BGU_ISRAEL

Many date the invention of plastic by Alexander Parkes (Parkesine) as far as 1856, back then plastic was made almost entirely of cellulose, a natural substance found in plants. With the advancements made in the field of polymer chemistry during the 20th century, many new polymers were introduced into industry and are known to us today as Polystyrene, Polyethylene and Polyethylene terephthalate (PET). Plastic immediately gained popularity, being cheap, durable and easily molded into different solid shapes, and can be even used as an ink in 3D printers. However, one of its best features was found to be one of its greatest drawbacks, the durability of plastic makes it virtually non-degradable. An average bottle of mineral water takes roughly half a millennium to decompose, thus, leading to a global accumulation of plastic waste. Many ideas were considered in dealing with plastic waste such as burning plastic or burying it, but these solutions are considered damaging to the environment due to plastics toxicity. Since the introduction of plastics, some microbial communities or species have evolved to successfully degrade plastics, however, from an evolutionary point of view, probably due to the relatively short period of exposure to plastics, they are yet to be efficient in plastic biodegradation. Our goal as the Ben-Gurion University IGEM team is to overcome this evolutionary hurdle by devising several approaches using synthetic biology tools for efficient plastic biodegradation. In addition, we plan to utilize the high energy stored in PET molecules, for electricity production. In order to achieve that, three courses of action were chosen: 1. An Organism Evolution Approach – since plastic is a new synthetic polymer introduced to the environment by mankind, only recently, not many organisms have adapted into using it as a carbon source and those that were able to utilize it, have yet to perfect their plastic consumption as well as its utilization as a sole carbon source. Hence, one of our approaches is to use an organism which has adapted into "finding a solution" to use plastic, and try to improve that "solution" using methods such as experimental evolution and serial passaging. We have chosen to improve Rhodococcus ruber that was found to degrade polyethylene. 2. A Protein Engineering Approach – another approach we have adopted, is the engineering of a protein. LC-Cutinase is an enzyme discovered from an unknown organism in leaf-branch compost, and has been found to be one of the most efficient enzymes in breaking down PET polymers into degradable substrates. Based on the LC-Cutinase structure that was solved in 2012, we have chosen to use a rational mutagenesis approach for our experiment. In this approach, we made various mutations using an algorithm that compares the sequence of the original protein with that of other homologous proteins and then chooses various mutations and calculates each one of the mutations differences in free energy (DDG) compared to the free energy of WT protein. After the process was completed, we have ended up with 4 different variants other than the WT. We plan to test these variants in order to check if we have succeeded in improving the enzyme’s activity and stability. 3. Genetic Engineering of Metabolic Pathways–we will modify two metabolic pathways using engineered enzymatic cascades which lead to two products, terephthalate and ethylene glycol resulting from the biocatalysis of PET by LC-cutinase. While the terephthalate will be used to produce succinyl co-A and acetyl co-A, the ethylene glycol will be transformed into malate by using a metabolic pathway that already exists in E. coli. This way, our engineered bacteria will degrade PET and will transform the electrons released from PET degradation into energy by using PET as the carbon source. We have chosen to work with Pseudomonas putida, which is a gram-negative bacterium that has a diverse metabolism, including the ability to degrade organic solvents. Moreover, Pseudomonas putida contains most of the enzymes required for the first enzymatic cascade required for breaking down terephthalate. Our goal is to genetically engineer Pseudomonas putida so it will contain two plasmids which will encode for three essential components: secretion of LC-cutinase that is required for the initial degradation of PET to its monomers; a membrane transporter that will carry the monomers into the cell and the necessary enzymatic cascades that will further degrade the monomers into TCA cycle metabolites. 4. Microbial Fuel Cells - Since PET is a polymer that contains high energy bonds in its carbon-carbon bonds, excess energy released by our engineered microorganisms from carbon-carbon bond degradation will be harnessed and utilized in microbial fuel cells devices, this way plastic biodegradation will be converted into energy.


CSU_Fort_Collins

Boolean logic is largely used in computer science but can be applied to various other disciplines. It regulates the occurrence of desired outcomes by stipulating necessary inputs. One operation from this system is AND. In its simplest form, an AND gate requires two simultaneous inputs in order for an output to be produced. An example of this operation is a driver moving a car forward. For this situation, the engine must be on AND the gearbox must be in drive before pushing the gas pedal will allow the car to move forward. Adhering to Boolean logic, our goal is to create a modular genetic circuit in the cyanobacterium Synechocystis sp. PCC 6803 to optimize expression of a desired product. Additionally, we want to eliminate the need for expensive induction molecules such as IPTG. To accomplish these goals, we selected two conditions to implement in an AND gate and regulate gene expression: light and a quorum of cells. These conditions make use of natural mechanisms of Synechocystis sp. PCC 6803 (herein referred to as Synechocystis ) and the quorum sensing mechanism from Vibrio fischeri . Synechocystis is a photosynthetic bacterium which has the ability to react diurnally (Labiosa 2006, Beck 2014), suggesting that it is able to change central metabolic flux following a circadian clock. In fact, studies using constant light found that about 2% to 9% of the organism's genes change following a circadian rhythm (Kucho 2005). Using data collected by Beck et al. about the relative abundance of transcripts during light-dark cycles, we identified two loci in the genome of Synechocystis that show peak abundance during the dark cycle. From these two loci, we aim to extract the promoter region and compare them to a known dark induced promoter called LrtA as well as a green light induced promoter called cpcG2 . Both LrtA and cpcG2 promoters are found in the genome of Synechocystis . After characterizing the four promoter regions, we will chose the one that expresses best during a dark cycle for further use in our AND gate. According to Merriam-Webster, a quorum is defined as ”the smallest number of people who must be present at a meeting in order for decisions to be made.” For our project, we are construing a quorum as the lowest density cell culture at which a product can be optimally produced. Quorum sensing is a communication mechanism bacteria may use to assess population density before allowing gene expression to occur. The bacterium Vibrio fischeri uses quorum sensing to provide bioluminescence for the bobtail squid. Bioluminosity isn’t easily visible until the V. fischeri population reaches a certain density, so to conserve resources, the population will act as a group and drive gene expression only when a quorum is met (Waters and Bassler 2005). Similarly, we want to optimize production in Synechocystis . We chose to implement the luxR-luxI intergenic region from V. fischeri strain MJ1S because its promoters and RBS result in considerably high expression of bioluminescence (Bose et al. 2011). The first portion of our AND gate will consist of a dark induced promoter driving expression of an antisense RNA (asRNA) that is complementary to our desired product. The asRNA interferes with translation of the product if light is not present. In the second portion, we have the luxR-luxI quorum sensing system allowing product expression only at a threshold population density. Beck C, Hertel S, Rediger A, Lehmann R, Wiegard A, Kölsch A, Heilmann B, Georg J, Hess WR, Axmann IM. 2014. Daily expression pattern of protein-encoding genes and small noncoding RNAs in Synechocystis sp. strain PCC 6803. Appl Environ Microbiol 80:5195–5206. 10.1128/AEM.01086-14. Bose, J. L., Wollenberg, M. S., Colton, D. M., Mandel, M. J., Septer, A. N., Dunn, A. K., & Stabb, E. V. (2011). Contribution of Rapid Evolution of the luxR-luxI Intergenic Region to the Diverse Bioluminescence Outputs of Vibrio fischeri Strains Isolated from Different Environments. Applied and Environmental Microbiology, 77(7), 2445-2457. doi:10.1128/aem.02643-10 Kucho K, Okamoto K, Tsuchiya Y, Nomura S, Nango M, Kanehisa M,Ishiura M. 2005. Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J. Bacteriol. 187:2190 –2199. http://dx.doi.org/10.1128/JB.187.6.2190-2199.2005. Labiosa, R. G., Arrigo, K. R., Tu, C. J., Bhaya, D., Bay, S., Grossman, A. R. and Shrager, J. (2006), EXAMINATION OF DIEL CHANGES IN GLOBAL TRANSCRIPT ACCUMULATION IN SYNECHOCYSTIS (CYANOBACTERIA). Journal of Phycology, 42: 622–636. doi: 10.1111/j.1529-8817.2006.00217.x Waters, C. M., & Bassler, B. L. (2005). QUORUM SENSING: Cell-to-Cell Communication in Bacteria. Annual Review of Cell and Developmental Biology Annu. Rev. Cell Dev. Biol., 21(1), 319-346. doi:10.1146/annurev.cellbio.21.012704.131001


Chalmers_Gothenburg

Current commercial production of many chemicals is based on fossil sources of carbon. This inevitably results in staggering amounts of carbon dioxide being released into the atmosphere of the Earth (in excess of 35 billion tonnes annually1). Though carbon dioxide itself is not very toxic, the current increasing atmospheric concentrations of this greenhouse gas has a massive effect on the ecosystems of the planet as well as human quality of life. Examples of this is the acidification of oceans and an increasing mean temperature of the earth. These problems can be mediated by replacing petrochemical-based production with a sustainable production method based on biosynthesis in microorganisms. This is currently applied in the production of bioethanol, which uses a process very similar to fermenting alcoholic beverages. However, this requires large amounts of sugars used as the carbon source, which is currently taken from plant-based materials such as corn and sugarcane2. This has a significant impact on the quality of life in developing parts of the world, where crops are grown and sold for fuel production instead of feeding the local population, leading to a substantial increase in food prices3,4. How can we solve the problem of increasing levels of carbon dioxide and the the social issues caused by current substrate production? Our solution to this problem is to use photosynthetic bacteria to produce the carbon substrate needed for industrial fermentation. The carbon fixation ability of cyanobacteria allows for the direct conversion of carbon dioxide into a usable carbon source that the cyanobacterium then secretes. The secreted carbon source can be converted into a useful product using biosynthesis. Biosynthesis refers to the production of complex molecules within living organisms or cells. A variety of microorganisms, such as Saccharomyces cerevisiae, Bacillus subtilis and many more, are already used in the industry today for this purpose.There are several approaches that can be used for this kind of system. The cyanobacterium could be grown separately and its supernatant could be used as medium for the separate fermentation for the production organism. This would mean that the fermentations would still be done in separate batches, similarly to how industrial fermentation is performed today. However, this method requires several purification steps: the cyanobacteria medium has to be separated from the bacteria, and the product of interest has to be separated from the production batch. How can we decrease the number of purification steps? To solve this issue, we will establish a continuous production system. The proposed system is a co-culture where both organisms are kept in the same container. To prevent one organism from outcompeting the other in the system, the organisms are modified to be metabolically dependent on each other, resulting in a symbiotic system. The modified cyanobacterium (Synechocystis) produces the carbon source that the production organism requires. In return, the production organism produces a specific amino acid that the auxotrophic cyanobacterium requires for survival. In this way we hope to create a self-regulated system that will maintain equilibrium between the two organisms. Furthermore, the auxotrophy of the cyanobacterium makes it non-viable outside the lab environment, preventing unwanted spread of the bacteria. Why not produce chemicals directly from Synechocystis? Converting carbon dioxide into useful molecules is an ability that makes cyanobacteria interesting as a production system for the biotech industry. However, with this ability a few disadvantages arise. One of them is a slower growth rate, and therefore a longer recovery time, after performing genetic modifications. Furthermore, the genetic tools needed for genetic modification are not as developed as for industrially used organisms like E. coli and S. cerevisiae. This makes introduction of new synthesis pathways slower in cyanobacteria than it is in other well-studied species. Therefore, we leave the production of chemicals to the organisms that have already proven themselves well suited for this task.The carbon source that the cyanobacterium is modified to overproduce is acetate. It was chosen since it is naturally present in the metabolism of cyanobacteria. Furthermore, acetate production by Synechocystis has been shown to be possible both in previous publications5 and iGEM projects6. Overproduction of acetate in Synechocystis is achieved by knock-outs and knock-ins of genes involved in acetate metabolism. The cyanobacterium is also made auxotrophic for arginine or glutamine to make it reliant on the production organism and prevent it from surviving outside the lab. In this case, the arginine auxotrophic bacteria will be co-cultured with prokaryotic production organisms and the glutamine auxotrophs with eukaryotic organisms. What production organisms will we use in this project?Four different industrially relevant organisms are modified to be compatible with the symbiotic production system. These are Saccharomyces cerevisiae, Escherichia coli, Yarrowia lipolytica and Bacillus subtilis. As described earlier, all production organisms will have to produce an amino acid that the cyanobacterium requires. Due to the difference in metabolism and regulation of amino acid synthesis, it proved difficult to make all organisms secrete the same amino acid. Therefore the eukaryotes (S. cerevisiae and Y. lipolytica) are modified to secrete glutamine and the prokaryotes (E. coli and B. subtilis) are engineered to secrete arginine.All of the production organisms except for Bacillus subtilis are capable of growing on acetate in their wild type state. An operon from its cousin Bacillus licheniformis is therefore incorporated into the Bacillus subtilis strain. We have chosen to work with B. subtilis over B. licheniformis due to the expertise available at our lab and the biobrick library available for this organism.With the four production organisms we will create a library of organisms compatible with the symbiotic production system. Our solution will provide a platform for a versatile system that converts carbon dioxide into everyday products in an environmentally friendly and sustainable way.


