, which becomes fusion antibody receptor in our system. When fusion antibody receptors on the surface come in contact with antigens, the pathway is initiated. The pathway ends with GFP expression as diagnostic display. The system will be tested with tuberculosis antibody, and simple replacement of antibody will make DiscoverY the universal diagnostic yeast. Health and Medicine Mycobacterium tuberculosis GFP In vivo N/A N/A yeast
Korea_U_Seoul 2010 Heavy Metal Gang Captured By Capsule Cop Yes Environment Toxic heavy metals such as arsenic, zinc, and cadmium in water are very harmful. Detecting these heavy metals is an important task. So we designed a heavy-metal-detecting E. coli. In order to design the system, we employed two fluorescence proteins (GFP, RFP) and aryl acylamidase as signal reporters. The aryl acylamidase converts a colorless acetaminophen(Tylenol TM) to a brown color substrate. Since the detecting E. coli has three heavy metal promoters, if more than two heavy metals coexist in a solution, the E. coli emit mixed fluorescence, so we simultaneously detect metals. Our goal is to synthetic modules put these three genes for different heavy metals in a row in E. coli and then utilized in the form of a lyophilized powder, which can be stored in a drug capsule to make it portable so that analysis of water is easily processed. We call it a "Capsule Cop". Environment arsenic
Cadmium
Zinc
GFP
RFP
not specified Silver Medalist N/A heavy
metals
Kyoto 2010 The Fantastic Lysisbox Yes Manufacturing The Fantastic Lysisbox: Genetically engineered cell death is essential for the application of biotechnology, such as in bioremediation area. In order to control the cell-death, we designed “Lysisbox”, which consists of a pair of modules: “Killer gene” and “Anti-killer gene.” As the Killer gene for Escherichia coli, we noted the lysis cassette [SRRz/Rz1 gene] of lambda phage coding for holin and endolysin. The holin form pores in the inner membrane and the endolysin access and degrade the peptidoglycan passing through the pores, leading the E.coli to death. As the Anti-killer gene, we chose SΔTMD1 coding for a dominant-negative holin that inhibits the formation of the fatal pores. The balance of these two genes' expression level has the key to the E.coli’s life or death. In addition, such controllable membrane pores should show critical functions for all living organisms with lipid membranes and a cell wall. “Lysisbox” will contribute a lot to all the future iGEM projects, thus you must say “FANTASTIC!!!" Foundational Advance IPTG cell death In vivo Gold Medalist N/A killswitch
anti-killer gene
killer gene
Macquarie Australia 2010 Engineering a Bacteriophytochrome switch – creating a controllable E. coli chameleon Yes New Application Photoreceptors are utilized by almost every organism to adapt to their ambient light environment. Our aim is to engineer a novel, reversible molecular ‘light switch’ within E. coli by introducing a photoreceptor from non-photosynthetic bacteria (Deinococcus radiodurans and Agrobacterium tumafaciens). By cloning the bacteriophytochrome coupled with heme- oxygenase, an enzyme producing biliverdin, the created colonies are able to respond to red and far-red light environments. This novel approach will result in the colour of E. coli to ‘switch’ from blue to green reversibly. Our E. coli chameleon will serve as a fundamental ‘bio-brick’ for future applications by providing a simple and photo-reversible switch. New Application light Colour In vivo Bronze Medalist N/A light
switch
far-red
METU Turkey 2010 E-CO Sensor Yes New Application Cells can sense and respond to the presence of various gas molecules such as oxygen, nitrogen and carbon monoxide using gas sensor proteins. CooA is a carbon monoxide (CO) sensing transcription factor. It is a member of the cAMP receptor protein (CRP)/fumavate nitrate reduction (FNR) family of transcriptional regulators. CooA switches on oxidation enzymes in Rhodospirillum rubrum (a purple, nonsulfur, phototrophic bacterium) which enables the bacterium to use CO as a carbon source. CO is an odorless and colorless gas which can be extremely lethal. Our aim is to develop a cell sensor which can detect a wide range of CO concentration in the environment. We are building CooA and CooA-responsive promoter biobricks which will be transformed into E.coli. Fluorescent proteins (GFP and RFP) will be utilized as dose-responsive signals of ambient CO. New Application CO GFP
RFP
In vivo Bronze Medalist N/A carbon
monoxide
Mexico-UNAM-CINVESTAV 2010 A very cool E. coli Yes Energy We begin by proposing a biosynthetic construction that enables Escherichia coli to produce an antifreeze protein, AFP at less than 15 degrees Celsius. This protein prevents ice crystal formation in the cell, which in turn allows survival at very low temperatures. We develop a switch by adapting the cold-shock E. coli operon with AFP from a fish (Macrozoarces americanus) using a positive feedback circuit. A very important potential application we are interested in is the use of AFP in designing systems helping crops to avoid potential damage from frosts. There are other possible important applications in tissue and organ preservation. Food and energy Temperature protein secretion In vivo Bronze Medalist N/A response
cold
shock
Neveda 2010 Development of Plant Biosensors for Environmental Monitoring Using Nicotiana tabacum Protoplasts as Yes Environment Our long term goals are to develop plant biosensors that reliably measure changes in the local environment. In the process of developing biosensors, the 2010 Nevada iGEM Team need to develop fundamental promoters, reporters, and plasmids for plants. Therefore, the 2010 Nevada iGEM Team has three goals for this year’s competition. First, we are going to test the validity of utilizing Nicotiana tabacum (NT cells) as a model for the expression of higher plant genes for future iGEM competitions. NT cells are a faster, cheaper, and safer model than traditional plant transformation. These cells can therefore be utilized as a quick proof-of-concept test model before moving synthetic constructs into plants of interest. We also aim to produce an iGEM-compatible plant-specific plasmid, several stress-inducible plant promoters, reporter genes containing Kozak sequences (ribosome binding sites) and terminators that conform to BioBrick standards. Lastly, we hope to measure the induction of these stress promoters in real-time by performing a fluorometry assay in which stress will be applied to NT cells and fluorescent output by a reporter (GFP) will be measured to detail induction in real time. This method has a distinct advantage over microarrays since microarrays are only one ‘snapshot’ in time. Environment Drought
Salinity
Temperature
RFP In vivo Silver Medalist N/A plants
remote
transgenic
sensing
Paris Liliane Bettencourt 2010 Every bacteria counts! Yes New Application Counting is the action of finding the number of elements in a set. Past attempts at developing counters in cells have mostly attempted to mimic the binary methods that computers use to count.Our first counter takes a new approach to counting in cells, essentially a mechanical rotary counter implemented on a micro scale. Each time the counter detects an input, it performs an excision and integration directly down-stream of the active site, turning on a reporter and rotating over one "notch" on the counter.Our second counter operates on the wholly different principle that the statistical occurrence of a rare event in a large population can be modeled. Each cell in our population harbors a construct that when stimulated has a small chance of excising a terminator and expressing a resistance gene. The number of resistant cells is thus an accurate count of the number of input stimuli. Foundational Advance Not specified Not specified In vivo Gold Medalist Best Foundational Advance binary
counting
Peking 2010 Heavy Metal Decontamination Kit Yes Environment During this summer, our group has developed a method to engineer bacteria into heavy metal decontamination kits. First of all, we analyzed the function, structure and operation of the transcription factor MerR, a mercury-responsive regulator in detail via bioware experiments and modeling. Then appropriate topology candidates for proper bioreporters were carefully searched. We selected a candidate and re-designed genetic components to accomplish certain bioreporter function in need, which was verified by following bioware experiments. For bioabsorbents, we engineered MerR into a metal binding peptide. This was followed by inductive expression of engineered peptide on surface, periplasm and cytosol of E.coli. This reverse engineering method was then expanded to lead-responsive regulator, PbrR, to confirm the validness of this method. Results demonstrated that the procedure mentioned above is streamlined enough to construct valid whole-cell bioreporters and bioabsorbents of various heavy metals for field application in the near future. Environment Cobalt
Copper
Gold
Lead
Mercury
Silver
Zinc
GFP not specified Advance to Championship
Gold Medalist
1st Runner Up
Best Environmental Project, Finals
heavy
metals
proteins
MerR
Purdue 2010 Development and Characterization of Hypoxic Stress Response Systems in Mammalian and Plant Models Yes Environment From water-logged soils to overpopulated regions of tumors, low-oxygen environments distress plant and mammalian systems. Plants with inadequate levels of oxygen move from aerobic respiration to alcohol fermentation to sustain their metabolism. This switch causes the accumulation of byproducts that are detrimental to the plant. A synthetic biological circuit, centering on the alcohol dehydrogenase (Adh) promoter, has been developed indicating when low oxygen levels (< 5% O2) are present in plants. Similarly, low oxygen zones can develop in solid tumors in numerous mammalian cancer models. Substantial evidence indicates that hypoxia in tumors initiates angiogenesis, a process that aids in tumor proliferation. Accordingly, an additional hypoxia-sensitive circuit that up-regulates the activity of a reporter protein in low oxygen (<1% O2) environments has been created for mammalian systems. The development and characterization of these circuits will provide tools to explore the consequences and identity of hypoxic environments in mammalian and plant systems. Food and energy Not specified YFP In vivo Bronze Medalist N/A plants
hypoxia
agriculture
Sheffield 2010 iCOLI: A water-borne pathogen detection system and an exploration of identity in synthetic biology Yes Environment The Sheffield iGEM 2010 team organised its activities around a general theme: ‘identification’. This notion, for instance, is at the heart of the scientific and modeling projects, which have made steps towards the design and production of a multi-target, water-borne pathogen detection system. Identification is also central to the human practices projects, which explicated and analysed the concept of identity in relation to the disciplinary backgrounds brought together in the project and the field of synthetic biology itself. Vibrio cholera was chosen as a test-case, giving us two potential routes to engineer E.coli to recognise the pathogen: 1. Fusion of cholera’s receptor (CqsS) for its quorum sensing molecule (CAI-1) with the internal apparatus of one of E.coli’s general stress detecting systems (BarA). 2. Engineer the whole cholera quorum sensing system into E.coli.Each of these would then be connected to a representation system (GFP or E.chromi) to visualize the pathogen. Environment CAI-1 GFP In vitro Bronze Medalist N/A cholera
chimeric
SJTU-BioX-Shanghai 2010 Synthetic-biological Approaches to Osteoarthritis Yes Health and Medicine Osteoarthritis (OA) is a chronic disease in which joint matrix is degraded and chondrocytes undergo disordered and hypertrophic differentiation, symptoms including joint pain, tenderness and stiffness. We proposed two synthetic-biological approaches to OA, one with a eukaryotic genetic circuit and another prokaryotic. Both circuits are composed of three systems: "Detector", "Actuator" and "Supervisor". As for Detector, we built tissue-specific promoters in the eukaryotic circuit, while inflammation factors are employed as signals of OA in the prokaryotic circuit. The same Actuator shared by two circuits generates proteins col2a1, which replenishes the degraded matrix, and oct4, which reverses the disordered differentiation. The eukaryotic Supervisor part has an original design in which a photo-sensitive cation channel crosstalks with certain cellular signaling pathways, resulting in the light-controlled expression of col2a1 and oct4; in the counterpart of prokaryotic circuit, both injected inducers and over-population lead the engineered bacteria to suicide, thus attenuating possible side effects. Health and Medicine light Calcium Signals In vivo Gold Medalist N/A Osteoarthritis
degenerative arthritis
Stanford 2010 EscheRatio coli: Novel Sensors to Detect a Ratio of Environmental Inputs Yes Miscellaneous The majority of sensors currently used in synthetic biology respond to the absolute concentration of a chemical. However, many important biological processes are governed by the ratio between the concentrations of multiple chemicals. To create systems capable of responding to more complex input data, the Stanford team designed two types of ratio-measuring sensors. The first sensor utilizes two unique small RNAs to inhibit the transcription of two operons, each responding to an environmental factor and having a specific flourescent protein (or output gene). By manipulating the number of small RNAs produced, a tipping point between outputs can be established for different input ratios. The second sensor uses a phosphorylatable protein to control the transcription rate of an output promoter. By linearly associating two chemical inputs to the production of a kinase and a phosphatase, the ratio of the two environmental factors indirectly dictates the activity of the output promoter. Foundational Advance Acyl Homoserine Lactones
Arabinose
GFP
RFP
In vivo Gold Medalist N/A sensor
system
ratios
two
Tec-Monterrey 2010 Development of a genetic frame for the creation of a concentration-sensitive bacterial sensor Yes Environment Bacterial reporters or whole-cell bacterial sensors have always been an area of application for genetic manipulation and synthetic biology. The first bacterial reporters appeared 20 years ago, although these early tests didn’t use genetically modified microorganisms. Further research and development in the area of genetic engineering has resulted in newer and more sophisticated bacterial sensors, capable of detecting the presence of contaminants, sugars and amino acids in different media such as soil and water. However, most bacterial sensors can only detect the presence of a compound at a certain concentration and currently there are few documented bacterial sensors that can detect and report different concentrations of the compound of interest. Our objective was to develop a genetic frame, compatible with the BioBrick standard, for the creation of a concentration-sensitive bacterial sensor. In the process we also developed and characterized BioBricks for two new families of phage activators. Environment Arabinose
MuC Protein
MuMor Protein
GFP
RFP
YFP
In vitro Gold Medalist N/A genetic
circuit
concentration-sensitive
Tokyo Metropolitan 2010 Life Design: Fine Clothing, Color Housing and Delicious Food by using E. coli Yes Manufacturing Our team theme is “Life Design.” We make our life comfortable by following three projects. [E. coli Fiber Project – Fine Clothing] Bacteria cellulose is very useful material. People try to get bacteria cellulose. But it is high cost and low efficiency. Aim of our project is to make low cost and high efficiency cellulose factories where E.coli works! [E. coli Pattern Formation Project – Color Housing] Give an experimental proof of Turing pattern. We use two kinds of E. coli and make various patterns! The patterns are dynamic and stereoscopic!? [E. coli Rice Master Project – Delicious Food] Japanese like rice, our staple food. We are particular about the quality of rice. Rice Master of E. coli judges the quality of rice. In future, other kinds of food “Master” provide us some information about quality of foods. Manufacturing Glucose concentration RFP In vivo Bronze Medalist N/A rice