HokkaidoU_Japan

Hydrogel is used in contact lenses and diapers. Some kinds of hydrogel are made of self-assembling peptides. They are amphiphilic peptides and they form nanostructured hydrogel under physiochemical conditions. Recently, they have been considered as a good biological scaffold for cell culturing and drug delivering. They are synthesized chemically such as solid-state synthesis, but it’s not efficient for production in large amount. So, we need another approach including biosynthesis.In this research, we expressed self-assembling peptides such as RADA-16 I and P11-4 in Escherichia coli and analyzed them by series of experiments. We also considered application of hydrogel to immobilized proteins, which may enhance the stability of proteins. Immobilized proteins will be used in medicine and environmental study in the future.


AUC_TURKEY

It takes several centuries for PET (Polyethylene Terephthalate) plastics to degrade in nature. With its extensive use in industry and ever-so-growing market, Polyethylene Terephthalate is everywhere around us. They are thrown out into nature, mixing into waters, contaminating seas and soil; degrading the quality of life and posing a threat to animals. Today’s commonly preferred recycling techniques need enhancement; in this light, alternative recycling technologies are pursued, albeit a competitive biological method is yet to be designed. Aiming to degrade Polyethylene Terephthalate effectively, we have generated a biological system based on E.coli; which will degrade Polyethylene Terephthalate, eliminating the toxicity by giving off non-toxic and safe products. Introducing enzymes with possibly higher activity than previously used PET degrading enzymes, our system enables a high quality and simple technique with highly pure results.


Dalhousie_Halifax_NS

Deep within the porcupine gut lies a concoction of microorganisms (called a microbiome) and their accompanying enzymes. We believe this fascinating microbiome holds the secret as to why porcupines are capable of digesting tree bark and sap, where as other mammals such as ourselves, are incapable of doing so. The Dalhousie iGEM team is working in close partnership with Schubenacadie Wildlife Park which has provided mammal fecal samples that we can use for microbiome analysis. As much as we are interested in learning about porcupines, we are also interested in learning about the other mammals living at the park. This will allow us to broaden our range, and find more microorganisms of interest. Once the organisms are identified, we can use online search tools like Blast to find enzymes and biosynthetic pathways within the microbiome organisms that are capable of utilizing cellulose or tree sap for the creation of bioplastics, biofuel and potentially many other useful products. The project has developed into three mini-projects that we hope will illuminate not only the porcupine microbiome but also the bacterial population found within the Schubenacadie ecosystem. The first project involves sequencing the porcupine microbiome. A preliminary test was conducted utilizing porcupine fecal samples collected on our first expedition to the park. The samples were prepared via a PowerFecal kit (Mo Bio) and then sent for 16s sequencing at the Integrated Microbiome Resource at Dalhousie University. We are still waiting for our results. On the second expedition to the park, we were provided with twenty fecal samples from mammals such as porcupines, black bears, beavers, deers, otters, and rabbits. These samples have recently been prepared for 16s sequencing using a PowerFecal kit. We hope that once we sequence the microbiome of these twenty mammals that we can produce a microbiome map for the park. The second project involves plating the fecal samples on various media and identifying what grows. To begin, cellulose media was prepared as we believe the media to be very selective. Furthermore, identifying bacteria capable of surviving in a cellulose environment will have down steam implications as future teams can study the cellulose degradation properties of these bacteria and their potential biofuel capabilities. Two rounds of plating occurred using porcupine feces from the first trip to the park and from the second. It appears that there is limited growth on the cellulose plates (in comparison to regular LB agar plates) but two colonies have emerged. As the team is interested in identifying the bacteria that allow for digestion of tree bark and sap, sap containing plates were prepared. Any bacteria that grow on the cellulose plates will then be transferred to the sap plates to see if they can survive in these even harsher conditions. We have yet to transfer any bacteria to the sap plates as the first round of cellulose plating was considered preliminary to ensure the selectivity of the media. The third project involves the formation of a genomic DNA library of the environmental DNA collected from the porcupine sample. This stage of the project is very much in its infancy as the team is still working on preparing the vector and the environmental DNA. Dalhousie iGEM hope that these experiments will not only provide immediate insight into the Schubenacadie ecosystem, and porcupine microbiome but will also lay the foundation for exploring biofuel production and cellulose degradation by characterized as well did novel porcupine bacteria.


BIT



BGIC_China

Open source Cell-free system based test paper platform1.2.3 To design, test and, if possible, manufacture test paper reader1.2.4 Pearl necklace-shaped test paper effectiveness assessment1.3.3.3 Creating Estradiol Receptor (E2R) and Progesterone Receptor (PR)1.3.3.4 The testing of cell-free system reaction on a paper discAs the first high school team of BGI-college, we endeavour to construct a paper-based cell-free system with whose function is to measure the concentration of target molecules in the sample within a certain range. What matters the most is that this attempt can be attributed into the application of bionics as the transcription and translation devices of the original cell is still present in the cell smear and thus a testing platform for a variety of molecules is created, and hereby being relieved of comprehensive limitations of using living cells for testing. This test paper integrated with biosensors for target molecules enabled the testing of the concentration of a variety of target molecules(various hormones, glucose, fatty acid or nitrates,etc.) in various clinical samples of plasma, urine or saliva. Quantitative results can be shown by the output of a variety of proteins.(light emission of GFP or the changing of colour initiated by LacZ,etc.). The high portability of the test paper and the small duration of the testing process of clinical samples, should the test paper be successfully manufactured, shall relieve millions of patients of comprehensive time-consuming and perhaps agonising medical inspections—these could be carried out at home! The test paper system, presumably, transcends mainstream medical inspections of clinical samples in means of efficiency and convenience.Our idea originated from comprehensive discussions that eliminated the alternatives of acetochlor test papers which already exists in the market at a feasible price and the cholinesterase injection plan for protection of nerve system against Sarin gas as the project relied upon the injected medicine’s access through the Brain-Blood Barriers——an unsolvable dilemma. The idea of cell-free test paper system came up before we came across two articles that outlined the feasibility of a paper-based cell-free system for inspection of clinical samples targeting at specific molecules(1)(2). With the solid theoretical foundation and overwhelming feasibility compared to the other ideas listed above, the cell-free test paper system was chosen by the team unanimously. In late April, the designing of our plasmids was initiated via comprehensive methods, which, upon finishing even as we post this passage, has gone through three phases. Upon the biosensor’s contact with the target molecule, the genetic circuit will produce an output with the fluorescence of a GFP.Our goals go as follows. The very foundation of our targets is to apply our cell-free system, the system of cell environment simulation which consists of cell-extract and substrate that enables DNA expression in vitro to a mature test paper module. Laboratory sample and clinical sample tests will be carried out to assess the effectiveness of the coalition. To make that happen, we will attempt on testing the feasibility of our test paper prototype in pursuit of building up a semi-quantitative test-paper system. Constant amendments, adjustments and improvements to the laboratory tasks specified in the original plans and/or to the plans themselves may be made for the better in accordance with the outcome of the attempt of putting theoretical research and arrangements into practice.1. A Courbet, D Endy, E Renard, F Molina, Jérôme Bonnet, Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates. Science Translational Medicine, Vol. 7, Issue 289, pp. 289ra83 (2015)2. Keith Pardee, Alexander A. Green, Tom Ferrante, D. Ewen Cameron, Ajay DaleyKeyser, Peng Yin, James J. Collins, Paper-Based Synthetic Gene Networks. Cell 159, 940–954 (2014)4.2.1 Risks to the safety and health of team members, or other people working in the lab4.2.2 Risks to the safety and health of the general public (if any biological materials escaped from our lab)4.2.3 Risks to the environment (from waste disposal, or from materials escaping from our lab)4.2.4 Risks to security through malicious misuse by individuals, groups, or countries4.2.5 What new risks might arise from our project's growth?4.2.1 Risks to the safety and health of team members, or other people working in the lab4.2.2 Risks to the safety and health of the general public (if any biological materials escaped from our lab) 4.2.3 Risks to the environment (from waste disposal, or from materials escaping from our lab)4.2.4 Risks to security through malicious misuse by individuals, groups, or countries4.2.5 What new risks might arise from our project's growth?


BNU-China

We established our team at about March. Our team consists of different majors, such as biology, math and computer science. Except the twenty team members, we also have two professors and a secondary PI to provide help for the experiment. We divided our members into five groups, they are experimental group, modeling group, wiki group, art group and human practice group. Each group has a leader to be responsible for the details. We organize the meeting with our instructors and secondary PI once a month. We decided the direct on 8th April. At the meeting, our members put up with a lots of ideas. microbic color palette In order to draw a picture using bacteria, we’d love to create a system which can sense different wavelength of the light, and make different pigment in specific areas. We can transform different kinds of photoreceptor genes into E.coli to form different kinds of cells, which can exhibit corresponding colors. So, when we illuminate an area with a certain kind of laser, different kinds of color can appear, and form images. microbic computing system in order to break the limitation of the theoretical physics in electronic computer, which cannot deal with the NP question until now, we want to design a Hin/hixC system in bacteria, to solve those NP questions which have a high value of practical application. ammonia production We already know that nif gene cluster controls the synthesis of nitrogenase in many organisms. We want to transform part of nif gene into E.coli, to create a new bacteria which can produce ammonia. Engineered Multi-domain Protein Machine We’d love to combine some functional domain of different proteins in order to make a protein machine which can finish a certain biological process more efficiently. microbial desalination cell (MDC) We’d love to design a device in order to desalinize sea water. In a battery, we place Lactobacillus amylovorus in anode chamber, and we place cyanophyta in cathode chamber as carbon source. After discussing over and over again, meanwhile consulting our instructors and advisors for so many times, we finally decided to reform the cyanobacteria into a proper chassis. Considering that the cyanobacteria has the characters of autotrophy, the capacity of fixing dioxide, high growth rate and a simple genetic background, we realized that it can be an excellent chassis for synthetic biology. To make the cyanobacteria a perfect chassis, several optimization measures have to be done, such as improving their efficiency of photosynthesis, enhancing their resistance to the environment and promoting the efflux of the products, after which the cyanobacterium can be applied to produce biofuel or other chemical substances with lower consumption of nutrition. Our present plan is to focus on the improvement of cyanobacteria's photosynthesis and try to make other optimization at the same time. In addition, we may as well try another project of making plants shining using the endophytic bacteria Bacillus subtilis to provide light at night because we think it also interesting. So our next step is to try both of the projects and then find the one more suitable to be our subject this year.


BostonU

Synthetic biologists seek to control the behaviors, specifically those behaviors dictated by gene expression. To do this, they look to cells to provide a blueprint for their designs. However, scientists like Timothy Lu have noticed a distinct dichotomy in the field of synthetic biology surrounding cellular blue prints, “Living cells implement ... both analogue- and digital-like processing ... In contrast to natural biological systems, synthetic biological systems have largely focused on either digital or analogue computation separately.” Currently in the field, most methods of gene regulation are either digital (transcriptional activators, repressors, and inducible circuits) or they are analog (oscillatory circuits). This summer our team desires to develop a synthetic promoter toolkit that can generate both digital and analog genetic expression. To do this, we have developed three main aims for our work this summer. The first aim is to develop a digital toolkit that is tunable, modular, and orthogonal. Tunable refers to a system with consistent replicable levels of gene expression similar across several activating complexes. Modular refers to a tolerance to several genes of interest and genetic architectures. Orthogonality refers a system that will not activate endogenous genes as well as produce cross talk over several activating complexes. The second aim is to develop the analog component of the toolkit by developing a grade genetic expression. By this, we are referring to a system that can produce low, medium, and high levels of gene expression with the same level of accuracy as the digital component of the toolkit. Finally, our system must be able to function in the complex cellular environment of human cells to prepare it for ultimate use in therapies. To perform these task, we discussed the various methods by with gene expression can be modulated in cells. These techniques include Zinc Finger, TALEN, and CRISPR/dCas9. The decision was reached that CRISPR/dCas9 would be the tool of choice for our toolkit due to both its ease to engineer as well as its legacy in the foundational research category of iGEM (see Freiburg 2013). As a foundational advancement focused group, applications for our project are years off, however there are several speculative areas of interest. In many cases production of proteins harmful to host cells, like antibiotics, are difficult to do in large quantities due to the risk of death to host cells. By introducing a scalable response, scientists can increase efficiency without killing the host cell by properly finding the point at which the cells metabolism can no longer contend with the stress. In regards to therapeutics, this system could either allow doctors to properly dose a patient with gene expression in a similar way to how traditional pharmaceuticals functions. In addition, if this system was integrated with genetic logic circuits, the level of gene expression during a therapy could be theoretically modulated after implantation to once again better address the needs of a patient.


ASIJ_Tokyo

We are surrounded by plastic everyday, specifically PET (Polyethylene terephthalate). Considered as the most common type of polyester, PET is a plastic resin often used for packaging consumer products. We can also find it in our water bottles, plastic toys, and even in the fiber of our clothing. PET is a combination of two monomers known as ethylene glycol and purified terephthalic acid that, when combined, form the polymer PET. The problem with PET is that although it is a convenient material for humans to use, it does not easily biodegrade. As PET accumulates in the ecosystems around the world, it poses detrimental effects on habitats worldwide. That is why it is crucial that we find an efficient way to degrade PET. Upon conducting our research on plastic degradation, shortly after deciding to focus on this topic, our team came across a joint collaboration research project from Keio University and the Kyoto Institute of Technology, two prestigious universities in Japan. Their paper explained their recent research on PET degradation into terephthalic acid and ethylene glycol using a new bacterium originating from Japan called Ideonella Saikaienis. We were inspired by Ideonella Saikaienis because it was a wonderful PET degrader (containing PETase) from Japan, our current home. Given this, when we realized that the production of PETase was from a uniquely Japanese context, we saw it only apt to center our project around this as it showcases a special (and scientifically recent) feature of the Japanese environment. Consequently, our aim and experimental idea were born: to optimize the use of PETase and hopefully add a new biobrick to the iGEM catalog. Turkey’s 2014 project on PET degradation as well as The University of Washington's 2012 project and Darmstadt's 2012 Project also provided us with inspiration on the potential applications for our project in addition to lab protocol ideas. We chose to optimize PETase as our goal to make a new type of biobrick available to future iGEM teams. We hope that this will make experiments in the following years easier to conduct. However, in order to even get to that stage, we recognized that we needed a well thought out procedure. Our team is currently working on this step. Thus far we have determined we will be using a western blot test to help us deal with the signal peptides. Currently we also have three promoters (one on the slightly weaker side and two on the stronger side) taken from the list of Anderson promoters to test in order to determine how to make PETase most efficient. Before testing such promoters though, we need to isolate evaluate each promoters' effectiveness and efficiency. This information is essential before we proceed onto our next steps and think about real world applications. Questions we may ask ourselves following this first step include: “How long will the degradation take?” and “Will the byproducts of the degradation be harmful in any way to the environment or to people?” Our aim, as stated above, is to find a faster, more efficient process to degrade plastic. Answers to such questions will be essential in seeking solutions to global environmental problems. In regards to the first question, to our current knowledge, 450 years is the timeframe for the natural biodegradation of PET. From our perspective this is much too inefficient when you consider how much PET we use daily. As a result, our experiment will focus on increasing the efficiency of the degradation of plastic through the manipulation of PETase. These are just some examples of the types of questions that we must first consider. Once our confidence in our research progresses, we can then fully focus on individual procedural steps of our project such as the Western Blot. Keio University and Kyoto Institute of Technology. (2016, March 30). Discovery of a Bacterium that Degrades and Assimilates Poly(ethylene terephthalate) could Serve as a Degradation and/or Fermentation Platform for Biological Recycling of PET Waste Products [Press release]. Keio University. Retrieved June 30, 2016, from https://www.keio.ac.jp/en/press_releases/2016/cb96u90000005501-att/160330_2.pdf P. (2015). FAQs - Frequently Asked Questions. Retrieved June 30, 2016, from Hampson, M. (2016, March 09). Science: Newly Identified Bacteria Break Down Tough Plastic. Retrieved June 30, 2016, from http://www.aaas.org/news/science-newly-identified-bacteria-break-down-tough-plastic How Long does it take to Decompose - Facts Analysis. (2012, January 24). Retrieved June 30, 2016, from http://www.hoaxorfact.com/Science/how-long-does-it-take-to-decompose.htmlT. (n.d.). Labjournal Metabolism. Retrieved June 30, 2016, from http://2012.igem.org/Team:TU_Darmstadt/Labjournal/MetabolismM. (n.d.). Team:METU Turkey project. Retrieved June 30, 2016, from What is PET? (2015). Retrieved June 30, 2016, from Yoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maehada, Y., . . . Oda, K. (2016, March 11). Supplementary Materials for a Bacterium that Degrades and Assimilates Poly(ethylene terephthalate). Science, 351, 1196th ser. Retrieved June 30, 2016, from file:///Users/lisawatanuki/Downloads/PETase supplemental (2).pdfYoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maeda, Y., . . . Oda, K. (2016, March 11). A Bacterium that Degrades and Assimilates Poly(ethylene terephthalate). Science, 351(6278), 1196-1199. doi:10.1126/science.aad6359


Denver_Biolabs

In 2015, over 300,000 women died during pregnancy and childbirth; 99% of these deaths occurred in developing countries. Postpartum hemorrhage (PPH), or severe bleeding after birth, is the leading cause of maternal mortality worldwide. Oxytocin is a naturally occurring hormone and a medication that is used to increase contractions in the uterus (i.e., induce labor). It has also proved effective in significantly reducing the risk of PPH. Oxytocin is now routinely used in industrialized countries, and is often given in small doses simply as a preventative measure in normal labors. However, oxytocin is not readily available in developing countries. Despite being on the World Health Organization’s List of Essential Medicines for developing countries and being relatively inexpensive (as of 2014, the wholesale cost of the medication is US$0.1–0.56 per dose), oxytocin requires storage at between 2 and 8 °C, which has led to a shortage of this critical drug in rural areas that lack reliable refrigeration, power, and infrastructure. Quality issues with existing oxytocin inventories have also been identified as a significant issue in rural areas.Our first goal is to build an oxytocin detection system using a G-protein coupled receptor in yeast that will allow us to verify the presence of active oxytocin. If successful, we will then focus our efforts on synthesizing oxytocin in various forms to increase its availability in resource-poor areas.Oxytocin is produced in the body by the OXT gene. It is synthesized as an inactive precursor peptide along with its carrier molecule neurophysin I. After several iterations of hydrolyzation via enzymes, the active oxytocin molecule is produced. In 2013 an iGEM team from Lethbridge Canada created a form of oxytocin still attached to its carrier molecule, neurophysin I, which prevents degradation until the carrier molecule is cleaved resulting in the activation of the oxytocin molecule. Our team plans to significantly build on this prior work by exploring several other approaches to improving the stability of oxytocin including producing a powdered form of the drug that can be activated using hydrolysis, adding trace metals to prevent oxidation, and using optogenetic techniques to activate oxytocin using light. In addition to these synthetic biology approaches, the diversity of our team’s skills will allow us to explore several mechanical and hardware solutions including simple, non-refrigerated single-injection systems; biological packaging solutions to prevent oxytocin’s degradation; and testing systems to evaluate the quality and effectiveness of current oxytocin inventories. The solutions we plan to explore will target practices ranging from manufacturing, transportation and storage, and distribution to drug administration protocols, drug quality monitoring and control, and improved documentation and inventory to support further research and quality care.The potential impact of any and all of these solutions will be to increase the availability of oxytocin for use in under-resourced maternity facilities.


ColumbiaU_NYC

If you were to ask your friend to list the most deadly animals, he or she would probably include lions, tigers, and bears (oh my!). However, they may be surprised to hear that the mosquito deserves a high place on this list. According to the World Health Organization, mosquitos account for more than one million deaths annually. These deaths are caused by mosquito-borne illnesses including West Nile virus, elephantiasis, dengue fever, yellow fever, malaria, and more recently Zika. With the recent outbreak of the Zika virus, the World Health Organization and the Centers for Disease Control and Prevention have labeled Zika as an international health concern. With no known treatments or vaccines currently available, prevention is the only option to combat Zika. Citronella oil and DEET are the main commercially available repellents against Zika-carrying mosquitos, yet these products possess several shortcomings. Each repellent stops being effective approximately three hours after application. However, many users are unaware of this time frame. Consequently, they are unprepared to reapply and are left unprotected. Applying current mosquito repellent can lead to a false sense of security, which can cause a person to be more prone to mosquito bites. While citronella oil has a lower efficacy than DEET, DEET has been shown to be harmful to skin, causing painful rashes. DEET is also harmful to the environment since its chemical runoffs can disrupt neighboring wildlife. Although DEET and citronella oil are viable mosquito repellents, they are by no means ideal. Our project hopes to provide a safe, long-lasting mosquito repellent using microbiome. Recent research has shown that the biomolecule di-rhamnolipids, naturally produced by Pseudomonas Aeruginosas, effectively repels mosquitos at low concentrations. This biomolecule is safer than DEET and more effective than citronella oil. However, di-rhamnolipids are expensive to produce synthetically. Furthermore, although naturally found on human skin, Pseudomonas Aeruginosas is known to be pathogenic. Pseudomonas Putida, an environmental strain found in soil, survives well on most surfaces, and is non-pathogenic. Using Putida, we are designing a safe bacteria strain to produce rhamnolipids. As a more long-term option, we will also be modifying Staphylococcus Epidermidis, a natural skin microbe, to produce rhamnolipids. The probiotics would be applied to the skin via a lotion rather than a spray like most repellents to prevent the loss of the product to the environment. These bacteria would continuously produce the mosquito repellent on the skin thereby increasing duration of efficacy as well as cost effectiveness as less repellent would need to be purchased. The experimental plan is as follows: building a recombinant plasmid with the genes necessary to produce rhamnolipids, transforming this plasmid into Pseudomonas Putida and Staphylococcus Epidermidis, and quantifying the amount of rhamnolipids produced by these engineered strains. Rhamnolipid will be quantified using TLC, CTAB assay, Orcinol Assay, and various spectrometry techniques such as MS, HPLC-MS, and SFC-MS. Additionally, we will do experiments to analyze the effects such biosynthetic repellent will have on mosquitoes. Ultimately, we plan to analyze the effects rhamnolipids have on skin by conducting experiments in mice. Lastly, we hope to conduct experiments that include both mice and mosquitoes to assess to what extent the repellent is effective.