amylose
TU-Delft 2010 Alkanivore: Enabling hydrocarbon degradation in aqueous environments Yes Environment Pollution of soil and water environments by crude oil has been, and is still today, an important environmental issue. This was once more confirmed with the oil-spill in the Gulf of Mexico, but is also an issue that has to be faced continuously during the process of oil extraction from oil sands. Cleaning has proven to be challenging, but synthetic biology may hold the key to sustainable bio-remedial solutions for the future. What if we could design a small, autonomous, self-replicating, inexpensive method to remove oil from aqueous environments? The TU Delft iGEM 2010 team spent their summer designing a system that can tolerate, sense, dissolve & degrade hydrocarbons in aqueous environments, which could open new doors for the oil-industry. Environment Alkanes
Glucose concentration
GFP
RFP
In vitro Advance to Championship
Gold Medalist
Best Presentation alkanes
oil
pollution
University of Calgary 2010 Translating Stress Into Success Yes Miscellaneous The majority of projects in synthetic biology involve the over expression of recombinant proteins in microorganisms. A major stumbling block however, is often an inability to express functional protein. This situation is difficult to manage and troubleshoot as it is often unclear why expression is failing. We have designed a system that can accurately and visually report whether a gene is being transcribed and/or translated. The system also differentiates whether expression is failing due to misfolding in the periplasm or cytoplasm. In the case of misfolding, our system can also fine tune expression levels of a given protein to optimize production, increasing the likelihood of obtaining functional protein. To further understand protein misfolding we have built an equation-based, multivariant model of inclusion body formation. Finally, we used a series of podcasts to explore the social implications of our project in the context of the growing synthetic biology industry. Foundational Advance Not specified
Stress
GFP
RFP
In vivo Gold Medalist N/A troubleshooting
kit
Uppsala Sweden 2010 Levande Klocka (Living Clock) Yes Health and Medicine Our project aims for building a biological concentration band detection sensor and demonstrating its usefulness in building a bio-clock. Many previous iGEM teams have come up with sensors for various applications ranging from toxic metals to life saving enzymes. Our attempt is to create a concentration band detect component that can quantify the signal. This concentration band detection sensor thus serves as a quantitative sensor, which can work in combination with any of these chemical sensors. Apart from this utility, we believe the concentration band detect sensor in different configurations can allow the creation of complex circuits ranging from simple oscillators to complex data processing machines which can exist on the same system without affecting other components of the system owing to its concentration band specificity. With the bio-clock we test the robustness of the concentration band detection mechanism and if it could be used to build more complex devices. Health and Medicine Acyl Homoserine Lactones Flourescence not specified Bronze Medalist N/A band detection
bio-clock
UTDallas 2010 Enlisting E. Scherichia Holmes: A modular whole-cell biosensor for the detection of environmental po Yes Environment Recalcitrant pollutants such as petroleum constituents and nitrates are regularly introduced to the environment through oil spills, natural geological seepage and eutrophication. The UN’s flagship water protection initiative enumerates a host of health risks associated with these chemicals. UT Dallas iGEM addresses the eminent need to mitigate their circulation by developing novel whole-cell biosensors that can detect alkanes, aromatics and nitrates and execute combinatorial logic, feedback and noise-reduction functions inspired by synthetic biology. This work has wide ranging applications requiring a cheap chemical sensor that can dynamically process heterogeneous inputs and express a user-friendly output. Environment Alkanes
Aromatics
Nitrate
GFP In vitro Gold Medalist N/A nitrates
aromatics
alkanes
Virginia United 2010 Quorum Sensing Amplifiers and a Codesign Approach for Information Processing Yes Manufacturing Synthetic biology endeavors to create information processing systems modeled on digital electronics. The use of quorum sensing can help transform an inherently analog molecular signal into a binary response and simultaneously allow the tuning of input response thresholds and signal amplification. This project demonstrates these capabilities through experimentation and modeling. Another candidate for reapplying an electronic engineering technique is the codesign of hardware and software to implement a function. In synthetic biology, codesign might mean implementing a design spec in different expression control regimes and comparing their relative merits. Our work examines the codesign concept by constructing an AND gate in three different design domains. We explore the application of these ideas with an environmental sensor. A unique aspect of our project is the collaborative nature involving five institutions at three locations, which fostered a codesign-like approach using two distinct assembly techniques. Information Processing Arabinose
arsenic
Copper
Mercury
Flourescence
Stimulation of Neighbouring Cells
In vitro Bronze Medalist N/A quorum sensing
stimulus
optimization
Waterloo 2010 Staphiscope: diagnosis of S. aureus through bacterial wiretapping Yes Health and Medicine Superbugs, or antibiotic resistant microorganisms, are microbes that have become resistant to traditional treatments. These types of infections are difficult to diagnose, treat, and eradicate, making the healing process time consuming and resource intensive. The native quorum-sensing unit from S.aureus (the Agr system), will be introduced into a non-pathogenic strain of E.coli. The E.coli will then effectively have the ability to eavesdrop on the activity of the pathogenic organism and emit an indication of the magnitude of the infection in the form of RFP. Using sensitivity tuners the system can be designed such that the response will occur at an exact level, when the size of the population poses a threat to the host. Upon a positive result from a diagnosis, further tests could be done to specify whether MRSA (methicillin-resistant S. aureus) or MSSA (Methicillin-sensitive S. aureus) are present. Health and Medicine Bacterial DNA RFP In vitro Bronze Medalist N/A MRSA
S. aureus
WITS-South Africa 2010 Lactoguard: A commensal whole-cell bionsensor for the diagnosis of sexually transmitted infections Yes Health and Medicine Whole-cell bacterial biosensors have been developed for a range of applications. In this project, the concept of a whole-cell biosensor has been adapted for medical use as a diagnostic for viral infection through engineering a commensal bacterium. Lactobacilli are the predominant commensal organisms in the human vaginal mucosa and are ideally placed to detect the presence of a sexually transmitted infection, such as Human Papillomavirus. A strain of this bacterium has been modified to produce a chromogenic reporter, which is visible to the naked eye, when ‘switched on’ through exposure to the input signal (viral infection). However, in order for this to be clearly visible in vivo, this signal needs to be transmitted throughout the entire bacterial population. Thus, this project focused on a) modifying a Gram-positive bacterium to produce the chromogenic reporter; b) using a heterologous quorum-sensing mechanism to propagate an auto-regulated feedback loop amongst a bacterial population. Health and Medicine Viral RNA Colour In vitro Bronze Medalist N/A HPV
whole-cell biosensor
British Columbia 2009 E.coli Traffic Light Yes Miscellaneous Biosensors have a diverse variety of real-world functions, ranging from measuring blood glucose levels in diabetes patients to assessing environmental contamination of trace toxins. The majority of these sensors are highly specific for a single input, and their outputs often require specialized equipment such as surface plasmon resonance chips. Our project aims to create a biosensor that recognizes a specific target and alters its output fluorescence from green, to yellow, to red as a function of concentration up to critical levels (hence, a biological "traffic light"). Foundational Advance Arabinose Flourescence
GFP
RFP
In vivo Gold Medalist N/A N/A
Cambridge 2009 E.chromi Yes Health and Medicine The Cambridge 2009 iGEM team has created two kits of parts that will facilitate the design and construction of biosensors in the the future. Previous iGEM teams have focused on genetically engineering bacterial biosensors by enabling bacteria to respond to novel inputs, especially biologically significant compounds. There is an unmistakable need to also develop devices that can 1) manipulate input by changing the behaviour of the response of the input-sensitive promoter, and that can 2) report a response using clear, user-friendly outputs. The most popular output is the expression of a fluorescent protein, detectable using fluorescence microscopy. But, what if we could simply see the output with our own eyes? We successfully characterised a set of transcriptional systems for calibrated output - Sensitivity Tuners. We also successfully expressed a spectrum of pigments in E. coli, designing a set of Colour Generators. Environment Arabinose Carotenoides
Colour
Flourescence
GFP
Melanin
mRFP
Violacein
In vivo Gold Medalist
Top 16
Winner of the BioBrick Trophy N/A
Cornell 2009 Cadmium Sensor Yes Environment To create a biosensor dependent on Cd(II) concentration, we decided to engineer the existing metal ion homeostasis system in Bacillus subtilis, in which metal ion transport is tightly regulated. The organism requires trace amounts of metals for normal growth, while high levels interfere with cellular processes. Cd(2+) enters B. subtilis through the manganese ion influx protein MntH. Intracellular Cd(2+) concentration is regulated by several factors, one of which is the CadA efflux protein. CadA is a P-type ATPase that pumps out Cd(2+). Transcription of the cadA gene is regulated by protein CzrA (formerly YozA), a ArsR/SmtB family repressor. CzRA binds and represses the cadA regulatory region and is released when bound by cadmium ions. [7] Environment Cadmium CFP
Flourescence
YFP
In vivo Bronze Medalist N/A 2
sensor
system
DTU Denmark 2009 The Redoxilator Yes Manufacturing In this project we have Designed and constructed a redox sensing device: The Redoxilator Performed extensive mathematical modelling on the operation of the Redoxilator device Written and submitted a novel biobrick assembly standard based on USER fusion that allows the assembly of several biobricks at once Made a program for the design of primers needed for USER fusion online: PHUSER Furthermore we have constructed and submitted four very useful biobricks to the registry. Manufacturing NAD/NADH Flourescence
GFP
In vivo Gold Medalist N/A cerevisiae
Saccharomyces
Gaston Day School 2009 Red Fluorescent Nitrate Detector Yes Environment For our project the Gaston Day School iGEM team decided to not only to attempt to create a biological nitrate detector but also demonstrate how a high school team with limited means similar to our situation could establish an iGEM team and compete in the iGEMs competition. Our local newspaper interviewed Sheran Hussain, our founding member, about our team, the iGEMs competition, and the difficulties we are facing. We have found that, although we do not have the same technology as a university or college, we have the ability to still do many of the experiments that we need to with simple manpower and ingenuity. Our hard work and determination allowed us to complete graduate level work all summer long. Nearly all of the team members hope to continue with the iGEM competition next year, both as incumbent high schoolers and as college freshmen. Environment Nitrate concentration Flourescence
RFP
In vivo N/A N/A N/A
IPOC1-Colombia 2009 no title Yes Environment Different gene parts are being assembled in order to construct a device that is able to detect different salinity levels in the sea. The device is tested against different concentrations of sodium chloride, fluoride, calcium and magnesium. Different parameters, such as reporter fluorescence, DNA concentration, growth of bacterial device will be used to measure the efficacy of the device. Computational modeling will be used in the project to complement the laboratory work. Importance of the project: Colombia borders two oceans, the Atlantic and the Pacific. Environment calcium
Flouride
Magnesium
sodium chloride
bacterial growth
DNA concentration
Flourescence
In vivo N/A N/A N/A
KU Seoul 2009 2009 Integrated Heavy Metal Detection System Yes Environment Our team project is designing synthetic modules for simultaneous detection of multiple heavy metals such as arsenic, zinc, and cadmium in E. coli. The ultimate goal is to build a micromachine sensing and determining of the concentration of heavy metals in a sample solution (e.g. the waste water). In order to design the system, we will employ two fluorescence proteins (GFP and RFP) and aryl acylamidase as signal reporters. Since each heavy metal promoter produces unique fluorescence or color by those reporters, if more than two heavy metals coexist in a solution, the results would be interpreted from the convoluted fluorescence and/or color rather than a single signal detection. The successful construction of the synthetic modules in E. coli can be utilizedin the form of a lyophilized powder, which can be stored in a drug capsule to make it portable. Environment arsenic
Calcium
Zinc
aryl acylamidase
Colour
Flourescence
GFP
RFP
In vivo N/A N/A N/A
Missouri University of Science and Technology 2009 Methanol sensor Yes Miscellaneous The purpose of this research is to use recombinant technology to culture yeast cells capable of determining the concentration of ethanol and using these cells to construct an ethanol sensor. Metabolic pathways exist for the metabolism of methanol and ethanol within some species of the Pichia taxa to include the yeast of our interest, Pichia pastoris. Alcohol oxidase (AO) appears to be the first and major enzyme produced in the methanol metabolic pathway of P. pastoris. However, if both ethanol and methanol are present, P. pastoris will utilize the ethanol before consuming the methanol. Consequently, the AOXI gene will not be expressed to produce the AO enzyme until the ethanol has been consumed. Fusing the AOXI gene promoter with the DNA sequence encoding a fluorescent protein will allow the expression of the AOXI gene to be detected. In supplying the yeast cells with ethanol and methanol simultaneously, the cells will produce the fluorescent protein once the ethanol is utilized. The concentration of ethanol can then be determined by measuring the time before fluorescence is detected. Food and energy Ethanol
Methanol
Flourescence In vivo N/A N/A N/A