ETH_Zurich

The inflammatory bowel disease describes the chronic inflammations of parts of the intestine and is a collective of several further specified illnesses. The most common conditions are ulcerative colitis and Crohn's disease. It is classified as an autoimmune disease for which no cure has been developed so far. Current treatments include immunosuppression, surgery, antibiotics and nutritional therapies. Unfortunately there aren't characteristic blood markers to distinguish the different forms of IBD. The diagnosis relies mostly on the location of inflammation observed during colonoscopy. Also the underlying trigger of the disease is not completely understood but correlation studies proposed factors such as diet, genetic predisposition, breach of the intestinal barrier and the composition of the microbiota, called dysbiosis. It is reported that the diversity of the microbiota is noticeably reduced in IBD patients and that the composition of the gut flora changes from symbiotic to predominantly pathobiotic microbes.And this is where our project comes in. We are developing a tool that allows for investigating the microbiota that is associated with inflammation, namely a harmless bacterial strain that can sense two inputs and store this information until readout. The inflammation of the intestine partially interrupts the integrity of the layer of epithelial cells lining the intestine. This cell layer separates the gut lumen containing trillions of microbes from the body. The damage to this essential barrier compromises the selectivity of it and allows for penetration of immunogenic antigens from the lumen across the epithelial layer1,2 what enhances the inflammation reaction. On the other side, there is also non-normal leakage of inflammation markers into the gut lumen. One of these molecules is nitric oxide (NO) and is one of the molecules we are going to sense with our system. The sensing of NO with E.coli has already been described by Archer et al.3 in 2012 what enables a faster adaptation of this system for our purpose. Aside a general inflammation marker we want to sense molecules secreted by bacteria in order to identify them. One well-known class of molecules secreted by many bacterial species belongs to the quorum sensing (QS) system. QS molecules act as bacterial hormones among and between species which control for example the formation of biofilms and growth behaviour. Furthermore, it was shown that QS molecules can alter the microbiota's composition4. The best known subclass of QS molecules are the N-acyl homoserine lactones (AHL) which will be identified by our living biosensor.Multiple genetic systems referring to QS have been described. In most cases, AHL molecules act as activators for the expression of proteins. But in our system a repressor of protein expression is favoured. A suitable repressor protein is EsaR that was first described in 2002 by Minogue et al5. As this regulatory protein naturally occurs in the plant pathogen Pantoea stewartii it is necessary to change the specificity towards an AHL related to IBD. This will be achieved by directed evolution with an optimized dual selection system similar to the one already used by Collins et al.6 for a closely related regulatory protein. Finally, our system integrates two inputs related to IBD and converts them - if encountered together - into an easy observable output. As there exist several intestinal markers for IBD that ideally are observed in parallel, our system aims at a high level of multiplexing and flexibility. Because the number of distinguishable reporters is limited, we integrate the concept of adaptive learning into our genetic circuit. This allows a potentially unlimited number of parallel measured markers. The information that two IBD related markers were encountered together is stored in the DNA of the bacterial reporter system. When these bacteria encounter just one of the markers again after recovery from the feces – in our case AHL - they express an observable reporter that gives the information that the added marker was encountered together with inflammation.The clinical procedure would look like the following: an IBD patient is given a mix of the bacterial reporter strains, each specific for a certain AHL or another marker along NO. After a certain time, the reporter strains are extracted from the patient's feces and sent to the laboratory. There, the bacteria are grown in different small cultures, each of them containing another marker. The cultures that change their colour give the doctor information on the composition of the inflammation-related microbiota and an appropriate therapy can be chosen as proposed by Thompson et al4.Our bacterial reporter system for IBD related markers gives an enhanced insight into the development and persistence of this chronic inflammatory disease of the intestine. It can be used as a diagnostic tool as well as for fundamental research of the underlying causes. The fact that only in Europe 2.5 million cases of IBD are reported and the number of IBD patients is increasing world-wide7 shows the significance of our project.


INSA-Lyon

Have you ever woken up with no memory of your last party? Your night may have spun out of control and you may have had a risky behavior. What if you could, in only 5 minutes, have the list of all the sexually transmitted diseases (STDs) you may have caught and the drugs you may have taken? What you would want to know is "Did I get a STD? And if so, which one did I get?! Is it the HIV, the syphilis or the hepatitis B?" Very-Bad-Trip is a small paper device that detects biomarkers at a very early state of the infection, and several at once. It's cheap, easy, and gives you multiple answers very quickly to help you remember what happened. Brainstorming Early on, our desire was to search for a cheap, maybe do-it-yourself project of "frugal biology". We rapidly thought of a test on paper. What for? The most documented important health problems are about STDs. Currently available STD self-test kits are expensive (av. $30), based on antigen-antibody detection and only work for one infection at a time. We want to develop something that combines several detections on one chip, and if possible, something fast, low-cost, and easy to use. To get another advantage on what already exists, why not try a more recent and very sensitive technology? We decided to focus our research on detection by aptamers. Principle The diagnosis is based on the interaction between a pathology biomarker (a protein) and a specific DNA sensor (an aptamer). This sensor, anchored on a piece of paper, will enable, from a drop of blood, a direct diagnosis thanks to a fluorescence emission. This project uses an innovative nucleic acid technology and a combination of existing parts, but no cells are used in this detection process. Cells are only used to produce the genetic construction, using synthetic biology. Proof of Concept The proof of concept will be made with ATP and thrombin aptamers. Then, we will work on the detection of HIV and hepatitis B. We are hoping to gather several different tests on a single paper chip in order to create a multi-detection device. Finality The goal is to build a simple, fast, eco-friendly, and cheap device that detects the most common STDs and drugs. Human Practices A reflexion about the conditions of use of our device seems necessary: should it be made available as a self-test kit, or should it be used under the control of a specialist? What about the consequences of the diagnosis? We are gathering opinions from experts who daily work with the detection of STDs, in order to know which major diseases necessitate the development of a new, faster and more sensitive detection test, who are the most concerned people in the population,... RK: DO NOT FORGET TO USE CONDOMS !


Groningen

Protecting data through encryption and storage in bacterial spore DNA. In 2002, the amount of information stored digitally had eclipsed information stored in analog format for the first time [1]. Just five years later, only 6% of the world’s data was still analog [1]. In 2015, an estimated 2,500,000,000,000 megabytes of new data were created every day, and this number is growing at an increasing rate [1]. It is not surprising that data breaches orchestrated by hackers are on the rise as well. Financial and legal records, military and government documents, these are examples of important information that must be preserved for a long time, but could cause great damage in the wrong hands. We have become a civilization dependent on information, and this information must be stored somewhere. As a result, we are faced with two problems: where do we store all of our data, and how do we keep it safe?Storage of data in DNA has been proposed as early as the 1960’s, but has only recently become a hot topic [2]. This is in part due to the ever-growing demand for data storage, as well as advancements in DNA synthesis and sequencing technologies. Our goal is to create a system for long-term data storage and data transfer which cannot be hacked by digital means. Digital methods of encrypting information and converting it into binary code are well established, and data storage in DNA has already been demonstrated. Our project combines these two approaches by first converting information into binary code, encrypting it, and then storing it safely in DNA. Additional measures based on molecular biology will prevent unauthorized access, ensuring the safety of the stored information. Our system will be useful for the kind of information that should be stored and transferred in a very secure manner, but does not have to be accessed quickly (within seconds). It will be possible to obtain the message in about 24-48 hours, however, this timeframe is likely to be reduced as new sequencing technologies are developed. For example, this system could be used to store patent and prototype information, genealogical records, legal and financial records, banking account details, login data or even top secret government documents. Given the stability and compactness of DNA, our system could also be adapted to serve as a time capsule for human knowledge. We use a layered approach with a combination of digital and biological security measures to ensure the information can only be accessed by the intended recipient. The first layer is digital encryption. The information is encrypted with the Advanced Encryption Standard (AES) algorithm, converted into a DNA sequence and integrated in the genomic DNA of Bacillus subtilis, a safe, thoroughly categorized organism capable of sporulation. The binary data obtained after encryption will be encoded into DNA according to the following logic: since DNA consists of four nucleotides namely T, A, C, and G, every nucleotide will represent a binary pair (combination of a 0 and a 1). The T will be represented as 01, A as 10, C as 00 and G as 11. The decryption key and the encrypted message are integrated into two different Bacillus strains and are protected from unauthorized access with additional security layers.Once the message and key are encoded in Bacillus DNA, the cells are cultured in a sporulation-promoting medium. Bacterial spores are among the most resistant biological entities currently known, and thus represent an ideal substrate for long-term data storage. The spores containing the encrypted message and key are freeze-dried and embedded in separate filter papers (or any other porous material) for storage and transfer, along with a spiropyran-ciprofloxacin conjugate [3]. The biological activity of this photoswitchable antibiotic is very low when the spiropyran photoswitch is in its stable closed form, but increases dramatically after irradiation with a specific wavelength of light (in our case, 365 nm) which brings the photoswitch into a less stable, open form. When the light source is removed, the compound slowly reverts back to its biologically inactive state. Irradiation with other wavelengths also results in deactivation. The strains carrying the message and key (which possess resistance to the antibiotic) are mixed with numerous decoy spores when brought onto the carrier material. The decoy spores are not resistant, and do not contain any encrypted information.When the intended recipients want to access the stored data, they place the filter paper with key carrying spores and antibiotic in a culture medium, and irradiate it with the activating wavelength of light. This wavelength must be known by the recipient beforehand. The activated antibiotic kills the decoys but not our key carrying strain. After culturing, their DNA is sequenced and the key is found. The key contains information necessary to culture the message carrying strain, and to decrypt the message. Without activation, all the spores germinate and grow, including the decoys. This makes it impossible to find the key by sequencing. Once the key is obtained, the message carrying strain can be cultured. Their DNA is then sequenced and the message can be decrypted.


EPFL

CRISPR-Cas9 has already revolutionized synthetic biology. To build upon this development we aim to implement digital-like circuits in yeast using a CRISPR-associated RNA scaffold system (Zalatan et al, 2015). Recently, a study published the use of the modular software CELLO which automates the design of DNA circuits using transcription factors in E. coli. As a proof of concept we will modify CELLO to use our dCas9 transistors in yeast for a so-called half-adder system, using AND and XOR gates, that we can then experimentally assess. With this approach we hope to pave the way for even more complex biological circuits in yeasts.We started brainstorming in December and quickly decided to work on the creation of a biological circuit.We were inspired by the EPFL’s 2015 iGEM team, who worked on bioLOGIC. This system uses a catalytically dead version of Cas9 fused with an RNA Polymerase recruiting element (VP64) to create transistors, and depending on the identity of the promoter that dCas9-VP64 binds, it will either be repressed or activated.At first, we created brainstorming groups to find applications of the project. The idea of creating a half-adder stood out from the rest for its possible applications as well as its suitability as a proof of concept. Later, we discovered a program called CELLO that automates the design of DNA based logic circuits.At this point, we split into two groups. The first group worked on the design of the system, the second on the understanding of Cello’s software in order to implement it with our system. The project was defined as to create simple gates using biological parts. We wanted to use d-Cas9 to target specific sequences of promoters and therefore be able to activate or repress the expression of the genes controlled by them. In order to build biosensors, we imagined a system that allows our gates to respond differently to various environments, such as presence of galactose. We also want to implement our system in yeast as they are well representation of mammalian cells and easy to handle. With this system we aim to create an half-adder which correspond to a XOR and an AND gate linked together.As mentioned before, we also plan to modify CELLO to be able to design genetic circuits in yeast using it. Fortunately, CELLO has a modular nature, allowing us to do this easily. CELLO has a User Constraint File that enables users to pass the program information about this system it is designing the circuit for. This file includes information pertaining to the species, the reactivity of gates to inputs, and the plasmids used. In order to obtain this new information, we plan on characterizing our system and gates using photometric experiments.During the process of designing our system, we stumbled upon a paper outlining a more intuitive way to activate and inhibit genes with dCas9, and we decided to improve our project using its results.This paper describes synthetic dcas9-based transcriptional programs in yeast. Instead of having the dcas9 unit fused to an activator or repressor protein, the guide RNA is extended to include an effector protein recruitment site, so that scaffold RNAs that encode both target locus and regulatory action.Using a dCas9 based system with scaffold guide RNAs offers numerous advantages with regards to previous biological circuit designing systems. Firstly, using gRNAs as parts of gates, instead of transcription factors reduces toxicity related to transcription factor density in the nucleus. In addition, our system can be even more complex than systems based on transcription factors since the amount of connections between gates are not limited by the amount of transcription factors available. Finally, the use of scaffolding RNAs simplifies design, since we can have just one dCas9, and it will also hopefully lead to more predictable repression and activation in the system.


Duesseldorf

The optogenetic induction of apoptosis in the budding yeast (S. cerevisiae) should serve us as a model for the future application in cancer cells. The application of optogenetic switches enables us to induct extremely precise and multiply regulated killing of cells. Thereby this system will represent an improvement in comparison to conventional, less target-specific methods. The sequential utilization of two optogenetic switches, namely a phytochrome-based expression system and a LOV2-based switch needed for the localization of apoptotic proteins to the outer mitochondrial membrane, allows the attainment of a very high level of spatiotemporal specificity for apoptotic activation.


Emory

Synthetic Biology is largely restricted to well-funded laboratories at major research universities in high income countries. One significant barrier to entry is the capital cost of instruments. The cloning and assembly of BioBricks, for example, includes the transformation of Escherichia coli, which requires the purchase of a refrigerated centrifuge and an ultra-cold freezer. Here we assemble BioBrick-compatible shuttle vectors for Acinetobacter baylyi ADP1, a naturally competent relative of E. coli that grows as rapidly under identical conditions. We will show that A. baylyi can be transformed with recombinant DNA simply by adding ligation reactions to mid-log cultures; transformants are selected as usual by spreading them onto LB agar plates supplemented with the appropriate antibiotics (kanamycin, spectinomycin, tetracycline, cefotaxime or amikacin). These experiments will show how BioBricks can be constructed and assembled in modestly funded laboratories in community colleges, high schools and even private homes. The resulting plasmid constructs retain their pSB1C3 backbones and will thus remain compatible with the BioBrick standard and capable of replication in the widely used E. coli chassis.


Ionis_Paris

Nowadays, Volatile Organic Compounds (VOCs) are commonly found pollutants that have been proved present in a wide variety of everyday life situations. Though they are dangerous and present almost everywhere, VOCs are not efficiently detected. Usual detection devices are very unprecise or requires a very long exposure time. This is why we developed the Quantifly project: a combination of a bacterial biosensor , perfectly adapted to on-field measurements, and an innovative drone that will allow us to easily and rapidly quantify the amount of VOCs in the air. The biosensor relies on bioluminescence , a biochemical phenomenon that is commonly used in cell imaging. We are trying to develop a new application for bioluminescence that should allow us to create a biosensor of a new kind, entirely different from the existing devices. As for the drone, it will be designed to safely contain our organisms and carry them on the field, thus acting as mobile detection platform Our brainstorming This project started when we had the idea to find a new application to bioluminescence, other than tagging or imaging. We noticed that bioluminescence seemed underestimated in the competition, which encouraged us to find a project using it in a very innovative way.The idea of using it in the detection of pollution came to us with the recent environment related conferences such as COP21 that took place in Paris. As a french team, we were very sensitive to this event and the issue of constantly increasing pollution levels, and decided to bring a contribution in order to fight the major flaws that actually exists in air quality measurement. We thus decided to focus on the creation of a drone transporting bacteria that would be able to detect and measure air pollution levels on field. The iGEM IONIS team is developping its project through different axes. We are focused on two areas : the development of our prototype and the realisation of our own european jamboree, the European Experience. Our prototype Our R&D team is working hard to develop a complete and functional prototype. This prototype is what we can call a biological system. It is composed of : - An engineered micro organism such as a bacteria containing our biosensor plasmid - A drone designed to allow the hermetic transportation of our micro organism while being able to react to the air pollution In order to lead this project to its realisation, our biology team works in pair with mechanical engineers and computer scientists to develop our product, making our project a multidisciplinary work, which is our strength and allows us to adopt a different approach to synthetic biology. The European Experience The iGEM IONIS team and the iGEM Evry team worked together to accomplish a great gathering of the european teams : a european jamboree ! We organized over a week end a symposium with more than 150 people that could assist to conferences and expose their projects, and create great network through the iGEM competition. We also wanted to give all european teams the opportunity to live an incredible weekend, by coming to Paris and being able to live the "science dream" in the city of light ! Though our project aims to realise a lot in a short period of time, we have objectives that would develop further our project Quantifly :


Edinburgh_UG

The last decade has seen an exponential increase in data and information generation, creating a storage demand that will soon outweigh supply. By 2040, global data storage demand will reach 3×10^24 (3 million billion billion) bits1.. Considering the amount of energy required to run a data centre (about 2% of global energy consumption2.) and the limited supply of raw materials like silicon for manufacturing memory devices, it is clear that novel storage methods are of the utmost importance in meeting demand and providing a sustainable, long term solution to the data storage problem. The University of Edinburgh 2016 undergraduate iGEM team held these considerations in mind when we set out to create a new DNA-based storage system. Over the course of weeks 1 and 2 our team explored and researched ideas for a project utilising DNA as an information storage device. Our brainstorming process evolved through discussions about the advantages and disadvantages of DNA synthesis and encoding digital information into nucleotide sequences. Major points of debate were cost, fidelity and efficiency of data storage. Following some constructive feedback from our supervisors, our team focused on developing a method that is accessible, sustainable and fits the iGEM format. Our project, given the name BabblED, is based on a simple idea: develop a modular system for encoding text, or any other unit of information, into DNA. We will prove the validity of our concept by encoding Ogden’s Basic English (a collection of 850-1,000 words that can be used to express most concepts in the English language). Each encoded word-a BabbleBrick -will be stored in a different PhytoBrick. Sentence assembly and unidirectionality is ensured by the stepwise addition of BabbleBricks that have alternating types of sticky ends; this also prevents repeats and minimizes the occurrence of missing words. The whole sentence construct can be melted off for easy retrieval and assembled back into a PhytoBrick for storage. Since the value that is assigned to each BabbleBrick is arbitrary, each one can be reused with any library or language. In this way, our encoding and assembly method can be optimized for many types of data. Furthermore, using tools such as checksums, optimal rectangular codes and, when appropriate, natural language processing techniques, we are able to ensure that each BabbleBrick sentence can be decoded with 100% accuracy. As of week 4, we have developed the computer program that converts our vocabulary to BabbleBrick sequences. We have designed the DNA sequences for error-correcting codes and researched the benefits and potential ways to utilize encryption in our method. We are in the process of ordering our first BabbleBricks in the form of gBlocks from IDT and testing our assembly method for efficiency. We have commenced the 2016 Interlab study and are pursuing another exciting project on bacterial growth-based logic. We have already had some fascinating discussions with data specialists and librarians; their feedback and expertise are vital to how we are shaping our project. We have also been in touch with other iGEM teams, such as Newcastle and Dundee, and are hosting a Scottish team meet-up in the beginning of July.


Duke

         Taxol, generically known as paclitaxel, is a chemotherapy drug highly efficient in combating multiple forms of cancer via interference with the normal breakdown of microtubules during cell division. Taxol’s efficacy has earned it a place on the World Health Organization’s Model List of Essential Medicines, a roster of the most critical medications needed for a basic health system.          Not surprisingly, there is an ever-increasing demand for taxol. Unfortunately, current production methods for the drug do not provide a long-term, sustainable supply. Taxol is derived from the bark of the Pacific yew tree, Taxus brevifolia, but isolation from its natural source is hindered by the slow growth of the tree and by the low concentration of the drug in the bark. Consequentially, large numbers of yew trees must be harvested for modest returns. Other production methods make use of chemical and semi-chemical synthesis, but the intricate stereoisomerism and multistep pathway of taxol production result in low yield rates and high production costs. Deriving taxol from nature is environmentally unsustainable; chemically synthesizing it is economically unsustainable. Biosynthesis of taxol is the best solution to the shortcomings of the aforementioned production methods. Plant cell fermentation has been shown to synthesize taxol somewhat effectively and requires minimal harvesting of the yew tree. As impressive as plant cell fermentation is, the potential for taxol synthesis in bacteria, an organism much simpler and far more optimized for fermentation, is vastly greater. Duke iGEM’s goal is to optimize the biosynthesis of taxol in E.coli.          Our primary objective is to individually characterize and then consolidate known enzymes of the taxol biosynthesis pathway into a single strain of E.coli. As such, our research plan consists primarily of two components: a cloning project and kinetic assays to characterize the system. Additionally, the existing enzymes as found in published literature may be insufficient for highly effective production of taxol. In their current states, the enzymes have a wide range of turnover rates that would lead to bottlenecks in the pathway even with high expression. Optimization projects targeting the enzymes with the lowest turnover rates will be undertaken to remedy the bottlenecks.          Currently, we have successfully cloned the majority of our enzymes into E.coli using Gibson assembly and are in the early stages of kinetic assays, most of which take advantage of CoA chemistry. Once cloning and assays are complete, we will combine the enzymes into one plasmid via Golden Gate assembly.          More efficient synthesis of taxol will lower the cost of the drug and its production, but this cost is not the only determining factor of accessibility. In order to understand how lowering the cost of drug production will translate into more available treatment, members of Duke iGEM with experience in bioethics, pharmaceutical patent law, and economics are analyzing and modeling the actual cost of taxol treatment by taking into account healthcare systems and distribution logistics.


NCTU_Formosa

Here is our preliminary team project descriptions! Abstract    Sustainability is the capacity to endure. It is how biological systems retain its diversity and productivity, whereas various food chains build up specious sustainability. Our ultimate goal is to eradicate pests and minimize human disturbance of the ecological equilibrium by engineering the venom of one of the most notorious predators on earth, spiders.     Through extensive research, we obtained the desired venom proteins. In our project, we called it PANTIDE. Unlike most commercialized pesticides, which are reported to be involved in the demise of bees, PANTIDE targets directly and specifically to the species from the orders, including Lepidoptera, Coleoptera, Diptera and Dictyoptera. Preliminary Project Brainstorming & Accomplished Work  We had several ideas on the table such as metal recycling coupled with electricity generation, optimizing heterologous protein production, bio- battery, conductive bio- cable, and bio- color printer. Through idea discussing and credible papers searching, biological pesticides prevailed as our project since we have foreseen the urgent need of it and how immense the use of chemical pesticide involves.      So far, for human practice, we have visited the green markets and Taiwan Agriculture Research Institute Council of Agriculture several times for improving the experimental design and get the knowledge of the general agricultural situation in Taiwan. Aside from farmers and researchers, we also intend to grasp general cognizance of the issues chemical pesticide brought about; consequently, we have done some internet survey for public in NCTU_FORMOSA Facebook page. Last but not least, we create a mind-boggling table game that promotes the concept of synthetic biology and propagates the ideology of our project. Ongoing Progression Except for the addition of a special protein that enhances PANTIDE’s orally-active toxicity, we will establish a small-scale experimental farm to simulate the real condition in nature for attracting pests, and we will raise the pests in the preparation of performing the experiment. Additionally, we utilize mathematical methods to set the modeling for the degradation of PANTIDE and differentiate the intrinsic factors and extrinsic factors that affect the toxicity of PANTIDE. For future human practice, we plan to pay field visits to several organic vegetable farmers and tea growers to further investigate the condition of farmland and ecology. In the ongoing progression, we strive to integrate technology into agriculture and create a novel system that cleverly tackle with the long-lasting problem that creepily devastates the sustainability of the environment and human health.