MIT 2009 MIT Phycocyanobilibuddies Yes New Application To maximize control over a biological system, it would beneficial to have quick, reversible control over each step in gene expression, from transcription to translation to post-translational processing. Much work has been done to create switchable promoters, toggled by pulses of light, to control rates of transcription for genes of interest. The MIT iGEM team aims to take this concept and apply it to post-translational control, more specifically protein targeting in yeast. Our goal is to make a system in which a pulse of light causes a protein of interest to localize to one part of the cell. When pulsed with another wavelength of light, the protein will diffuse. In this way, a user can easily control both localization and delocalization of a protein of interest. Our system takes advantage of the machinery used by plants and algae to respond to changing light conditions. Small pigmented proteins called phytochromes allow plants and algae to sense the amount and quality of the light available to them and to adjust rates of transcription accordingly. They are composed of a small pigment called a chromophore covalently bonded to a polypeptide. PhyB, our phytochrome of interest, binds to a chromophore called phycocyanobilin, or PCB. In red light, PhyB changes conformation into it’s active form and can bind to a transcription factor called PIF3. A pulse of far-red light returns the phytochrome to its inactive state. This mechanism provides the foundation of a a fast, reversible switch. We have two main goals for our project. Our first goal is to be able to engineer yeast to produce the chromophore PCB endogenously. Right now, PCB has to be extracted from plants or cyanobacteria or from strains of E. coli that have been designed to produce PCB. We would like the switch to be self-contained in the strain we engineer, so we would like to engineer a strain of yeast to produce PCB. Our second goal is to engineer a system that adopts the PhyB-PIF3 switch to control protein localization within the cell. We plan to have either PhyB or PIF3 constitutively anchored to the target location (e.g. mitochondrial membrane, nuclear membrane, vacuole etc). The other will then be bound to a protein of interest and diffuse within the cell. When pulsed with red light, the PIF3 and PhyB will bind, causing the protein of interest to localize to the target. Such a system would be useful in creating a reversible switch for many purposes. For example, one could synchronize a culture of cells in one part of the cell cycle without having to deal with temperature sensitive mutants or adding chemicals externally to arrest the cell cycle. The system would also be useful to study the kinetics of localization and delocalization, as well as provide an easy on-off switch for expression of essential genes. Light switchable transcriptional regulation has shown to be an effective way of increasing or decreasing gene expression quickly. By applying the concept of light switching to post-translational control as well, we aim to have greater control not only over gene expression, but also how the protein functions within the cell. Foundational Advance light of different wave lenghts protein diffusion
protein localization
In vivo Bronze Medalist N/A PIF3
BCP
PhyB
NTU-Singapore 2009 pLaqUe Out! Yes Health and Medicine Atherosclerosis is a growing healthcare concern, affecting millions of people worldwide every year. Conventional medical regimens only treat the symptoms, but do not provide a means for prevention or cure! The NTU iGEM ’09 team is proud to announce that we are working on a proposed alternative treatment for this disease. This year, we will be working on an in vivo approach to visualize and degrade atherosclerotic plaque. Our system, pLaqUe Out!, ideally in a T-helper cell chassis, can be introduced into the bloodstream. It will be activated by a symptom that is typical of plaque buildup. Upon activation, our system will release a cholesterol degrading enzyme, a novel reporter protein and a vasodilator. The sensing construct triggers the system in response to falling nitric oxide concentrations. The cholesterol degrading enzyme breaks down the plaque. The reporter protein, with its unique fluorescent property, allows the plaque site to be visualized in vivo. Finally, the vasodilator will simultaneously dilate the blood vessels for better flow, as well as switch off the extended activity of our system. Health and Medicine NO biliverdin
IFP
infrared
In vivo Gold Medalist N/A Atherosclerosis
NYMU-Taipei 2009 Viro Catcher Yes Health and Medicine The title of our project: ViroCatcher The Fact: Although traditional medical treatments for viral diseases usually have a high specificity, the treatments will likely fail to cure diseases once viruses mutate. Our Motivation: Is there any chance to create an universal solution to fight against viral diseases? Our Strategy: Fight inconsistency with consistency. Counter changing viruses with specific binding. Our Objective: Use engineered bacteria which are safe for the bloodstream to bind and remove many kinds of viruses. Our Method: Design bacteria that can catch viruses using constant binding regions between viruses and viral receptors/specific anti-viral antibodies. Health and Medicine Binding of HIV to receptor
Binding of influenza virus to receptor
Binding of other viruses to receptor
Not specified In vivo Bronze Medalist N/A viruses
sense
+
detect
eliminate
PKU Beijing 2009 Conditioned Reflex Mimicking in E.coli Yes Miscellaneous We are engineering our E. coli cells to process the correlation information of two enviornmental signal, similar to the process of conditioning in higher orgamisms. We have constructed and tested a series of AND gates which can sense the two signals: the conditioned and unconditioned stimuli. With the presence of both signals, the AND gate outputs a repressor protein and then changes the state of the bistable switch, which acts as a memory module. In this way, our E. coli cells can convert the information about the concurrence of the two signals into its memory. After the memory module is switched and given the "conditioned stimulus", the E. coli cells will pass the information to the reporter module and thus exhibit the "conditioned response." Information Processing Acyl Homoserine Lactones
Arabinose
aTc
IPTG
Salicylate
Flourescence
GFP
mRFP
In vivo Gold Medalist N/A gates
Logic
Sheffield 2009 SWITCHED ON !!! Yes Environment By modifying E.coli so that it can use a phytochrome- with a light receptor- from cyanobacteria as a trigger of protein generation. This pathway is controlled by a certain wavelength of red light, acting as a system switch for lacZ production. LacZ can react with substrate X-gal and form a blue precipitate as a reporter. However, other reporter genes can be attached to the lacZ gene, so different reporters can be expressed. From the fact that this mechanism is sensitive to a certain wavelength of light, we hope to create a system that can be sensitive to various wavelengths and hence triggering different protein generation. Through this the E.coli can become a wavelength sensor; a different wavelength can trigger a different production of protein, for example various types of fluorescent protein, giving a different a colour-scaled indication of the wavelength of the environment around the E.coli. Our aim is to design an E.coli system that is sensitive to multiple wavelengths of light and therefore produce a colour indication of the specific wavelength it is exposed to. Foundational Advance light Colour
EGFP
Flourescence
LacZ
In vivo N/A N/A N/A
Stanford 2009 Immuni-T. coli Yes Health and Medicine Inflammatory Bowel Disease is an autoimmune disease that results in inflammation of the colon and small intestine. IBD is a huge problem in developed countries, vastly growing with no effective therapy in sight. This disease is caused by an imbalance of immune T-cells, Th17 and T regulatory, which control inflammation and immunosuppression responses respectively. We propose a novel mechanism using synthetic biology that aims to regulate this balance in vivo. This involves a two-part device: one that regulates inflammation and the other immunosuppression. We cloned a device that recognizes superoxide producers, a byproduct of inflammation and Th17 proliferation, to produce retinoic acid, which blocks the further differentiation of Th17 cells. This device has been characterized, is well behaved and capable of recognizing superoxides, like paraquat, at optimum levels of 40 to 80 uM without growth inhibition. To control immunosuppression, we cloned and mutated the trp operon so that it recognizes 5-Methyl tryptophan, a target substrate of an enzyme involved in Treg immunosuppression, and designed a potential IL-6 excretion device to regulate Treg proliferation. The behavior of this novel tryptophan sensor has been studied by our group through the development of a mathematical model. Our results suggest that our construct has potential applications as a diagnostic or therapeutic tool for post-operative Crohn's patients. Health and Medicine 5-Methyl tryptophan
nitric oxide (NO)
Flourescence
GFP
Interleukin 6 (IL 6) production
retinoic acid (RA) production
In vivo Gold Medalist Best Health or Medicine Project, Finale Inflammatory Bowel Disease
SoxR gene
retinoic acid
2 device system
SoxS promoter
Tianjin 2009 no title Yes Environment Taking use of Yeast Gal4 system which is aimed at Microcystins(MCs, induce liver cancer) detection in waters. Why we design a detector? The threat of MCs in seas, rivers, lakes and Reservoirs has become more and more severe worldwide due to eutrophication in pulltion waters. As we know, there are far more nitrogen and Phosphor elements in polluted waters, which is called eutrophication, resulting in algal blooms and red tides. Fishes, prowns and almost all the living creatures in these waters are killed by the high concentration of MCs that are produced by algea. It is also a severe threat to drinking water and water in daily use, for MCs induce liver cancer. What's more, the existed detecting technologies are complicated, expensive, time-consuming and require an expert to handle the devices. Environment Microcystins Colour
LacZ
In vivo Silver Medalist N/A GSH
PP1
Yeast Two-hybrid system
UAB-Barcelona 2009 no title Yes Environment We are trying to develop a biosensor which can detect chloroform and other trihalomethanes in water. The idea is based on the ability of a recombinant Nitrosomonas europaea strain to detect those contaminants by expressing the exogenous gen of green fluorescent protein (gfp). It is thought that the capacity to detect trihalomethanes is due to ammonia monooxigenase (AMO), the enzyme responsible for oxidizing ammonia to nitrite. It seems that AMO recognizes chloroform nonspecifically and oxidizes it to phosgene, that is somehow able to activate mbla and clpb promoters and start the expression of GFP. Our aim is to transform an Escherichia coli K-12 strain with a plasmid containing the sequence that codifies for AMO and other plasmid containing mbla or clpb promoters and gfp, in order to achieve an E. coli strain which could detect chloroform and express GFP. Environment chloroform
trihalomethanes
Flourescence
GFP
In vivo N/A N/A N/A
UCL London 2009 The Traffic Light Stress Sensor Yes Miscellaneous Our project “Stress Light” will produce a series of synthetic biosensor devises, which can improve on the traditional sensors in bio-processing; by using green fluorescent protein (GFP), yellow fluorescent protein (YFP), cyan fluorescent protein (CFP) and red fluorescent protein (RFP) expression as indicators of different stresses for e.coli bacteria during cultivation. Our product and system is called "The Traffic Light Stress Sensor”. It is constructed to express fluorescent proteins of different colors in response to different stimuli which are inhibiting growth or harming production. Description We aim to build a sensor that can detect shear stress and low oxygen levels. We believe these two stresses are critical in a bioprocessing environment. We are applying e.coli’s native or modified promoters for DegP, Spy and NarK in order to induce transcription. Ideally the cells responses to stressed conditions should be sufficiently accurate, reliable and rapid for the stresses to be detected and mitigated in a timely manner.Objective Besides making bioprocesses easier to monitor, analyse and hence optimize, we believe that well functioning biobricks responding accurately to processing conditions (e.g. oxygen levels) can have a broad set of general applications; e.g. to make more efficient induction systems or be used to develop self inducible or increasingly self regulated bioprocesses. Foundational Advance acetate production/concentration
cell growth phase
oxygen level
shear stress
CFP
Flourescence
GFP
RFP
YFP
In vivo Silver Medalist N/A N/A
Alberta NINT 2008 Logi-Coli Yes Miscellaneous Two major hurdles facing the development of complex genetic logic circuits are device connectibility and device extensibility. Connectibility refers to the ability to connect the output of one device to the input of another device, while extensibility refers to the dual abilities to rationally design new devices and to combine multiple devices in one organism. Our project uses terminator/attenuator (T/A) hairpin sequences (gates) to control transcription and anti-sense RNA as input/output signals to/from the devices. We call this approach Terminator/Attenuator anti-sense Logic (T/AasL – pronounced “tossle”). It solves the connectibility problems of common protein-based approaches because the anti-sense output of one device is used to disrupt formation of T/A hairpin structures of downstream devices, thus activating them. In addition, because RNA secondary structures can be rationally designed (using our m-fold derived analysis program) we can readily construct a large family of devices with minimal cross-talk for inclusion in a single cell. N/A Not specified Not specified In vivo Bronze Medalist N/A N/A
Bay Area RSI 2008 Cardiac Cells Yes Health and Medicine Every year over 1.2 million people suffer myocardial infarction (MI). The resulting heart damage requires new approaches for effective repair. Stem cell therapies provide hope. However none of the stem cell therapies currently in clinical trials addresses the need for efficient stem cell targeting to cardiac tissue or the need to replace efficiently dead tissue with new cardiomyocytes. To address these problems, we have built several genetic circuits that work sequentially to repair the heart. First, we have built an inducible differentiation circuit that closely resembles the endogenous differentiation pathway, to program cells to become cardiomyocytes. Second, we have built circuits that use the extracellular domains of chimeric proteins to target cells to damaged cardiac tissue. Upon binding, novel receptor-coupled intein-mediated signaling domains activate effector genes that then aid in integration, inhibition of cell death, and the alteration of the tissue microenvironment. We have shown that both the targeting and signal transduction circuits work in cell culture models of MI. N/A CRP/FCGamma Receptor
Dammaged Tissue
Colour
Flourescence
In vivo N/A N/A N/A
BCCs Bristol 2008 Bacto-Builders Yes Manufacturing Assembling particles at microscopic scales into desired patterns or structures is currently either extremely difficult, or in most cases impossible. Some structures have been shown to naturally self-assemble under specific conditions [1], but this is limited to a very small subset of all those possible. Other techniques, such as the use of optical tweezers [2], although promising, are human-intensive, a possible disadvantage in certain applications where structures need to change dynamically in response to certain conditions. With this in mind the BCCS iGEM 2008 project aims at developing miniature “Bacto-Builders” to help. All construction projects require the manipulation of varying size components, many much greater than any individual. To make this possible, teams of individuals work together with a common outcome in mind. In aim of transferring this behaviour to our “Bacto-Builders”, we will investigate the possibility of utilising large numbers of E. coli to perform a task too great for any individual cell. Specifically, this will involve the physical movement of particles through direct contact with a swarm of bacteria working together in a co-ordinated manner. The ultimate goal is to make collective behaviour emerge by bacteria adhering to a set of simple rules so that particles are assembled according to some desired pattern. Furthermore, patterns or structures could be evolved in real time with bacteria adapting to new dynamic requirements or autonomously forming new ones. To create these structures, each bacterium searches randomly through an environment to find a suitable particle. On contact, it attempts to push the particle towards a goal (chemoattractant gradient). It also sends out a short range quorum signal to tell nearby bacteria, in a position to help with particle movement, that a particle is in the vicinity and therefore to move towards the goal chemoattractant. By altering the pattern of the chemoattractant gradient, it will be possible to place particles in a specific configuration. For the longer term, we envisage different sets of bacteria performing complementary tasks. For example, one group, the ’architects’, may have the job of finding the locations that particles need to be placed. Once found, they emit a chemoattractant signal that the second group, the ’workmen’ (which could be engineered in order to exert more force than normal), can use to move the particles to the necessary location. This could then be extended to allow bacteria to set locations that change over time leading to structures that evolve either due to a defined genetic program, or environmental cues, whereby bacteria would assimilate necessary environmental information, and then decide on the best course of action. N/A chemical
Quorum sensing
Motility In vivo Bronze Medalist Best Model N/A
BeijingNormal 2008 Intelligent PCB Detector and Degrader Yes Environment We are aiming to create some magic intelligent bacteria to track and ‘eat’ pollutants PCBs (Polychlorinated Biphenyl) and dioxins efficiently, based on the methods of synthetic biology.Polychlorinated biphenyls (PCBs) are a family of compounds produced commercially by the direct chlorination of biphenyl using ferric chloride and/or iodine as the ctalyst.The total amount of PCBs produced in the world is estimated 1.2 million tons.Because PCBs have been released into the environment in many countries over decades, these compounds have become serious and global environmental contaminants.PCBs tend to accumulate in biota owing to their lypophilic property. The biphenyl molecule is made up of two connected rings of six carbon atoms each, and a PCB is any molecule having multiple chlorines attached to the biphenyl nucleus. Two distinct classes of bacteria have now been identified that biodegrade PCBs by different mechanisms, including aerobic bacteria which live in oxygenated environments and anaerobic bacteria which live in oxygen free environments such as aquatic sediments. The aerobes attack PCBs oxidatively , breaking open the carbon ring and destroying the compounds. Anaerobes, on the other hand, leave the biphenyl rings intact while removing the chlorines. Polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) were introduced into the biosphere on a large scale as by-products from the manufacture of chlorinated phenols and the incineration of wastes. Due to their high toxicity they have been the subject of great public and scientific scrutiny. The evidence in the literature suggests that PCDD/F compounds are subject to biodegradation in the environment as part of the natural chlorine cycle. Lower chlorinated dioxins can be degraded by aerobic bacteria from the genera of Sphingomonas, Pseudomonas and Burkholderia.However, higher chlorinated dioxins requires anaerobic degradation process. Organic pollutants such as PCB and dioxins, produced in human beings activities in the last century, are toxic and carcinogenic which are able to promulgate widely and accumulate to a high level of concentration by food chain. Due to their inherent thermal and chemical stability, it is commonly considered as indestructible under normal incineration or burial. Nonetheless, by endowing some bacteria ability of utilizing such molecules as carbon source, cooperative evolution makes all possible! Enzymes assembled from related degradation pathways into our host strain serve as the function part. We introduce popular components involved in chemotaxis, quorum-sensing to regulatory parts, sense the environment signal, respond to move, accelerate growing and produce related degradation enzymes. After the cleaning work being finished, bacteria will return to the normal state. Taking the condition of our lab into account, we decide just deal with the aerobic degradation path way. And do some work on increasing the degradation effeciency. N/A Polychlorobiphenyls Activation of degradation In vivo N/A N/A environmental
PCB
beijing
asia
contaminant
degrade
in vivo
2008
detector
degradation
environment
polychlorinated biphenyl
Bologna 2008 EPROM Yes Miscellaneous The specific goal of our project was to design a bacterial reprogrammable memory, i.e. colonies of genetically engineered E. coli immobilized in solid medium where they work as an array of binary memory cells. To engineer the bacteria we designed a modular genetic Flip-Flop composed of two parts (Figure 1): a binary memory block and an induction block, sensitive to UVc radiation. UVc has been chosen to have a fine spatial selectivity in programming the memory cells, whereas IPTG should be used to reset the entire memory. The molecular circuit can switch between two different stable states (LacI-ON and TetR-ON), driven by the external stimuli UVc and IPTG. LacI-ON represents the stable state in which LacI gene is active and LacI protein represses the TetR gene expression, with a positive feedback. Therefore, the LacI-ON state coincides with the TetR-OFF condition. On the contrary, the TetR-ON represents the state with the TetR gene active and the LacI gene silenced (LacI-OFF). Owing to the coexistence of two stable states (bistability), this circuit is capable of serving as a binary memory. We denominated it genetic Flip-Flop since it works as a SR Latch: LacI state is the q output and TetR state is the output. Uvc is the set signal and IPTG is the reset signal. Indeed, IPTG stimulation inhibits LacI repressor, thus can cause the transition from the LacI-ON state to the TetR-ON. UVc radiation, inactivating LexA repressor through the SOS response [Friedberg et al. 1995] can cause the opposite transition from LacI-ON to TetR-ON. The core elements of this epigenetic memory are the two mutually regulated promoters (see Figure 1), each designed as a constitutive promoter flanking an indipendent operator site. In this way, the promoter transcriptional strength and the repressor binding affinity can be independently fixed. Mathematical model analysis and computer simulations were used to obtain a rational design of the regulated promoters. By the model we found the analytic relationships to quote the regulated promoter in terms of transcriptional strength and sensitivity to the repressor and we established such a relevant circuit properties as the bistability and the dynamical response to inputs. N/A Ultraviolet Activation of gene expression In vivo Bronze Medalist Best Experimental Measurement N/A
Brown University 2008 Toxipop Yes Environment "Brown iGEM's 2008 Team focused on designing a novel electrical reporting system that could be used as a method of toxin detection, particularly in third-world countries, where water pollution is a prevalent problem.Through the use of a lysis gene cassette bound to an inducible promoter in E.coli bacteria, the biosensor will have the ability to detect the presence of a certain substance (for example a water toxin)and report that information back via a change in the conductance of the bacterial solution. Through the use of minimal biological machinery and a versatile construct, our system can provide for a sensitive and compact system for substance analysis." N/A Not specified
Toxin
Electrical Resistivity
Electrochemical
In vivo Bronze Medalist Best Environmental Project, Finals N/A
Calgary Wetware 2008 Quorum Coupled Bacteriocin Release Yes Health and Medicine Autoinducer-1 (AI-1) from Vibrio fischeri and Autoinducer-2 (AI-2) from Vibrio harveyi put into two populations of E. coli (termed Bad guy #1 and Bad guy #2, as per their respective Autoinducer). third population of E. coli (termed Champion cell) acts as a biosensor by receiving these signal inputs and subsequently initiating transcription of specific E. coli-targeted bacteriocins (i.e. colicins). The presence of AI-1 induces the Champion to produce a colicin to which Bad guy #1 is susceptible, but to which Bad guy #2 is resistant, and vice-versa for AI-2. An additional aspect is the ability of the Champion cell to report the presence of each specific Bad guy by producing a specific fluorescent protein (i.e. either green or red fluorescent protein) in tandem with the specific colicin as determined by the presence of either AI-1 or AI-2 N/A Pathogen
Quorum sensing
Bacteriocins In vivo Silver Medalist N/A N/A
Caltech 2008 Engineering multi-functional probiotic bacteria Yes Health and Medicine The human gut houses a diverse collection of microorganisms, with important implications for the health and welfare of the host. We aim to engineer a member of this microbial community to provide innovative medical treatments. Our work focuses on four main areas: (1) pathogen defense either by expression of pathogen-specific bacteriophage or by targeted bursts of reactive oxygen species; (2) prevention of birth defects by folate over-expression and delivery; (3) treatment of lactose intolerance by cleaving lactose to allow absorption in the large intestine; and (4) regulation of these three treatment functions to produce renewable subpopulations specialized for each function. Our research demonstrates that synthetic biology techniques can be used to modify naturally occurring microbial communities for applications in biomedicine and biotechnology. N/A Quorum sensing Oxidative Bursts In vivo Gold Medalist 2nd Runner Up
Finalist
Winner of Synthetic Standards
N/A
Cambridge 2008 iBrain Yes Miscellaneous "In order to simulate neural activity in bacteria, a mechanism resembling a synapse is necessary. At the synapse, neurotransmitter molecules are released from the presynaptic plasma membrane. The neurotransmitter diffuses through the synaptic cleft and binds to chemical receptor molecules on the membrane of the postsynaptic cell. These receptors cause ion channels to open so that ions rush out, changing the transmembrane potential. Attempting to mimic this in a prokaryotic system is particularly attractive as, in a more general sense, it provides an interface between chemical or biological and electrical systems.Using the amino acid glutamate as our 'neurotransmitter', we have successfully demonstrated a voltage response in bacterial cells." N/A Glutamate Change in voltage
Electrochemical
In vivo Bronze Medalist N/A N/A
Chiba 2008 E.coli Time Manager Yes Miscellaneous We are constructing delay switches to control/preset the timing of target gene expression. Our project uses two classes of bacteria: senders and receivers. Senders produce signaling molecules, and receivers are activated only after a particular concentration of this molecule is reached. The combinatorial use of senders/receivers allows us to make a ‘switching consortium’ which activates different genes at the preset times.As signaling molecules, we utilize molecules associated with Quorum sensing, a phenomenon that allows bacteria to communicate with each other. Although different quorum sensing species have slightly different signaling molecules, these molecules are not completely specific to their hosts and cross-species reactivity is observed (1),(2). Communication using non-endogenous molecules is less sensitive than the original, and requires a higher signal concentration to take effect. This reduced sensitivity results in the slower activation of receivers, thus creating a system in which different receivers are activated after different amounts of time following signaling molecule release. N/A Quorum sensing Time measurement In vivo Silver Medalist N/A lux
asia
in vivo
2008
AHL
time
clock
quorum
chiba
Davidson-Missouri Western 2008 E.nigma/Vis-a-brick Yes Miscellaneous Our team designed, modeled, and constructed a bacterial computer that uses XOR logic to compute a cryptographic hash function. Hash functions are used to authenticate the integrity of a document by computing its digital fingerprint. Our bacterial computers are designed to recognize the presence or absence of two chemical signals via intercellular communication. Mathematical modeling of these computers has shown that our hash functions are difficult to corrupt. We designed and built a number of new parts, and improved and gained experience on existing parts. We also produced a graphical interface for exploring the Registry of Standard Biological Parts called Viz-A-Brick, and other web-based tools to improve the construction of new parts with BioBrick ends. N/A Quorum sensing Not specified In vivo Gold Medalist N/A relative
EPF-Lausanne 2008 Genetic Network Generating Spatial Patterns Through Cell-Cell Communication Yes Miscellaneous Biological systems are unique in their ability to combine information and energy to generate complex entities. Genetically encoded networks drive many of these patterning processes. Furthermore, developmental studies have highlighted the importance of gradient formation and cell-cell communication for the generation of cellular patterns in the early stages of life. It has been shown that simple networks can form both static and dynamic patterns. Nonetheless, a system whose pattern formation is dependent on combinations of multiple signals has yet to be demonstrated. Here we address this question by designing a network, involving two different quorum-sensing based signaling mechanisms. Upon introduction in E.coli, the system can sense the relative amounts of two input molecules. Using a pre-define set of rules which was selected on its ability to generate spatial patterns, the cell can then express its final state by emitting red or green fluorescence and transmit its state to its neighbors. N/A Quorum sensing Colour
Flourescence
In vivo Bronze Medalist N/A relative
differential
ESBS-Strasbourg 2008 Yeast Cell Cycle Measurement Yes Miscellaneous Our project is about establishing a regulatory network over several cell generations in budding yeast (Saccharomyces cerevisiae). We want to construct a toggle switch that is triggered by cell cycle dependent factors. This would result in a binary expression pattern like for example GFP expression in every other cell cycle (0-1-0-1). There shall be the possibility to easily extend the system by adding further "bits" of similar construction (e.g. for the second bit the pattern 0-0-1-1). The resulting device would be the basis for a binary cell division counter. N/A Not specified Colour
Flourescence
In vivo Bronze Medalist N/A N/A
Freiburg 2008 Modular Synthetic Receptor System: Yes Miscellaneous Signaling through membranes is a characteristic of life. Transmembrane proteins control proliferation, differentiation, and cellular response and are key for the formation of multicellular organisms. Controlling such proteins enables modifying cellular behavior and ultimately programming cells at will. The complex rules for transmembrane signaling often require engagement of several proteins in a fine-tuned spatial and temporal manner. To tap possibilities of transmembrane programming, the Freiburg 2008 iGEM team provides an extensible system comprising an external framework with spatial resolution, a concept for modifying natural receptors, and a modular set of fusion-Biobricks for the construction of synthetic receptors. Spatial resolution in the nanometer scale is provided by DNA-Origami modified with distinct patterns and combinations of ligands. Receptors are decoupled from their natural ligands by fusion with artificial binding domains. The Biobrick collection contains signal sequences, binding domains, transmembrane domains, and effector domains featuring split enzymes and split fluorescent proteins for immediate readout. N/A Haptens
Not specified
Scaffolded Target
Colour
Flourescence
In vivo Gold Medalist 1st Runner Up
Finalist
Winner of the PoPS Prize
N/A
Groningen 2008 Conway’s Game of Life in real life Yes Miscellaneous Conway’s Game of Life is a simple cellular automaton famous for generating complex ‘life-like’ patterns. The goal of this project is to explore the possibility of implementing cellular automata, particularly the Game of Life, as a regular spatial arrangement of bacteria. Communicating the number of neighbors is implemented using the well-known Homoserine Lactone (HSL) quorum sensing system. A novel component is the circuit implementing the automaton’s ruleset, to determine the state to switch to upon detecting ‘too few’, ‘enough’ or ‘too many’ neighbors. This ‘interval switch’ was designed and implemented by altering the binding site affinity of the signal molecule complexes to correspond to the levels of HSL coming from the neighbors. Finally, the ON state of the cells is indicated by GFP production and production of new HSL signals, and the OFF state by their absence. The system was implemented partially in vivo and we have developed in silico models. N/A Quorum sensing Colour