Lethbridge_HS

When our team started meeting, we had many great project ideas, such as taking on autoimmune disorders or treating fetal alcohol syndrome. We also considered bacterial fuel cells, terraforming bacteria, biofilm inhibitors, and synthetic ivory production. After a gladiator-style fight to the death, we narrowed it down to clotting blood. We asked ourselves who we wanted to help, what kind of wounds we wanted to treat, and how we could interact with our community. We decided that we want to focus on the medical field, more specifically medical treatment in emergency situations. We recognized that in most emergency situations, excessive blood loss is a threat that could result in hypovolemic shock, anemia or even death. Preventing or reducing blood loss would greatly increase the chances of survival as well as speeding up the healing process. After discussing different wound sizes and how our project could be applied to each, we decided we would focus mainly on treating medium to large sized wounds. Then, we started designing a construct based around snake venom. Some snake venoms are very effective at inducing blood clotting by skipping many steps of the clotting pathway and thereby greatly increasing the rate of blood clotting. The Cerastes cerastes snake venom acts similar to thrombin in the blood clotting cascade, causing inactive fibrinogen to be converted into active fibrin monomers. Along with Factor XVIII, the fibrin monomers form a crosslink structure that traps red blood cells, resulting in a blood clot.For human practices we have been contacting professionals in relevant fields to ensure that our project is applicable in real-world emergency situations. Another component of our human practices is the community outreach we have been conducting. For example, we have gone to schools in Southern Alberta to educate students with respect to our project and iGEM. In addition, we have devised a public survey, went door to door, and created a social media account to try and establish an amicable rapport with those affected by severe bleeding and members of our community.In the lab, we hope to successfully express our recombinant DNA in E.coli, and produce an effective solution for clotting blood. After that, we hope to develop a fast-acting and effective prototype that will be able to clot pressurized blood being pumped through a simulated wound. If this is accomplished, we’ll attempt to design a tool or delivery system to make sure that we apply the right amount of our system to the wound in order to get the best clot. In addition, we want to test whether or not the clotting factors can move through the body causing an embolism elsewhere. This is something we want to prevent and need to test if our system can remain local in the wound.Our team hopes that our inexpensive and effective technology will be able to help military personnel, disaster victims, and other people affected with severe bleeding survive their ordeals, and have a better quality of life afterwards. In doing so, we will reduce strain on healthcare systems, simplify treatment of major bleeding for EMTs and doctors, and keep families together.


Lanzhou

Heavy metal contamination has become a serious problem in fishery in recent years. Now with Lanzhou's GM bacteria, the heavy metal ions can be captured in the fish gut. This can be a new method to solve the problem.


Nagahama

To innovate a refrigerator without electricity, we invented a prototype of FRAVORATOR that is possible to preserve food by antibacterial volatiles synthesized by Escherichia coli. For high-efficiency synthetic processs, we tried two methods. 1, 1-deoxy-D-xylulose 5-phosphate(DXP)synthase, Dxs, is down-regulated when its downstream material has been produced to some extent. So, we tried to over-express, another DXP synthase, nDXP, that rarely has been used in normal conditions. 2, Using genomic editing method, we tried to knock out synthase, that we used to produce unnecessary by product.


NYU-AD

In many developing countries, rapid urbanization leaves people with limited access to cooking facilities, resulting in a large dependence on reasonably priced and conveniently available street foods. These foods, however, pose a high risk of food poisoning due to microbial contamination. According to WHO statistics, food poisoning kills 420,000 people a year worldwide. One of the primary microbial contaminants is the Shiga toxin-producing E. coli O157:H7 (STEC). These particular pathogenic bacteria cause severe diseases in humans worldwide by secreting a toxin called Shiga-like toxin (SLT). Research shows that E. coli causes 73,000 illnesses in the United States every year. It is even estimated that STEC causes 2,801,000 acute illnesses worldwide annually, leading to 3890 cases of Hemolytic Uremic Syndrome, 270 cases of End-stage renal disease, and 230 deaths. Currently, there is no detection method for Shiga-like toxin outside of a lab setting, so consumers have no way of protecting themselves without strong legislation.Lack of action taken by governments and street food vendors in developing countries lead to the prevalence of street food-related illnesses, and call for the necessity of consumer awareness. Our project ultimately aims for a consumer-focused mechanism to detect Shiga-like toxins in foods.Shiga-like toxins are exotoxins, which consist of a toxic enzymatic A subunit and a cell-binding B subunit. The latter binds to a globotriaosylceramide (Gb3) receptor, expressed on the surface of the target cells. This interaction is responsible for the toxin's entry into the host cell. Through our device, Gb3 will be expressed in non-pathogenic E. coli. When the receptor is exposed to the food sample, the STL subunit B, if present, will bind to Gb3. Crosslinking will occur to stabilize the interaction. Next, a recombinant subunit B will be fused with a reporter and then applied to detect whether the Gb3 binding sites are available. If the binding sites are vacant, the sub-unit B will bind to them and elicit a signal, indicating the safety of the food sample.In summary, we will be creating a portable device that would evaluate the safety of food by detecting a specific contaminant, Shiga-like toxin, for consumers who rely heavily on street food in developing countries in which there are weak food safety regulations.Before making our final decision, we explored an extremely diverse range of project topics such as blockage of oil pipes, controlling fruit ripening, detecting milk adulteration, biodegradable plastics, bioelectronics, preventing the coral reefs bleaching, bio-art, smoking, monitoring air quality, and more. After extensive research and intense discussion, we decided to move forward with the idea of detecting pathogenic SLT-producing E. coli in street foods. SLT is highly toxic due to its low LD50 and the A subunit’s protein synthesis inhibitory action, so it would have been too dangerous to work with given our lab environments. Keeping the validation process in mind, we decided to use only the SLT B subunit as our method of verification.


SDSZ_China

Bovine milk, something so common that people consume every single day, inevitably contains antibiotics from the drugs or fodders that prevent them from mammary glands inflammation. Though strict protocols for diary products are enacted worldwide to make sure the drug residues are under the dosage that could lead to health problems for human, the current testing methods are not of great efficiency or accessibility, because of the high cost and complex procedures. This disadvantage leaves potential risks of letting milk containing antibiotics that are over the limit into the market. Our project aims at speeding up while lowering the cost of the method used to detect antibiotic residues in milk. We take β-lactams as the target, and implement a penicillin binding protein, which recognizes all β-lactams, in our testing device. First, we improve the ELISA (enzyme linked immunosorbent assay) method, making the raw materials cheaper by replacing the immune response that occurs on the ELISA plate with a simple competitive binding reaction, in which the penicillin (or other β-lactams) on the plate and in the testing sample compete to bind with GFP-PBP5 (green fluorescent protein - penicillin binding protein 5). We can then measure the concentration of penicillin in the sample by measuring the fluorescence intensity on the plate. To even further reduce the budget and strengthen the sensitivity of the test, we created a testing paper by binding our fusion protein CBD (cellulose binding protein)-PBP5 to filter paper. When the paper is dipped in a milk sample, the presence of β-lactams alters PBP5’s enzymatic activity, which can be measured through electric conductivity test. Its electric conductivity therefore indicates how much of this type of antibiotic exists in our milk. So far, we have constructed pET-GFP-PBP5 and pET-CBD-PBP5. The plasmids are to be integrated into bacterial genes and express the fusion proteins that will be used in our device. Our methodology provides new solutions for simplifying and reducing the cost of a standardized antibiotic residue testing procedure, making bovine milk safer to drink in China, and maybe someday throughout the world.


SCAU-China

Team SCAU-China set up in March, 2015. In the first three months, we actively come up with various thoughts in the meetings every twice a week, exchanging our idea with all the team members. Delightfully, we always got inspiration from other's sharing. After that, we divided our team into several small groups to work over several ideas, which were thought to be viable and meaningful. We dedicated to our issue and cooperated with other group members to complete them. Eventually, two projects stood out among all, with their name astaxanthin biosynthesis in rice endosperm and PHBV biosynthesis in E.coil. In June of 2015, both two projects started their experiments respectively and in March, 2016, the astaxanthin one was selected to be our final project for iGEM competition due to its satisfying progress and surprising innovation. Now our wet-lab experiment is well progressing and we have made some plans for human practice, wiki making and other sections. We will try our best to complete our project, which will be the debut of rice endosperm with a safe and productive bioreactor in the iGEM competition.


ShanghaiTechChina_B

At the very beginning of our project we brainstormed various FORMs of a synthetic biology product. Editing and rearranging genes are basic methods in synthetic biology just like coding in information science and technology. The most obvious form is a MACHINE which responses to an input (chemical molecules , physical stimulus etc) with corresponding outputs. That's why this competition is always mentioned ' genetically engineered machine '. A deeper view of gene ' programming ' suggest that a general algorithm is another exciting form of products. An algorithm can be adjusted to be applied in different problems with multifarious variables. The first several ideas we came up with, though seems to be naive, were aimed at only one form of the mentioned above. A machine which transfers chitin into drugs or glue was defeated by cheap chemical processes in factories . An algorithm of sending a spy with survival advantages and a effective kill switch to remove harmful species was denied, for we did not determine a suitable example and we were not sure about its safety when the kill switch fails to work.After months of debate we focus on gut microbes. People suffer a lot if they have trouble with the most important organ of their digestive system. Diseases come and go, but gut microbes are faithful residents. How we wish they participate in defense with their nature of being living creatures!We need an example, anyway. Our research shows that gut diseases did not receive sufficient attention in China, such as IBD , the inflammatory bowel diseases. Mechanisms remain a riddle and scientists are still seeking for therapies. We may have a try!Our aim is to program gut microbes to sense the diseases, to supply curing molecules,to adjust the dose automatically and to terminate the treatment when necessary. This will be our ' algorithm ', and IBD is the specific example as well as the entry point. Parts with the features and therapies of IBD will be applied and we hope the engineered gut residents would stand up for their homeland !


NYMU-Taipei

Background of our Project This year, we are focusing on the entomopathogenic fungus Metarhizium anisopliae, which is currently used as a biological control agent for different arthropods. However, its uses has been limited by poor efficacy. That is why many experts genetically engineered various M. anisopliae strains in order to improve its virulence. While genetic engineering is a great way to improve upon what mother nature has given us, biosafety has always been a big problem with genetic engineered organisms. For this reason, we hope to build a biosafety system, which includes one optogenetic module and one kill switch, to limit the persistence of our genetically engineered fungus in the environment. Details of our project In our biosafety system, our design consists of an optogenetic module and a kill switch. We used the optogenetic system VP-EL222 which containing the VP-EL222 genes and a promoter that activated by the VP-EL222 proteins blue light inducible dimerization and DNA binding. We only want the kill switch to be induced when the fungi have already killed the insect. To achieve this, we put VP-EL222 under the control of the hemolymph-induced promoter, Pmcl1. This allows the production of VP-EL222 proteins in the darkness of the insects’ interior. The fungus will breach the the dead host’s cuticle from inside after killing its host and expose to blue light, then lethality can be induced by built-in killswitch, which will be activated when the light-inducible promoter drives the expression of the proteins in the kill switch system due to VP-EL222 dimerization and the DNA binding. When it comes to the kill switch, we employ a simple, versatile, and filamentous-fungi-specific CRISPR/Cas9 system developed by the authors of the 2015 paper “A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi.” Because virtually any gene can be targeted by RNA-guided Streptococcus pyogenes Cas9, we target several genes that could disrupt the life cycle and reduce the survivability of the genetic engineered M. anisopliae. Two of our target genes, MrPHR1 and MrPHR2, encodes photolyases in Metarhizium. Removing them will seize the production of UV-induced cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) photoproducts [(6-4) PPs]. The effect is supported by 2012 paper “Enhanced UV Resistance and Improved Killing of Malaria Mosquitoes by Photolyase Transgenic Entomopathogenic Fungi” which shows that deleting native photolyase genes will strictly contain M. robertsii to areas protected from sunlight, alleviating safety concerns that transgenic hypervirulent Metarhizium spp. (We will blast the same genes in the M.anisopliae strain’s genome.) What NYMU team has been working on so far? We are still waiting for our Metarhizium anisopliae ARSEF549 which we booked from ARSEF, US. Thus, we conduct our experiences in E.coli. now. We have already completed the design of our system. However, we can't sure whether will our Metarhizium arrives on time or not. All we can do is to prepare all the other thing and as soon as the Metarhuzium arrived we can really start our project! What we hope to accomplish We have also chosen some other essential genes for M.anisopliae as our potential target genes. The repetible DNA regions in these essential genes will serve as the sgRNA template allowing the Cas9 to mutate many positions within the gene with high off-target activity, differing from mostly other CRISPR researches insisting Cas9 must have high on-target activity, resulting in the transformed M.anisopliae that will easily die under blue light.In conclusion, we want our project display one solution to the biosafety problem of genetically engineered entomopathogenic fungi. We also want to show the world that the CRISPR-Cas9 system is not just one of those lab tools that have no real impact on the lives of the non-scientific community, but a marvelous gene editing system that could change the daily lives of many people and help our strive towards a cleaner and better future.