Flourescence
In vivo Gold Medalist N/A N/A
Harvard 2008 Bactricity Yes Energy "Our project sought to combine the detecting capabilities of bacteria with the speed and ubiquity of electricity by creating an inducible system in Shewanella oneidensis MR-1 with an electrical output, allowing for the direct integration of this biosensor with electrical circuits via microbial fuel cells." N/A LacI induction
Temperature
Electrochemical In vivo Gold Medalist Best Food or Energy Project
Finalist
N/A
Hawaii 2008 Cyanobacterial toolkit Yes Environment "Cyanobacteria are photosynthetic bacteria that can convert carbon dioxide to sugars. The main goal of the Hawaii team is to make a ""toolkit"" for cyanobacteria, which hold promise as producers of biofuels and other bioproducts. We constructed a number of tools to more easily and effectively engineer cyanobacteria, including1) a BioBrick switch that turns on a downstream gene when nitrate is added,  2) a BioBrick that mediates protein export from the cell into the surrounding medium and 3) a naturally occurring shuttle vector to BioBrick format to allow easy transfer of existing and new BioBricks into cyanobacteria. Our toolkit was designed to allow controlled production and recovery of bioproducts. Additionally, our vector has the potential to transform other gram negative bacteria and possibly even plants via Agrobacterium. " N/A Nitrate Activation of gene expression In vivo Bronze Medalist Best Rookie Team N/A
Heidelberg 2008 Bacterial killers from a genetic construction kit Yes Health and Medicine Ecolicence to kill: Engineering E.coli for targeting pathogenic microorganisms Pathogenic microorganisms represent a major challenge to both medicine and industry. Microbial communities known as biofilms prove to be particularly resistant to conventional therapies [1] and demonstrate the need for alternative methods to fight bacterial growth. The formation of biofilms, as well as other processes such as virulence, antibiotic production, and sporulation, are regulated by communication circuits that depend on small signalling molecules called autoinducers. Our aim is to exploit this communication mechanism by engineering synthetic bacteria that are able to target potentially harmful autoinducer-secreting species and kill them. Working with E. coli as a model system, we plan to engineer separate “killer” and “prey” cells, and divide our project into two complementary modules. The “sensing module” comprises the modification of E. coli’s chemotaxis [2] system to make killer cells move towards prey cells. This requires the engineering of a “sensing module” which propagates a prey-specific stimulus to the downstream signalling cascades, prompting the cells to swim towards the gradient of such a stimulus. The directed swimming stops only in the region where the stimulus is maximal, i.e. in the vicinity of the prey. The “killing module” ensures that once in the vicinity of the prey, a bacteriocidal mechanism is activated. Computer models will show how both modules behave in concert and probe the efficiency of the system in defined spatial environments. Future directions, which are beyond the scope of this project, include the modification of the sensory and killing modules, adjusting the range of targets to real pathogens, but also other organisms, specific cell types or even cancer cells. N/A Pathogen Bacteriocins
Phage
In vivo Gold Medalist Best Human Practices Advance
Best Poster
Best Presentation
N/A
iHKU 2008 Formation of new patterns by programming cell motility Yes Miscellaneous The ability of living organisms to form patterns is an untapped resource for synthetic biology. The HKU iGEM2008 team aims to generate unique patterns by rewiring the genetic circuitry controlling cell motility. Specifically, E. coli cells are programmed to autonomously regulate their movement by sensing local cell density. Interesting patterns are formed by two types of newly engineered cells. The low-density mover cells spread outwards and spontaneously form a distinctive ring of low cell density surrounded by rings of high cell density whilst the high-density mover cells form a Mt.Fuji-like structure. Moreover, we build a theoretical model that satisfactorily fits our current experimental data, and also predicts some parameters which may significantly affect the ring formation. The study of this self-organized spatial distribution of cells helps us to understand principles underlying the formation of natural biological patterns, and synthetic non-natural patterns have various potential applied uses. N/A Quorum sensing Motility In vivo Bronze Medalist N/A pattern
AHL
iHKU
quorum
asia
2008
motility
Illinois 2008 Pathogen Detection Yes Health and Medicine The unifying motivation behind our research this year is the creation of novel diagnostic tools for medicine. To this end, we are conducting three parallel research projects to create cell-based biosensors. We are currently engineering a bimolecular fluorescence system in which two halves of a fluorescent protein, each fused to an antigenic epitope, will bind to the two sites on an antibody in human serum to cause a detectable fluorescent signal when antibodies against this specific antigen are present. These proteins can be produced in bulk through a bacterial expression system. We are also pursuing similar diagnostic objectives using a eukaryotic system; we are designing strains of yeast able to respond specifically to immunogenic epitopes or antibodies, and activate a fluorometric or enzymatic response accordingly. We are fusing antibodies against immunological targets to cell surface receptors of transcriptional signaling pathways, which would become activated only in the presence of these pathogens. N/A Pathogen Activation of gene expression
Colour
Flourescence
In vivo/in vitro Bronze Medalist N/A N/A
Imperial College 2008 Biofabricator subtilis Yes Manufacturing For the 2008 iGEM competition, the Imperial College Team aims to develop a genetically-engineered Biofabricator, using the Gram-positive bacterium Bacillus subtilis as our chassis. Our Biofabricator aims to produce self-assembling biomaterials in specified 3D shapes, using light as the trigger. N/A light Activation of gene expression
Motility
In vivo Gold Medalist Best Manufacturing Project
Best New BioBrick, Natural
N/A
Johns Hopkins 2008 S. cerevisiae mating type elucidation Yes Miscellaneous "As our inaugural project, we set out to simplify one of the somewhat belaboring tasks in the field of molecular biology: S. cerevisiae mating type elucidation. Baker’s yeast, S. cerevisiae, has become an invaluable eukaryotic model for molecular biology research for many reasons. One, it utilizes many proteins and biological pathways homologous to those in humans. Consequently, investigating these molecules and systems in yeast has provided unparalleled insight into the genetics of humans. Two, because yeast is unicellular and therefore grows fast, it can be studied more readily than many other organisms, especially higher eukaryotes. Another useful characteristic of yeast is its ability to exist in populations of different ploidy, either diploid or haploid. The process in which ploidy arises is governed by the yeast mating pathway, which is well studied. A haploid yeast cell is either mating type ‘a’ (MATa) or mating type ‘α’ (MATα). In the elucidation of biochemical and genetic processes in yeast, many times it is necessary to initiate sporulation of diploid yeast cells. After sporulation occurs, there are four haploid cells; two MATa and two MAT α. To continue analysis, differentiating between the haploid cells is often crucial, and the necessary assay to do this can take 2 to 3 days. We propose to cut this time to a matter of seconds by constructing a plasmid with fluorescent markers that preferentially activate depending on the mating type. If the cell is MATa, one fluorescent protein is produced. If the cell is MATα, another fluorescent protein is produced. Simply shining a UV lamp over the cells will reveal the mating type, allowing for the cells to be easily separated." N/A MAT(alpha) or MATa Colour
Flourescence
In vivo Bronze Medalist N/A N/A
KULeuven 2008 Dr. Coli Yes Health and Medicine Our team’s project is Dr. Coli, an E. coli bacterium that produces a drug when and where it is needed in the human body. It does this in an intelligent way, such that the drug production meets the individual patient’s needs. And when the patient is cured, Dr. Coli eliminates itself from the body. To achieve this goal we divided our project into several subsystems. A detailed description about every subsystem can be found by clicking on one of the following pictograms. N/A light Colour
Flourescence
In vivo Gold Medalist N/A N/A
LCG-UNAM-Mexico 2008 Singing bacteria Yes Miscellaneous The aim of this project is to make bacteria sing, and it will be done by modifying the extracellular medium's resistivity through the modulation of the RcnA (E. coli's natural efflux pump) which will in turn change the concentration of nickel outside the cell. By doing this we expect to gain insight into a fundamental aspect of ecological dynamics which is currently not well understood. On the other hand, we expect to show that measuring changes in resistivity is an effective way to determine the activity of the efflux pump, and that this can become an efficient indicator of real time transcription for in vivo experiments. To achieve this, we designed a system where rcnA is under the regulation of the lambda repressor CI which itself is under the regulation of Vibrio fisheri’s quorum sensing core components: LuxR and AHL. The former is constitutively produced and the latter is our input signal. Further regulation of the system is achieved by constitutively synthesizing AiiA, which degrades AHL, and by RcnR, RcnA's natural repressor which is inactivated in the presence of nickel. All the protein components of the system are encoded in two devices: the first one contains the efflux pump, and the second one the regulatory cascade. The reason for this partitioning is that in this way RcnA can be integrated with any desired regulatory upstream signal. Once the system is built and implemented on E. coli, we will measure the medium's resistivity on a real time basis through a set of copper electrodes connected to a multimeter. The monitoring device will be connected to a computer which will filter the noise in the signal and return a sound depending on the resistivity N/A Quorum sensing Electrical Resistivity
Electrochemical
In vivo Bronze Medalist N/A N/A
Melbourne 2008 Binary and linear clock Yes Miscellaneous We want to build a biological clock that can count up when it is "ticked" by input light pulse signals. As the signal "ticks" the clock, the clock changes color and observer can use the color or combination of colors to tell what "time" it is.There are two types of clocks proposed by our team.The first type is a Binary Clock. In the Binary Clock, there are identical units (in fact not totally identical but almost) which are connected in series to make the entire clock. We call each unit a bit-unit. Each bit-unit can be turned on and off by its input signal and give its output as the input signal for the next bit in the series. So for example Bit1 can have 2 states ON or OFF, Bit1's output is the input for Bit2 to turn Bit2 ON and OFF. So with 2 bit-units, there are totally for states and these 4 states happen in a sequential order 00 -> 01 -> 02 -> 03, because Bit2's input is Bit1's output. If we extend to 3 bit-units, the number of possible states will grow exponentially to 8.Each bit-unit is said to be modular because, apart from input receptor and output molecule, the internal machinery are identical.We also proposed a Linear Clock. The linear model is similar to and simpler than the Binary model. The difference is that each bit-unit is turned ON only once and once it is turned OFF by the next bit-unit, it will stay OFF forever. So you can imagine this system as a string of light globes, the light jumps from one globe to the next and people can read the time by just looking at which globe is on. This model is also highly modular and the internal machinery is considerably less complex than the binary system.The ultimate goal of these systems is to construct a biological production pipeline of which the systems can keep track on what stage it is and decide what reagents to release for the next step. N/A light Colour
Flourescence
Time measurement
In vivo Bronze Medalist N/A time
clock
asia
linear
binary
melbourne
2008
color
METU Turkey 2008 Light controlled heavy metal carrying E. coli machine Yes Environment Light controlled heavy metal carrying E. coli machine Heavy metals are natural components of the Earth's crust. They cannot be degraded or destroyed. To a small extent they enter our bodies via food, drinking water and air. As trace elements, some heavy metals (e.g. copper, selenium, zinc) are essential to maintain the metabolism of the human body. However, at higher concentrations they can lead to poisoning. Heavy metal poisoning could result, for instance, from drinking-water contamination (e.g. lead pipes), high ambient air concentrations near emission sources, or intake via the food chain. We designed a E.coli machine to control heavy metal concentration in water by using phototaxis induced tunable carrying system on E.coli membrane. In our system, there are two light sources. One of them is for the metal source and another is for the destination to where we want to carry metal atoms. And our machines have phototaxis ability. In addition to this, they have metal binding domain in outer surface and bacteriorhodopsin. When we open light at the metal source, they start to move toward source and catch the metal atoms. Then we open the light at the destination while closing the light at the source. So our machines move toward the destination. After the arrival our machines will be exposed to light with specific wavelength to activate bacteriorhodopsin leading to small local pH changing at the outer surface. This pH changing causes the release of metal atoms from the metal binding domain. Eventually, system starts from the beginning and so on. As a result we will make E.coli cells act as trucks that carry metal ions on our medium from the metal uptake location to the release locations and also the path are illumintated by lights at specific wavelenghts. N/A light Bacteriorhodopsin
Motility
In vivo Bronze Medalist N/A N/A
Mexico-UNAM-IPN 2008 Horizontal Transfer and Turing Patterns Yes Miscellaneous Horizontal gene transfer is an evolutionary mechanism that contributes to the acquisition of new genetic material among organisms; as such it helps bacteria to acquire antibiotic resistance and other genetic devices. The main goal is to design a devise that would detect events of horizontal gene transfer among bacteria. N/A Horizontal Gene Transfer Event Colour
Repression of Gene Expression
In vivo N/A N/A N/A
Michigan 2008 Circadian Clocking... in E. Coli! Yes Miscellaneous The human body's "clock" regulates the daily cycles of many physiological and metabolic processes, such as the sleep/wake cycle and feeding rhythms. It is controlled by the interplay of numerous molecular factors that orchestrate complex feedback loops and processes that are fundamentally mediated by gene expression and the events that follow it. We are working on constructing a synthetic clock, affectionately deemed "The Sequestillator," that is analogous to the mammalian clock. Our clock consists of two parts: an activator with constitutive expression and a promoter that drives the production of a repressor that binds and "sequesters" the activator away from the promoter. While intuitively it seems that this system may reach a steady state rather than oscillate, simulations have shown that under certain rapid equilibrium and tight binding conditions, this circuit does exhibit oscillations. We are currently involved in building and testing of this device. N/A NifA Colour
Flourescence
In vivo Bronze Medalist N/A N/A
Minnesota 2008 Time Bomb Yes Miscellaneous Control systems are an integral component of almost all aspects of life. Whether it is in industrial, biological, or chemical applications, controllers provide a way to keep systems functioning properly. A vital part of any control system is the comparator. This component compares a set point value and a measured value, and determines which is larger. It then sends the appropriate signal to the controller, which reacts to bring the system back to the set point. In typical applications, the controller equipment is electronic. However, our team set out to create a comparator using only genetic components. This comparator could potentially be used as part of a new, solely biological control system that could be used to treat many diseases afflicting humans, for example diabetes. This comparator could compare the blood sugar of a patient to what it should be, and send this result to a control system that could compensate, for example by changing the levels of insulin. In order to undertake this task, a system involving six genes was designed. For our system, the two inputs (one representing the set point and one representing the measured value) are IPTG and aTc. These inputs will activate the transcription of the LacI and TetR proteins, and set in motion the rest of the system to produce the outputs. Depending on the amounts of the two inducer molecules added to the system, either green fluorescent protein (GFP) or red fluorescent protein(RFP) will be produced. The actual design of the system can be seen below. In order to complete this project, a total of six genes will have to be cloned into plasmids, and two new BioBrick parts will be produced. One will be a TetR and p22-MNT dual-repressed promoter, and the other will be a LacI and lambdaphage cI dual-repressed promoter. We will also build mathematical models and conduct computer simulations that will help with the designs. This project will pave the way for other parts of a true genetic PID controller to be produced, which could be an exciting scientific development in the near future. N/A aTc
IPTG
Tetracycline
Colour
Flourescence
In vivo Silver Medalist Best New BioBrick, Natural (Runner Up) relative
Missouri Miners 2008 "Methanol Sensor, FUTURE PROJECT - Microbial Fuel Cell Yes Energy The goal of this research is the manipulation of yeast cells; granting them the capability of measuring the concentration of ethanol present. This project utilizes the metabolic pathways of the yeast Pichia pastoris, which are capable of metabolizing ethanol and methanol. The enzyme, alcohol oxidase (AO), encoded in the AOXI gene appears to be the major enzyme involved in methanol metabolism. If both carbon sources are present, however, P. pastoris prefers to utilize ethanol first. This preference is controlled by the AOXI promoter. Fusing the AOXI promoter with a fluorescent protein gene will allow visible detection of the expression of AOXI. In supplying the yeast with ethanol and methanol simultaneously, the cells should produce the fluorescent protein after ethanol consumption; resulting in a visible color and fluorescence. The concentration of ethanol can be determined by measuring the time before fluorescence and in doing so, will make plausible the development of a breathalyzer device and additional sensor systems. N/A AOXI Promoter
Ethanol
Methanol
Colour
Flourescence
In vivo Bronze Medalist N/A N/A
MIT 2008 Biogurt Yes Food "Streptococcus mutans, the main cause of dental caries, binds to glycoproteins on the teeth. A clinical study (Kelly CG et al.; Nature Biotechnol. 1999) isolated the 20aa functional segment (p1025) that S.mutans uses to attach to the teeth. p1025 competitively inhibits the binding of S.mutans, causing unharmful bacteria to grow in its place, preventing the recolonization of S.mutans for 90 days.The peptide p1025 could simply be added to any food. But production of this peptide by L. bulgaricus is an independent process, so inserting the gene into live bacteria in yogurt will enable continuous production. Since a new batch of yogurt can be made using the bacteria from a smallAlso, the p1025 gene could be replaced by any other gene, so this same expression system could be used to produce other useful peptides. Yogurt with modified bacteria will provide a cheap, efficient, and delicious way to distribute vitamins, vaccines and more. amount of the old batch, a continuous supply of teeth-cleaning yogurt will be available from the first successfully engineered batch. This could be the key to providing effective dental health care in underdeveloped rural communities, especially if yogurt is already an integral part of the diet." N/A lactose Activation of gene expression
protein secretion
In vivo Gold Medalist N/A N/A
Newcastle 2008 Bug Buster Yes Health and Medicine We aimed to develop a diagnostic biosensor for detecting pathogens. We wanted this to be cheaply and readily available for deployment in areas where access to medical resources, such as refrigeration and sophisticated laboratories, is limited or absent. We chose to use Bacillus subtilis as a method of delivery due to its ability to sporulate. The sensor bacteria could then be dried down as spores, which are very stable and extremely resilient to hostile environmental conditions, and rehydrated when required. The ambient temperature of much of the developing world is ideal for the growth of Bacillus spp. without the use of incubation equipment. Gram-positive bacteria communicate using quorum communication peptides. Research has shown that these peptides are extremely strain-specific. We chose to engineer B. subtilis 168 to detect four Gram-positive pathogens by their quorum communication peptides. The different combinations of quorum communication peptides would be sensed by the engineered bacterium, and this signal converted into a visual output as fluorescent proteins such as mCherry, GFP, CFP and YFP. Mapping multiple inputs to three output states is a multiplexing problem. The design of the genetic circuitry to do this is non-trivial and is not feasible manually. We therefore chose to use a biological implementation of an artificial neural network (ANN). Our team members wrote, designed and implemented a complete suite of tools that allowed the design and simulation of regulatory networks. We aimed to use this software to design an appropriate gene regulatory network that behaved as an ANN. An essential part of the approach was the use of computational evolution to design circuits with predictable behaviour even when the details of the required topology are unknown in advance. Models were encoded in the modelling language CellML because of its ability to model individual virtual parts that can be easily assembled, in a bottom up fashion, into a circuit which can be simulated. We aimed to translate this model into a sequence that could be implemented as BioBricks. N/A Pathogen
Quorum sensing
Colour
Flourescence
In vivo Gold Medalist N/A N/A
NTU-Singapore 2008 Detection and Lysis System Yes Health and Medicine N/A (this wiki is broken) N/A Pathogen
Quorum sensing
Bacteriocins In vivo Silver Medalist N/A detector
bacteriocin
colicin
asia
pathogen
in vivo
2008
NTU-singapore
NYMU-Taipei 2008 BacToKidney Yes Health and Medicine After ingesting our BacToKidney capsule, it passes the through stomach without taking any action, nor being digested, and proceeds to the small intestine. Once in the small intestine, the pH Sensor detects the change in pH and activates the clearance processes of Urea, Phosphate, and Guanidine from the body. To allow itself more time to perform its tasks, the pH Sensor also activates the Attachment process, making the capsule attach itself to the small intestine. After a pre-selected amount of time has passed (controlled by the time regulating oscillators), the capsule detaches itself from the small intestine and exits the body. N/A pH Activation of gene expression In vivo Silver Medalist Finalist NYMU
kidney
NYMU-Taipei
gene expression
in vivo
ph
2008
Taipei
Paris 2008 The BacteriO'Clock Yes Miscellaneous Have you ever dreamed of a new way of thinking everyday life objects? Be sure, this could one day become true, under the form of our BacteriO'Clock ! A simple test tube containing our modified bacteria might give you the time, directly from living organisms, the hours of the day being color-coded, and oscillations ensuring the repeated periodic behavior. Inspired by the flagellar motor machine, our clock at this stage of developpement serves as a chassis to be used in building future modular molecular machines in an optimized and coordinated manner. It may serve as well to control in an optimized fashion multi-reaction pathways. To achieve this incredible project, we relied on a well characterized genetic structure that allows a specific sequence of fluorescent proteins expression to occur in a First In - First Out order. This FIFO behavior enables us to define a rich color encoding of day time. An additional negative feedback loop generates clock oscillations! Based on in-depth studies and experimentally measured parameters we developed predictive models that suggest that this core system is not likely to demonstrate stable oscillations due to damping phenomenon leading to a stationary steady-state. Importantly, our modeling approach provided us with alternative improved designs that should lead in principle to an optimized BacteriO'Clock. In particular, this is achieved through synchronization at the population level by adopting a quorum sensing feedback mediated by HSL production that enforces a necessary delay and provides an elegant cellular synchronization mechanism : N/A Quorum sensing Colour
Flourescence
Time measurement
In vivo Bronze Medalist N/A N/A
Penn State 2008 Bioproduction Control Yes Miscellaneous Microorganisms typically preferentially utilize glucose over other sugar carbon sources such as xylose. This is largely regulated through control of gene expression based on the response of regulatory elements to sugars available to the cell. In E. coli, the xylose metabolism operon is controlled by both the xylose-inducible XylR activator protein and the cAMP receptor protein (CRP). In this project we attempt to eliminate glucose control over xylose-inducible gene expression in E. coli by altering the natural transcriptional control region of the xylose operon. Designs constructed and tested include scrambling the CRP binding site, increasing the strength of the xyl promoter, and overexpressing XylR. Xylose-inducible gene expression that functions independently of glucose regulation provides a useful approach to improving microbial utilization of biomass feedstocks containing mixtures of glucose and xylose. N/A Bisphenol A
phthalates
xylose
Activation of gene expression
Reversal of Auxotrophy
In vivo Silver Medalist N/A N/A
Prairie View 2008 Cation Detector Yes Miscellaneous "biosensor for the detection of cations by introducing electron network system proteins into the chassis best suited to receive an enhanced energy flow.Through our electron network system, we can enhance the expression of DNA, increasing cell replication along with the fluorescence of our reporters. Together, these incorporated proteins enhance the capacity of our sensor device." N/A cations Colour
Flourescence
Increased Growth Rate
In vivo Bronze Medalist N/A N/A
Princeton 2008 Toggle Switch with Neurons Yes Miscellaneous The goal of the Princeton iGEM team is to utilize the considerable capabilities of neurons and in particular of neuronal networks – in terms of speed of transmission of information, physical and programmable versatility – by designing neural networks using gene-regulatory circuits and microfabrication of surfaces. Gardner et al. showed in 2003 the construction of a toggle switch using gene-regulatory circuits. Our project is to design a similar toggle switch with neurons. Highly differentiated neurons can be made to produce and/or respond to specific neurotransmitters; and have receptors for these neurotransmitters also. The genetic regulation determines what kinds of neurons embryonic stem cells differentiate into. The toggle switch is constructed as follows: a cluster of pacemaker neurons constantly excites two clusters of neurons that are designed to cross-repress each other. With an external inhibitory input, either of these neural clusters can be repressed, immediately following which it ceases to repress the other cluster of neurons. This in turn represses the first cluster of neurons, which remains repressed even if the external repression is taken away. Thus, it can be held in a steady state. N/A dopamine Not specified In vivo N/A N/A switch
toggle
Purdue 2008 UV Biosensor Yes Food safety Purdue's project this year is creating a biosensor for UV radiation. Essentially, we are combining the SOS pathway promoter with a lacZ gene. This will lead to transcription of lacZ whenever the bacterial DNA undergoes significant damage. By plating these bacteria on X-gal plates, a blue color will be an indicator of intense UV irradiation. N/A DNA Dammage
SOS Response
Ultraviolet
Activation of gene expression
Colour
In vivo Bronze Medalist N/A N/A
Slovenia 2008 Immunobricks Yes Health and Medicine Bacteria Helicobacter pylori infects half of the world population causing gastritis and contributing to increased incidence of ulcers and gastric malignancies. This infection can be treated with multi-drug regime, but this is often associated with induced antibiotic resistance and does not protect individuals from re-infections. Vaccination against H. pylori can therefore be a viable alternative to control this widespread infection. However, developing an effective vaccine against H. pylori has presented a challenge because H. pylori or its components, which have frequently been used as parts of vaccines, are modified by bacteria such that they evade host defense mechanisms. Using synthetic biology approaches we managed to assemble functional “immunobricks” into a designer vaccine with a goal to activate both innate and acquired immune response to H. pylori. We successfully developed two forms of such designer vaccines. One was based on modifying H. pylori component (flagellin) such that it can now be recognized by the immune system. The other relied upon linking H. pylori components to certain molecules of the innate immune response (so called Toll-like receptors) to activate and guide H. pylori proteins to relevant compartments within the immune cell causing optimal innate and acquired immune response. Both types of vaccines have been thoroughly characterized in vitro (in test tubes or cells) as well as in vivo (laboratory mice) exhibiting substantial antibody response. Our strategy of both vaccines’ design is not limited to H. pylori and can be applied to other pathogens. Additionally, our vaccines can be delivered using simple and inexpensive vaccination routes, which could be suitable also in third world countries. N/A Pathogen Activation of gene expression
Immune Response
In vivo Gold Medalist Best Health or Medicine Project
Finalist
Grand Prize Winner
Winner of the BioBrick Trophy
N/A
Tokyo Tech 2008 Coli Touch Yes Miscellaneous What is "Coli touch"?“Coli Touch” has a pressure sensitive display composed of an E. coli lawn. When you touch its display, touched section is colored.Next I'll tell you about “Coli Touch” work system. Display of “Coli Touch” contains many E. coli. When you touch this display, pressure applies to E. coli in this display. Pressure applied E. coli expresses GFP.Why pressure?“Coli Touch” uses pressure as input. Why do we use pressure? Past input methods (small molecules, heat and light) are difficult to induce uniformly. Pressure can induce uniformly. N/A pressure Colour
Flourescence
In vivo Gold Medalist N/A tokyo tech
touchpad
touch
pressure
asia
in vivo
2008