NRP-UEA-Norwich

We are a group of undergraduate students from the University of East Anglia, which is renowned for its environmental awareness and climate change research. We are studying subjects that range from Biological Sciences, Biochemistry, Biomedicine, Computing Sciences, Molecular Biology and Natural Sciences. Having been selected for this year’s iGEM team, we are identifying ways to bring synthetic biology techniques to an interdisciplinary research project that is currently ongoing within our university. The Science Increasing fuel poverty and global climate change are driving the global demand for clean energy. Renewable sources of energy, such as sunlight, remain largely untapped due to challenges arising from the intermittent nature of the source. In a coal fire power plant or a nuclear fission reactor it is possible to control energy output in line with fluctuating demands for power. However with renewable sources, such as wind or solar power, electricity is only generated when the wind is blowing or the sun is shining. Thus, a major challenge for renewable energy sources is in converting these types of renewable energy into fuels that can be used to release the harnessed renewable energy as it is needed. The aim of our project is to use the methods of synthetic biology to prepare biological systems that will store solar energy as hydrogen due to the channelling of electrons from photovoltaic cells into bacteria via proteins termed “molecular nanowires”. In this way bacteria can then use this energy to drive the production of hydrogen, and this can be used to sustainably power vehicles or be burned to produce electricity on demand. The Research ‘Rock-breathing’ bacteria such as Shewanella oneidensis MR-1, are microbes that couple the generation of proton-motive force across the cytoplasmic membrane to reduction of minerals, located outside of the cell. The MtrC, MtrA and MtrB proteins come together to form the MtrCAB complex that spans the outer membrane in S. oneidensis MR-1. This complex has been shown to contain a network of iron atoms that conduct electrons between the cell and its environment, leading to them being termed “molecular nanowires”. The electrons transferred across the membrane can then be used by hydrogenase proteins that catalyse the reduction of protons (2H+) to dihydrogen (H2). The process is inefficient however and we aim to explore ways of increasing its efficiency, for example through use of alternative hydrogenases or alternate subunits. Additionally we wish to control protein expression at a genetic level in order to optimise the protein ratio for maximum cellular H2 production. Lastly we are also looking into ways of increasing the efficiency of electron recruitment to hydrogenase by experimenting with various modifications to the enzyme. The MtrCAB proteins have been the focus of several previous iGEM projects and one additional aim of our project will be to improve the utility of biobricks that are already housed within the iGEM repository. Ultimately, we hope to increase the yield of clean hydrogen produced from S. oneidensis MR-1 in a microbial-photovoltaic fuel cell. The development of efficient mechanisms for storing of energy produced from renewable sources will help counteract intermittency costs and aid their development and economic viability.


ShanghaitechChina

The recent work based upon Bacterial (M. thermoacetica)-quantum dots hybrid system to harvest value-based products has suggested great future for artificial photosynthesis system [1]. Despite important advances, the current efficiency and scope of application have been limited due to the damage of quantum dots on biological systems arising from direct contact of quantum dots with cell membrane, less efficient integration between bio-abiotic interfaces as well as poor conductivity of most biological systems. To address these issues, we develop a solar hunter platform that can seamlessly integrate conductive bacteria biofilms, high-efficiency photon-electron transformation of quantum dots with efficient metabolic pathways of biological systems. The biofilm system that came into our sight is type IV pili in Geobacter sulfurreducens, which is conductive microbial nanowire [2]. The wire can be expressed in genetically manipulated strains as long wires with binding sites for quantum dots and efficiently conduct electrons. With the more surface area of biofilms for quantum dots and indirect contact between quantum dots with cell membrane, we expect a significant boost in the energy of light harvested by our Solar Hunter without sacrificing normal cell growth and regeneration. Specifically, we propose three demo examples here based on our newly developed artificial photosynthesis. The first one is a simple artificial photosynthesis based on non-conductive biofilm; to increase system complexity and promote the efficiency of electrons transferring, we design the other two systems in which we use conductive biofilm of G. sulfurreducens to develop the electrons transferring tracks and connect the quantum dots with microorganisms. 1) At first, we want to establish the Solar Hunter system on E. Coli, whose biofilm serves as a synthetic nonconductive biological platform for self-assembling function materials. The amyloid protein CsgA , which is the dominant component in E. Coli, can be programmed to append small peptide domain and successfully secreted with biological functions. Then we propose that our Hunter family member can be an enzyme. Nitrogenase complex is the central enzyme in the natural nitrogen-fixing process. Previous researches have demonstrated the viability of using semiconductor CdS nanorod to harvest light and supply the electrons as a substitute for the Fe protein in the complex where electrons are generated from ATP [3]. The heterotetrameric MoFe protein, the other part in nitrogenase complex, will use the electrons provided to reduce N2 to NH3. We will explore the possibility of an increase in the efficiency of the semiconductor-enzyme system usingE.Coli’s biofilm, on which biofilm subunit are engineered with SpyTag and SpyCatcher system from FbaB protein to provide binding sites for proteins [4]. 2) The solar source in the solar-chemical system is, in its essence, energy with electrons. In an attempt to apply our quantum dots-pili hybrid to a wider extent, we decide to try out this model on another amazing archaea, Methanosaeta harundinacea, which is likely to have a pathway to simply use carbon dioxide, electrons and protons for the biosynthesis of methane [5]. Geobacter can naturally express nanowires and transfer electrons between each other or do direct interspecies electron transfer(DIET) with other microorganisms; for our project, Methanosarcina. Extern light is absorbed by the Geobacter and is transferred into electrons. Semi-conductors are bind to the biofilm of Geobacter to enhance its conductivity. The electrons are then transported to Methanosarcina in the form of succinate and fumarate, used as the input material to produce value-added products like methane. 3) In addition, solar hunters will include a pathway for leucine synthesis from acetate (acetyl-coenzyme A) [6], since leucine is of higher value. They use carbon dioxide as a carbon source to synthesize isoleucine via a combination of two pathways. The first pathway is the acetyl-coenzyme A (acetyl-CoA) pathway [7], gaining electrons to reduce carbon dioxide and synthesizing acetyl-CoA which is a vital intermediate. As acetyl-CoA is synthesized, it can be the raw material of the second pathway, which is the pathway for isoleucine biosynthesis in G. sulfurreducens, to give the final product isoleucine [8]. There are three main reasons for us to choose this combination. Firstly, these two pathways are found in G. sulfurreducens. Secondly, carbon dioxide is a kind of environmentally friendly carbon source. Thirdly, comparing to carbon dioxide, isoleucine is a high value-added chemical that will bring us a high level of economic efficiency. Additionally, the second pathway can be replaced by other pathways to synthesize other value-added chemicals, such as butanol. Collectively, we envision that these three parallel systems should build a powerful solar Hunter system to push the boundary of current artificial photosynthesis.


Stockholm

The Team iGEM Stockholm 2016 team consists of 14 members from diverse backgrounds and different schools; from biotechnology to medicine, to design, currently or previously studying at Karolinska Institutet, KTH Royal Institute of Technology and Konstfack, the University College of Arts, Crafts and Design. Our diverse team collectively came up with different project ideas after brainstorming in smaller groups. Subsequently each subgroup presented their prospective ideas for the whole team to vote for the two finalists. These two ideas were further researched and developed to fulfill criteria based on the iGEM requirements. We saw so much potential in both ideas that we fused them into our final core project. The Problem - Chronic Wounds We are focusing on a common medical issue: chronic wounds. Around 1% of individuals living in the western world will suffer from a chronic, non-healing wound in their lifetime, with those affected by diabetes, poor vascular health and increasing age being particularly at risk. It is a painful and expensive problem that does not receive the attention it deserves. The wounds may begin as an insignificant break in the skin which fails to heal and serves as a breeding ground for bacteria. When the bacteria reach a certain population density they develop the formation of biofilms. The biofilm is an important bacterial survival mechanism; a 3D structure built upon the wound surface to facilitate colonisation of multiple strains of bacteria, providing channels for nutrients to flow through and mediate resistance against both the immune system of the patient and conventional antibiotic treatment. The Solution - Protein Infused Spider Silk We aim to use spider silk combined with functional proteins to degrade biofilm in chronic wounds. By incorporating additional proteins the biofilm structure will be destabilized and various functions disrupted. Spider silk is an ideal material for this application since it is one of the strongest biomaterials in the world. We will use three BioBrick parts for the expression of proteins that target different components of biofilm: Lysostaphin, Nuclease 2 and Esp. Lysostaphin is used to attack cell walls and degrade exopolysaccharide which make up the complex 3D structure of biofilm. Nuclease is an enzyme that digests extracellular DNA, resulting in the disruption and destabilisation of biofilm. Esp is used to break down various structural and metabolic proteins that make up biofilm and cleaves off virulence factors from the cell wall. To attach the expressed proteins to the spider silk, we will use sortase A. This is a transpeptidase used for the formation of peptide bonds between proteins with recognition motifs LPETGG and an oligo-glycine sequence. We will tag each expressed protein with LPETGG on the C-terminus and the spider silk has an already existing glycine on the N-terminus. We will also isolate srtA gene from staphylococcus aureus to create our own BioBrick for sortase expression. To test the efficacy of our wound dressing, we are forming a staphylococcal biofilm to be treated with our modified spider silk and observed using crystal violet assay. And finally we would like to contribute to the medical field with our invention that targets biofilm formation in chronic wounds. We really hope to be a part of a bigger movement to draw attention to this subject and get one step closer to treating chronic wounds.


TJUSLS_China

TJUSLS China's subject of the competition for this year is the surface display to modify PET hydrolase(PETase). PET hydrolase was found from a kind of microorganism living on PET as the main carbon source. It can degrade macromolecular polymers into monomers. Surface display can reveal the protein whose gene code is coalescing the gene code of target protein or polypeptide with the counterpart of ankyrin on the surface of the host cell wall to harvest the whole cell catalyst. The protagonists of our project, which are PETase and the surface display technology, will act in two aspects. Firstly, create the mutant of PETase in order to improve the degradation efficiency and thermal stability. Secondly, useing surface display on the surface of the prokaryotic (Escherichia coli) and eukaryotic (Pichia yeast) for whole cell enzyme catalysis reaction.