Tsinghua 2008 Interchangeable Biosensor Yes Energy Poor Driver In a Strange Car.The car is strange because it can only run forward or tumble. The probability of the two states is controlled through a handle in it. Even worth, there are no windows on this car but a barometer showing local altitude. How should the driver do to reach the top of the hill and stay at there? ... If you think about the design of bacterial chemotaxis pathway, you will find that this pathway just plays the role of the driver in the story above. Interestingly, we find E. coli chemotaxis pathway realizes this delicate dicision-making process through the interactions amount handful molecules. Our project will show how we learn the design principles from native pathway to complete our device. N/A chemical Motility In vivo Bronze Medalist N/A N/A
TUDelft 2008 Biothermometer Yes Miscellaneous The goal of our project is to construct temperature-sensing bacteria Escherichia coli that changes color at different temperatures. Such a thermometer can be applied e.g. as a temperature reporter system in large-scale fermentations, or as a temperature-inducible protein production system. The functionality of this thermometer relies on the post-transcriptional regulation of a temperature-sensitive RNA structure: it opens and enables the ribosome to bind, only when the temperature exceeds a certain threshold. N/A Temperature Activation of gene expression In vivo Gold Medalist Best Wiki N/A
UC Berkeley 2008 Clonebots Yes Miscellaneous In an effort to optimize the manufacture of parts, we have designed Clonebots - a collection of devices and strains that aid in the synthesis and analysis of new parts. Building engineered biological systems requires cumbersome laboratory protocols that provide a significant impediment to the advancement of our field. However, there are some unit operations that can be cost effectively automated at scale in the laboratory such as small volume liquid transfers, fluorescence measurements, and heating/cooling steps. If we can reduce all synthesis and analysis methodology to these simple operations, it will be readily possible to automate all aspects of synthetic biology research - a cost-effective, BioCAD-friendly approach to large-scale projects. The Clonebots project is an effort to solve these basic technical problems of synthetic biology with the substrate of our own medium - a live cell. We initiated the construction of several genetic devices for protein purification and standard assembly. At the jamboree we will focus on two successfully constructed devices designed to automate sythetic biology: a genetic self-lysis device and a Gateway cloning device. N/A Arabinose
Magnesium
Bacteriocins
Holin
In vivo Gold Medalist Finalist N/A
UNIPV-Pavia 2008 Multiplexer (Mux) and Demultiplexer (Demux) logic functions in E. coli. Yes Miscellaneous We are trying to mimic Multiplexer (Mux) and Demultiplexer (Demux) logic functions in E. coli. N/A Quorum sensing Not specified In vivo Silver Medalist N/A N/A
University of Alberta 2008 Bisphenol Eh? Yes Environment The aim of our project is to create a biosensor that will detect BPA and other estrogen-like compounds in the environment. BPA is a toxin that has been shown to leech from certain types of plastic that are used in everyday life. Animal studies have shown that BPA is linked to various forms of cancer and other detrimental effects, which are likely to affect humans as well. Having a biosensor that can detect soil and water contaminated with BPA would be a useful tool indeed. Our project relies on the mechanism by which BPA affects cells. As an estrogen-like compound, BPA has the ability to mimic estrogen. When taken into the cell, it can bind to the cytoplasmic estrogen receptors, and activate genes related to estrogen, tricking cells into thinking they are in an environment containing estrogen when they are not. By introducing the estrogen receptor into "E. coli", we can use it to activate transcription of reporter genes to allow for easy visual identification of environments contaminated with BPA. Furthermore, the system can be used to activate recently characterized genes for BPA metabolism (BisdA, BisdB) in order to help with bioremediation of contaminated areas. While proving the principle in an "E. coli" system is our main goal for this year’s project, we are thinking ahead to future development of other applications. For example, a BPA detector system put into a plant could serve as convenient 'BPA-sentinel plant' and early warning system if planted in areas at risk for contamination. Project 2 is focused on developing the tools that would allow us to move our project into plants. These will comply with the standard iGEM parts requirements and will allow anyone to use any standard biobricks in plants, opening iGEM up to the plant realm. Also, we plan on developing a "cell free" version of our system that would allow for cheap and quick detection of BPA "in vitro". This could prove to be of much benefit to poorer or third world nations, which may not be able to afford the resources necessary to maintain the plant system, or where poor regulations regarding BPA have lead to a very high risk of environmental contamination. N/A Bisphenol A Activation of degradation
Colour
In vivo Bronze Medalist N/A N/A
University of Lethbridge 2008 Baccum Cleaner Yes Environment The tailing ponds created when water is used to extract oil from the Alberta tar sands or other mining operations pose a major environmental dilemma. How can we isolate the tailings and byproducts of the extraction process? Despite the efforts of the corporations responsible, chemicals can leech from the ponds into the surrounding ground water and soil. These toxic and often corrosive water beds not only affect the immediate land and water environment but also cause severe repercussions to larger ecosystems as much of the wildlife relies on getting their food and water from the now disrupted bionetwork. The exact composition of tailing ponds is highly complex, often laced with heavy metals and other toxic chemicals, such as aromatic hydrocarbons, and are difficult and expensive to filter or degrade. One powerful example is the high level of mercury in our fresh water fish, stemming from the tailing ponds of gold mining operations and the refinement of chloralkali metals. It is our goal to create a bacterial vacuum cleaner, or “Bacuum”, which will seek out and degrade a particular harmful hydrocarbon. We intend to use the theophylline riboswitch we worked on last year as a platform for directed evolution to create a novel riboswitch capable of binding a particular aromatic hydrocarbon or class of hydrocarbons. The riboswitch will be used to control expression of the motility protein cheZ in Escherichia coli at low concentrations, thus directing the bacterium towards local areas of high ligand concentration. At a threshold level, a second riboswitch will be used to activate a pathway capable of metabolizing the aromatic hydrocarbons. Ultimately, the resulting product will be funneled into an anabolic pathway, such as the TCA cycle or fatty acid biosynthesis, from which an alternative fuel source can be produced, thereby turning toxic tailings ponds into a bioreactor with the help of a self-guiding "search and destroy" bacterial operative. N/A PCB
Polychlorobiphenyls
Motility In vivo Bronze Medalist N/A N/A
University of Ottawa 2008 The Pulsilator Yes Miscellaneous Large-scale production of recombinant proteins typically involves growing genetically modified microorganisms in bioreactors in which metabolic stress and selective pressure tend to diminish culture productivity over time. To alleviate the detrimental effects of continual high-rate synthesis, we have designed a yeast strain capable of producing bursts of gene expression in a controlled and inducible manner. These "pulses" are generated by the action of an inducer molecule that triggers the synthesis of a protein of interest and simultaneously induces a repressor protein to terminate expression as well as an enzyme to degrade the inducer signal, thereby returning the system to its initial state. By co-culturing populations of inducer-synthesizing cells and pulse-generating receiver cells, we hope to achieve self-sustaining oscillatory gene expression dynamics that could render long term culture-based recombinant protein synthesis more sustainable. This would open the door for the production of considerably toxic proteins for numerous applications including anti-cancer therapeutics and antiseptics. N/A cytokinin Activation of gene expression In vivo Silver Medalist N/A N/A
University of Sheffield 2008 Cholera Sensor Yes Health and Medicine Hygiene related diseases have an undeniably huge impact on the world we live in, where many deaths are preventable if sanitary conditions could be improved. This issue is not limited to developing countries: outbursts of diseases caused by water contamination still occur all around the world including the most developed regions. Efficient testing of water is an essential part of preventing these incidents, especially after natural disasters. It needs to be quick, easy enough for anyone to use, cheap and reusable. This was the idea behind the University of Sheffield’s project in its first entry into iGEM. N/A Pathogen
Quorum sensing
Colour
Flourescence
In vivo N/A N/A N/A
University of Washington 2008 Vector-jector Yes Miscellaneous Transferring novel abilities into eukaryotes has many potential applications. Our project attempts to control transfer of genetic material across phylogenetic domains. We attempt to direct the prokaryote Escherichia coli (domain Bacteria) to transfer DNA encoding potentially useful traits from to the yeast Saccharomyces cervisiae (domain Fungi). The design utilizes standard engineering and synthetic biology techniques to modularize this process, in order to enable usage across varying organisms and conditions. To achieve control over our system, bacteria transfer DNA via conjugation only if certain conditions are met. In our design, E. coli transfers the genes to metabolize lactose in S. cerevisiae, but only where lactose is prevalent, glucose is minimal, and yeast proximity is sensed via a yeast-produced signaling molecule. It therefore provides a means for conditional, not constitutive, gene transfer between diverse organisms. Applications might include the production of transgenic plants and animals, clinical gene delivery, and interacting multiple-organism systems. N/A Glucose concentration
lactose
Quorum sensing
DNA Conjugation In vivo Bronze Medalist Best Presentation, Runner Up N/A
USTC 2008 self-organized multiple-cell system Yes Miscellaneous It is an amazing process in nature that the evolution from Protozoa to Metazoa. Even in the development of each Metazoa, it is still unknown how the genome regulates stem cells to differentiate into different kinds of cells, which can compose different tissues or organs, according to where they are in the body. There should be a self-organized process. Here we are trying to build a self-organized multiple-cell system based on the quorum sensing system to understand the mechanism of this process. We employed small molecules in the AHL family as messengers to transmit the orders of differentiation, and we use Cre recombinase as the executor of differentiation. With the use of an artificially designed network, we are trying to construct a new kind of cells, through which a ring composed by GFP will be seen on the plate if the colony is big enough. N/A Quorum sensing Colour
Flourescence
In vivo Silver Medalist N/A N/A
Utah State 2008 systems to monitor PHB production in microes Yes Manufacturing The Utah State University iGEM team project is focused on creating an efficient system for producing and monitoring PHA production in microorganisms. One goal of our research is to develop and optimize a method, using fluorescent proteins, for the detection of maximum product yield of polyhydroxybutyrate (PHB, a bioplastic) in recombinant E. coli and in C. necator. In order to develop an optimal PHB detection system, we worked to identify the most efficient reporter genes, and the best promoter sequences that would allow the GFP reporter to indicate maximum PHB production. N/A PHB Colour
Flourescence
In vivo Bronze Medalist N/A N/A
Valencia 2008 Hot Yeast Yes Miscellaneous The present project aims to demonstrate that the temperature of a microbial culture might be modulated through the expression of the mammalian uncoupling protein UCP-1. Saccharomyces cerevisiae strains genetically modified to express wild type UCP-1, mutant sequences with increased uncoupling activity, as well as a control strain were cultured in an Liquid Culture Calorimeter (LCC) we developed. The system consisted of a modified thermo flask with an inserted thermocouple allowing real-time accurate temperature measurements. Different conditions, such as initial densities, amounts of inductor, or shaking speeds were tested. We succeeded to obtain significant temperature increases in the mutant strains compared with the other strains. We also developed an effective model of our system. Although the system is not always stable and might be sensitive to external perturbations, this is the first time a significant increase in temperature associated to UCP-1 expression in yeast is reported. N/A Not specified Heat In vivo Gold Medalist N/A N/A
Warsaw 2008 Interactor Screen System Yes Miscellaneous A novel system for generation and screening for new interactors targeted against any bait N/A Interacting Protein Colour In vivo Bronze Medalist N/A N/A
Waterloo 2008 Genome-free Bacterial Bioproduct Factory Yes Manufacturing The aim of our project is to engineer a genome-free, cell-based expression system capable of producing a desired protein or activating a pathway in response to an environmental signal. Genome degradation is achieved using the combined activity of a restriction endonuclease to fragment the genome and an exonuclease to hasten degradation. The gene for the protein of interest will be located in a plasmid lacking recognition sites for the endonuclease, allowing it to remain intact after genome degradation. The plasmid genes will be expressed using the remaining cell resources until they expire. The primary application of this design would be an in situ compound production and delivery system for agricultural, industrial or therapeutic use to continue for a period of time. N/A DNA Dammage
SOS Response
Activation of gene expression In vivo Bronze Medalist N/A N/A
Brown University 2007 Cellular Lead Sensor Yes Food safety About 40% of the world does not have access to clean water. Lead is a major contaminant worldwide. In the US alone, over 1 million children ages 1 through 5 have elevated levels of lead in their blood. Current lead detection systems are expensive and require lab analysis. Home lead testing kits are inaccurate and only detect lead at very high levels. We have created a genetic circuit in E Coli that responds to lead. The promoter and lead binding protein we use are ten times more selective for lead than for other similar heavy metals. We have also incorporated a genetic amplifier into our circuit to allow us to detect fairly low concentrations of lead. Having found a Lead Binding Protein and its corresponding Lead Promoter in the literature, we began to generate a number of ideas for our lead detector design. We began with a simple detector: The lead promoter could be placed in front of Green Fluorescent Protein, GFP. Once lead enters the cell, it activates the Lead Binding Protein, which activates our Lead Promoter, which in turn gives us some GFP output. But we realized that we could make this simple detector much more effective with an amplification circuit. N/A Lead Flourescence
GFP
In vivo Gold Medalist N/A AHL
Amplifier
Colombia-Israel 2007 No Title Yes Environment The Colombian-Israeli team is made up of students from different cities in Colombia and Israeli high school students. The students who are currently attending different universities pursue careers within the sciences and engineering. Each and every one of us has a different personal motivation that drives us in our daily work for this year's IGEM project. As a group, we also shar a motivation that brings us together withing our team: to put into useful practice our passion for biology, math and computer science but most of all, to be creative. We want to find new solutions and new ways of solving problems and overcoming obstacles found in science through synthetic biology. For this year's IGEM project, our team's objectives are to enhance the detection levels of the sensing device with the implementation of ion channels and to use these results as reference to develop other types of sensing devices to be used in different conditions. Biosensors are useful molecules and/or cellular tools that allow detection of the presence of different metals including iron (II/III) and other compounds, even at detection levels beyond the limits of conventional methods (Colombian IGEM. IET Synthetic Biology Journal. 2007). Last year, the Colombian IGEM team developed a microbial biosensor device for iron detection under UV irradiation using synthetic biology. This year, in association with the Israeli team, we will develop a more sensitive biosensor device, in order to detect different levels of iron, including those below that of 0.5 ppm. The device will also be tested at different levels of oxygen and UV irradiation. Plasmid isolation, preparation of competent cells and cell transformation are being currently carried out in the laboratory at the Universidad Agraria in Bogota, Colombia. New parts designed by the Colombian group as well as parts from the MIT BioBrick will be assembled, in order to construct the genetic machine. This year, sequences from both upstream and downstream will be used for our project. One of the main new features of our device will be exposed to different environmental conditions such as oxygen levels, temperatures and varied light intensities. As we carry out all of our experiments within our laboratory, we are also developing a mathematical and computational model. N/A iron
UV irradiation
not given In vivo Bronze Medalist N/A N/A
ETHZ 2007 EducatETH E.coli Yes Miscellaneous Our combined team of biologists and engineers is coping with the problem of implementing memory capabilities in bacterial colonies. First, E.coli are able to respond differently (with distinct fluorescent proteins) to two different inputs (we used chemicals). Second, they remember which input was presented to them. Finally, when confronted with a new input, they are able to recognize whether it is the one that they were trained with or not. In other words, in this project we are educating the E.coli! Our system has the ability to behave in different ways according to an internal toggle inside it switching states based on the chemical substances that the system is exposed to. The toggle states could generally be used to trigger events such as enzyme synthesis, transcriptional regulation, virion production, or even cell death. Therefore, one may view the bacterial cell line containing this system as a multipurpose cell line. By adding a certain chemical to a cell line, the latter may be trained to exhibit a desired behavior, and then it is not necessary any more to construct two independent cell lines. This means that one applies an “input engineering” instead of a “DNA engineering” approach. If one extends this idea to several multi-inducible toggle switches being harbored in the same cell line, the number of possible phenotypes increases to 2n, where n equals the number of toggle switches. For example, if one would have 5 such toggle switches inside a cell line, 32 different behavior patterns would be possible. For the purpose of creating a toggle switch that is activated in a specific phase only and not always (a multi-inducible toggle switch), as is required for stable biological automatons, we introduced the concept of double promoters to the Registry of Standard Biological Parts, which can be helpful for engineering systems which exhibit a desired behavior only at specific times. N/A AHL
aTc
cI
IPTG
p22cII
ECFP
EYFP
Flourescence
GFP
RFP
In vivo Gold Medalist Best Presentation, Finale Educating
Toggle Switch
Modelling
Glasgow 2007 ElectrEcoBlu Yes Environment ElectrEcoBlu combines an environmental biosensor for common organic pollutants with a microbial fuel cell which can produce its own electricity. These cells produce their own electrical power output which increases in the presence of one or more organic pollutant stimulants. This system has the potential to be used for self-powered long term in situ and online monitoring with an electrical readout. It is based around novel reporter genes encoding electron carrying mediators which aid the transfer of electrons from the cells to the electrodes resulting in enhanced electricity generation. N/A Benzene, Toluene, Ethylbenzene and Xylenes (BTEX chemicals)
DmpR and Phenolic Compounds
DntR and Dinitrotoluenes
XylR
Change in voltage
Pyocyanin
In vivo/in vitro Gold Medalist Best Environmental Project, Finals Pyocyanin
microbial fuel cell
Imperial 2007 Infector Detector Yes Health and Medicine Infector Detector tackles the ongoing problem of catheter-associated urinary tract infections. To do this, we looked at how infections develop - as biofilms - and designed a system which would be able to detect their presence. We have created a system which is capable of detecting one of the types of signalling molecules found in biofilms, AHL, and visibly report its presence by producing a fluorescent protein. N/A AHL
LuxR
Flourescence
GFP
In vivo/in vitro Gold Medalist N/A Infection
Biofilm
MIT 2007 Mercury Sensor Yes Food safety Mercury contamination of drinking water is a significant problem in both developed and developing countries. Techniques to filter it out are both costly and intensive. Thus, the MIT iGEM 2007 team is engineering a biological mechanism to cost-effectively sense and remove Mercury ions from contaminated water through a two cell system. One cell will use the Mer promoter to sense the presence of Mercury ions, then activate the GFP fused downstream. The other uses a cell surface display mechanism to exhibit a Mercury capturing peptide, extracting the Mercury from the water. Both cells also display polystyrene binding peptides, and will thus be attached to a polystyrene filter. This setup would be easy to use, cheap to manufacture, and economical to distribute. It could be used from very small scales to even an entire village's drinking water supply. N/A Mercury Flourescence
mercury filtering
In vivo Gold Medalist N/A N/A
Naples 2007 YeSOil: A Yeast Sensor for real Extra Virgin Olive oil Yes Food safety The aim of our project is to engineer a synthetic biological network in yeast. This system will help in evaluating the quality of olive oil, one of the wordly famous product of Italy. Detection of oil quality is now possible only through expensive and bulky machines. In order to render this process easy and cheap we will modify Saccharomyces cerevisiae cells so that they will act as sensors and indicators of different oleate concentrations. N/A high oleic acid concentration (ot edible oil)
low oleic acid concentration (extra virgin olive oil)
Flourescence
GFP
PHO8 promoter
In vivo Silver Medalist N/A N/A
Penn State 2007 Dosimeter Yes Environment A dosimeter is a device which measures the amount of ionizing radiation an individual or object has received over time. With the renewed interest in nuclear energy in response to dwindling fossil fuel reserves, concerns over nuclear waste storage and disposal, and fear of radiological terrorism, the need for a cheap dosimeter is clear. A biological system that acts as a dosimeter would be a cheap and readily producible first response indicator that could be interpreted without training or calculation. The Bio-Dosimeter In order to monitor radiation dose the bio-dosimeter would need to sense incoming ionizing radiation, a trait that organisms do not normally possess. However, the genetic damage that makes radiation dangerous is also readily monitored by several highly specific systems in nature. One such example of this is the Lambda Bacteriophage, which switches from the dormant lysogenic state to the active lytic state in response to genetic damage in its bacterial host. Our project uses the lambda phage genome as a radiation biosensor as it has been extensively characterized and has tight control over gene expression. Lambda Bacteriophage The lambda bacteriophage controls switching between the lysogenic/lytic states once lysogeny has been estabilished through a bi-directional promoter (PR, PRM) with three binding sites with different affinities for repressor (Cl) and activator (Cro). The lysogen normally maintains lysogeny through a feedback loop with repressor Cl that simultaneously maintains Cl concentration within a set range and represses the Cro activator by activating the PRM promoter which expresses Cl and repressing the PR promoter which expresses Cro. However, in response to genetic damage the lambda phage exploits the host’s SOS response to cleave the repressor. As Cl concentration declines, the stronger PR promoter begins to express Cro, which competes with Cl for binding sites and represses Cl’s production. Using the Bacteriophage as a Dosimeter By taking the PR, PRM bidirectional promoter and placing desired response proteins such as GFP downstream of the activator Cro, the operator acts as a tightly regulated dosimeter with little chance of accidental false positives. N/A Ionizing radiation bi-directional promoter (PR, PRM)
Flourescence
GFP
SOS response
In vivo Gold Medalist N/A N/A
Prairie View 2007 Development of a Biosensor Device for Detection of Several Metals Simultaneously Yes Environment Assembling parts for developing microbial biosensors for detection of toxic metals and for organic compounds. There exists two essential needs which enabled us to design the trimetallic probe. The need for alternative forms of oil, in fact their methods and the bioremediation of metals ions from the environment. Micrococcus luteus strain (ATCC 4698) was transformed by plasmid pUC57-S-3M, in which Fe (II), Ni (II) and V (II) were fused to the fluorescence proteins (ECFP, EYFP, and mRFP respectively and to a fluorescent protein coding region [C0061(lux I)] ligated with a signaling sequence BBa_I13207. The pUC57-S-3M was standardized for its specific sensoribility response to three metal ions and to sulfur (S), in order to detect metal contamination and/or hydrocarbons associated to these metals. Single and combination of the tree metals were used at different concentrations (0.2, 2, 50 ppm). The pUC57-S-3M was grown in the presence and absence of oxygen and/or hydrocarbon (Thiophenol). Only results from combined metals are reported. The biosensoribility was determined by the response of the pUC57-S-3M to the different concentrations of the metals. This response was measured by bioluminescence, fluorescence, DNA concentration, bacterial growth. These parameters were related to sensoribility of the pUC57-S-3M. Develop and standardize microbial biosensors that respond specifically to toxic metals (nickel, vanadium, iron) simultaneously at different concentrations. Combine parts such as lux and lacZ gene reporters with inducible promoter and flourescent proteins to develop a microorganism (chasis) with the functions of detecting the toxic metals and or organic compounds. N/A iron
nickel
vanadium
[C0061(lux I)]
ECFP
EYFP
mRFP
In vivo N/A N/A N/A
Princeton 2007 An RNAi-Enhanced Logic Circuit: Cancer-Specific Detection and Destruction No Health and Medicine Using standard engineering practices, we have designed, and are in the process of implementing, a novel system that utilizes RNA interference (RNAi) to detect and destroy cancer cells in a tissue-specific manner. We are interfacing RNAi components together with promoter and repressor elements to form logic circuits, which allow the use of multiple criteria to target cancerous cells in a unique and highly specific manner. As a measure of safety, we utilize mutant lentiviral integrase to deliver our construct into the cell as a non-integrated plasmid, preventing any disruptive effects that could be attributed to pseudorandom integration by the lentivirus. This also ensures that the daughter cells will not inherit the cancer-detecting circuitry, thus preventing unintended proliferation of our construct and allow for more extensive and comprehensive cancer treatments. We have constructed many components of our system and are in the process of testing our plasmids in a proof of concept manner. Where possible, we will revise and improve upon our components based on mathematical modeling and experimental results. N/A GATA3 (non-neuronal ectoderm cell fate regulator and a transcription factor)
RNAi
Apoptosis of cancer cells
Expression of Bax
RNAi enhanced logic gates
In vivo Gold Medalist N/A N/A
Saint Petersburg 2007 Copper Biosensor Yes Environment In our project we intend to create a copper biosensor, that would sense copper ions in growing media (based on a water sample). The advantage of biosensor over FAAS and MS techniques is, that it will sense true free copper concentration, available to biological system. It will not react to strongly ligand-bound copper and fine dispersed metallic copper. To make our sensor more robust we intend to supplement it with a threshold device, that will provide the response on a “all or nothing” basis, when copper level will exceed the critical concentration. So, our project falls into two distinct parts. The first part is a copper-responsive element, that will convert measured copper level to POPS. The second part is a threshold device with hysteresis (a Schmitt trigger), that is designed as a individual part, so that it may be used with any input. N/A Copper cooper-regulated promoter
Flourescence
Schmitt-Trigger - all or nothing
In vivo Gold Medalist N/A N/A
Sounthern Utah 2007 Cyanide Biosensor Yes Environment Southern Utah University's iGEM team is developing a cyanide biosensor. This project idea was inspired by the 2006 University of Edinburgh iGEM team which developed an arsenic biosensor. Like arsenic, cyanide is a toxic compound that can contaminate water. Currently, the most common ways for cyanide to come into contact with humans are through industrial wastes and through the root crop cassava. Cassava is a major part of the diet for about 300-500 million people living in the tropics and subtropics. There are currently already several methods for detecting cyanide in water. However, these methods are time consuming and require many steps. We would like to engineer a strain of bacteria that could produce a signal in response to the presence of cyanide. There are already some strains of bacteria such as Pseudomonas fluorescens PfO-1 that produce enzymes such as nitrilase/cyanide hydratase to degrade cyanide. We believe that the transcription of the genes for these enzymes may be dependent on the presence of cyanide. Therefore, we would like to modify the currently existing genes in the Pseudomonas strain so that GFP is produced in response to this toxic compound instead of the usual cyanide degrading enzymes. A bacterial strain with these capabilities may provide quicker detection of cyanide in the future. N/A Heavy metals (Cyanide) Cyanide Nitrilase Promoter
Flourescence
GFP
In vivo Gold Medalist N/A N/A
Taipei 2007 GlucOperon No Health and Medicine Diabetes mellitus is a significant problem especially in developed countries and leads to several severe long-term complications. Compared to well-known type 2 diabetes mellitus, manifested with different degrees of insulin resistance, type 1 diabetes mellitus is caused by insulin deficiency following destruction of the insulin-producing pancreatic beta cells. Controlling blood sugar in a reasonable level and avoiding severe emergency as diabetes ketoacidosis (DKA) are very important clinical issues. Thus, the NYMU_Taipei iGEM 2007 team is designing a biological system to sense environmental glucose concentration and decrease the level of glucose by releasing insulin. Besides, life-protection functions for removing toxic ketoacids produced during DKA and preventing hypoglycemia status will also be established. This system will be a convenient and safe design for those patients with diabetes mellitus, and further improve their quality of life by avoiding them from diabetes-related morbidity and mortality. N/A Glucose concentration Activation of glucose degradation by insulin In vivo Gold Medalist N/A N/A