UCAS

During the course of brainstorm, our team members came up with several ideas including treating diabetes using gut microbes, degrading PCBs in the environment and degrading antibiotic residues.After consulting professionals, we decided to work on degrading antibiotics for several reasons: (1) Antibiotic resistant crisis has become a major threat to human health and it has attracted much attention worldwide in recent years. Since antibiotic contaminant is more eminent than others like PCBs, we decided to tackle this problem; (2) China is by far the largest antibiotic producing and consuming country in the world, but it was not until recently that the public has been aware of the consequence of antibiotic abuse;(3) Researches show that connection of antibiotic residues in city river is relatively high, so this is the practical use of our project; (4) Thanks to the works finished by previous teams, we can utilize and enhance some of the submitted parts; (5) While most of the previous teams focused on testing the antibiotics in natural environment or some products, we will focus on degrading the antibiotics. Evaluating the degrading efficacy of enzymes is a primary goal of our work;Antibiotics have long been extensively used in agriculture, livestock husbandry and medical treatment, but the harm caused by the abuse of antibiotics has not been realized by human society until recently. Researches show that antibiotic residues in water seriously affect human health and ecological safety. China, as a country which uses excessive antibiotics, would suffer from the harm of drug residues more severely. In order to effectively degrade the antibiotic residues in water, the UCAS iGEM team 2016 hope to construct a kind of microorganism which is able to decompose antibiotics with high efficiency. We choose several oxidative methods to solve this problem, and screen several productive oxidases.(1)The selection of degrading enzymes: Before enzymatic reaction, we first used some active small molecules to test the degradation efficiency of antibiotics. However, the results are not promising, indicating that chemical compounds alone are not sufficient to degrade antibiotics. Next, we will try to practice enzymatic reactions to decompose antibiotics in vitro, and will compare the efficiencies with those of natural resistant genes, so that we would select one or a few oxidases. The enzymes we will screen includes a form of manganese peroxidase(MnCcp) and myoglobin mutants. We choose E. coli as the chassis organism, and evaluate the degrading efficiency in vivo.(2)Genetically modified microbes(GMMs) threaten the environment once the artificial genes are transformed to other organisms or released. So we designed a kill-switch to prevent the horizontal-gene-transfer based on Type II TA modules commonly found in prokaryotes. In this summer, we will measure the toxicity of different types of TA modules, in order to screen out the most toxic ones. In addition to test the activity of different toxins independently, we will also come up with a method to label and quantify the amount of toxins expressed in cells, and to compare the toxicity per unit between varies kinds of toxins.(3)Circuit design: We hope that the expression of antibiotic degrading enzyme and the TA module could be tightly regulated by signals outside. So in this part, we will utilize the tetracycline sensor constructed by BIT and make improvements to it by adding a positive feedback. We are also expected to further characterize this circuit. We will also test the TA module regulation circuit reported in some research papers.


Tec-Chihuahua

We have previously carried out experiments with Myxobacteria, poorly studied bacteria with great biotechnological potential because of its capacity of producing a large number of secondary metabolites. They are also known for their properties of predation, fruiting bodies formation, and desiccation resistance.We isolated this bacteria from our region and we got proof they are able to inhibit fungus and other bacteria. Therefore, we saw a potential iGEM project on enhancing Myxobacteria’s properties to attack some specific endemic fungi.We decided to apply enhanced Myxobacteria to solve a diffused problem in our local agriculture. The state of Chihuahua is the 2nd producer of alfalfa in Mexico. This legume has a significant impact on our economy, but it is often put at risk by different biological factors such as bacteria, fungus, plagues, extreme temperatures and hydric stress.Our team set to work with Myxobacteria to battle Rhizoctonia solani, a fungus affecting alfalfa by rotting different parts of the plant.


TP_CC_SanDiego

Fungal infections have detrimental impacts in agriculture by decreasing crop yields. Particularly, Fusarium wilt, a fungal disease caused by Fusarium oxysporum, affects a wide variety of foodstuffs. Current treatments for Fusarium wilt involve the cultivation of resistant crops; however, ever-evolving fungal pathogens can circumvent said resistances and induce blight within the resistant crop strains. As a result, an inherent component of all fungal cell walls, chitin, was targeted to combat fungal infections in plants.A diversely found glucose-derivative, chitin provides rigidity in all fungal species and also acts as a similar constituent of arthropod and insect exoskeletons and harder external tissues in various organisms. Our proposed mechanism for the antifungal treatment was to degrade chitin through the use of the enzyme chitinase. Various chitinase isozymes act upon the varying chitin structures in different organisms, so chitinase LbCHI31 was selected as the chitinase of choice for Fusarium oxysporum.


TEC_GenetiX_CCM

The idea of the project this year consists on the bioremediation in aqueous media of molecules that are similar to estrogen, such as BPA and phthalates that are common secondary products in the manufacture of many common plastics. We plan to use and/or improve one of the previous estrogen biosensors developed by past iGEM teams and then use the production of human proteins TGB and TTR for the bioaccumulation of the toxic molecules.


Leiden

In the near future, we will finally set foot on our neighbour planet Mars. The soil, however, is highly toxic, which makes agriculture problematic. Luckily, the bacteria of the Leiden iGEM team will be able to detoxify the soil and even produce oxygen out of it! Almost 47 years ago, Neil Armstrong spoke his famous words: “That’s one small step for man, one giant leap for mankind”. The first man on the moon was a fact. Since then, scientist from all around the world are trying to put the first man on Mars. However, before this is even possible, an important obstacle needs to be overcome: 0.5 - 1% of all mars soil contains the, for humans, very toxic perchlorate (ClO4-). This perchlorate is toxic for humans because it disrupts iodine uptake by the thyroid gland, thereby interfering with our overall metabolism. This would mean that, once humans are able to go to Mars, it isn’t even possible to survive there for long. Luckily, we have found a solution. Like the beginning of life on earth, bacteria can possibly be the beginning of life on Mars. By transferring eight genes to an E.coli bacterium, we will engineer a system that is capable of turning perchlorate in non-toxic chloride ions and oxygen. This way we will not only detoxify the soil, but also produce oxygen, which is fundamental for human life. Possibly, the small step made with these bacteria, can be a great leap for mankind.


USTC

Coming up with a fancy idea is easy, however, coming up with a promising as well as feasible one is hard, harder than we imagined.Our leader encouraged every member to think about ideas, and we successfully did that. Initially, we acquired about 10 ideas and discussed each one of them. After 2 weeks, three ideas left to be further determined whether they are appropriate or not. They were: 1. Bacteria feeds on plastic 2. EEEEE(Extremely Enhanced Expessing Engineered E.coli ) 3. Prion and its aggregating 2. EEEEE(Extremely Enhanced Expessing Engineered E.coli ) Our criteria for ideas are as follow:Will our team members have fun? Is our time enough for it? Is our experiment equipment enough? Does it meet iGEM safety requirements? Is it innovative enough?We finally decided to select "Prion and its aggregating" as our project carrier. Information found is as below:In yeast cell, there is a non-Mendelian inheritance system.Figure 1: The effect of [PSIC] on Sup35 and translational termination. (A) A complex of Sup35 (see legend at bottom) and Sup45 binds ribosomes at stop codons and mediates translational termination. Sup35 is composed of two regions, a prion-determining-domain (PrD, rectangle) and a termination domain (Sup35C, sphere). In non-prion [ psi¡] strains, translational termination occurs efficiently at stop codons at the ends of open reading frames, and the completed protein is released from the ribosome.(B) In [PSIC] cells, most Sup35 proteins adopt the prion conformation and self-assemble into an aggregated, possibly amyloid structure (depicted as large cylinder). This conformational change impairs Sup35’s ability to participate in translational termination and consequently, stop codons are read through occasionally, producing proteins with a C-terminal extension.Moreover, it shows that the PrD can be modularized, which means we can combine this domain to another protein we want to make them aggregate, and even impair its function.Here is the most magical part ,not only can we make them aggregate, we can also cure our yeast by a great variety of chemical, environmental, and protein-based agents. Then these proteins will be depolymerized, and spread uniformly in the cell once again. In the first design (figure 2), we just use R9 to depolymerize the SUP35’s aggregation to allow the yeast to produce functional GFP. Then we can calculate the concentration of R9 through the fluorescent brightness. In the second design (figure 3), we build a double direction switch. In the third design (figure 4), GFP1 and GFP2 are not able to give out light separately. However, when they touch each other physically, they will reconstruct and give out light.We hope to construct a bio-reaction controller, which functions directly on protein level rather than on DNA level in advance. Such strategy is highly possible to reduce the time it takes for the controlling effect to appear, as DNA->Protein process is skipped.


Valencia_UPV

The aim of this project is to develop a new and more efficient strategy for genome editing in plants using the CRISPR/Cas9 editing system. To reach this goal, we have made a Tool&Kit in order to decrease current technological barriers for plant breeders. It combines the split Cas9/CPF1 technology, viral systems, a CRISPR target database and laboratory equipment. Plant improvement with Agrobacterium - the most common method - is inefficient, long and difficult. The alternative chosen in our project are viral vectors, due to their higher rate of plant transformation. This advantage of virus is used to improve plants using CRISPR/Cas9 system. Nevertheless, viral vectors are small, so Cas9 and CPF1 endonucleases - necessary for editing - need to be splitted in two parts to fit into the viral vector. The reassembly of these parts is accomplished by inteins. In order to provide the necessary information to use the editing system, it has been created an optimized database that provides target genes and optimal gRNAs to knock-out them. This gene modification leads to a phenotypic improvement. A Testing System using Agrobacterium allows us to know how efficient is the gRNA selected in the database for any particular variety. To fulfill this process, we have made a Tool&Kit which includes all the necessary laboratory equipment for genome editing in a compact and affordable way, in addition to the technologies and techniques mentioned above. Together, they make an innovative and complete set of tools for accessible and more efficient genome editing in plants. Imagine a farmer who wants to have an orange tree that produces more oranges. But he knows that his variety tastes better than the ones offered by seedbeds. To get this goal he could cross varieties, but it takes a long time and it is expensive. The better way would be to genetically modify the plant. However, he doesn’t have the necessary knowledge nor the technology to make it possible. Plant breeders are the ones with the required knowledge to deal with his problem. They do have some of the necessary tools to make genetic edition, but they will need to invest a substantial amount of time and money to do it with them. With the current technologies the whole process will need between 2 and 12 years and around XX $ to develop an improved variety. Problem Currently, the most serious problems for plant breeders are time, money, and legal aspects regarding transgenic crops. That reduces the accessibility for those who want to modify the plant varieties. Using our new and revolutionary strategy based on CRISPR/Cas9 or CPF1 and viral systems, plant breeders will be able to modify any variety in order to get the desired features. Thus, those users could get their new crops spending less time and therefore less money. How will we do this? With HYPE-IT, a technology that will allow to Hack Your Plants Editing with the tools created by our team. We pretend to bring this new technology from laboratories closer to land. We will create an optimized database containing target genes whose silencing with gRNA lead to a phenotypic improvement. The plant breeder will select in our database the desired modification or gene to be edited for his variety, and it will return the optimal guide RNA to target and knock-out the selected gene. Open source will be the main philosophy of this database, allowing breeder to update new known modifications. The plant breeder could test the guide RNA directly in his plant, but it would take a long time just to check if it works or not. To avoid this, we have designed a gRNA Testing System which does this in a fast and simple way. Using Nicotiana benthamiana, Agrobacterium infection system, a short sequence of the gene of his plant and a luciferase assay, the users will surely know if the guide RNA works on his own variety. To genetically modify the plant, the Agrobacterium infection system is inefficient , long and difficult. Thus, we decide to use a viral system to enhance plant infection. Since the viral vectors are small, the Cas9 and CPF1 endonuclease - necessary for editing - need to be splitted in two parts. To reassemble them inside the plant cells, we will use intein proteins. All these innovative tools can overcome the problems that plant breeders have nowadays. Bearing this in mind, we want now to make genetic plant edition more accessible for all potential users. We have made a Tool&Kit that contains all these technological tools. For users who have few resources we have included all the laboratory equipment required to make the genetic edition, with simple protocols.


Vanderbilt

Every Gene Harbors a Vulnerability At the foundation of the field of synthetic biology lies a seemingly irreconcilable paradox. By applying our mastery over life’s genetic code, we aim to turn biological systems into devices that we can control and program in predictable ways. Yet the same genetic elements that we incorporate into our designs owe their existence to the unpredictability of evolution operating to mutate and change DNA. Evolution and mutation work hand in hand to select against the maintenance of synthetic DNA sequences, taking the biological engineer’s best-formulated designs and eroding them to nothing. No matter if it is a complex gene circuit or single-gene expression, a single mutation is enough to render an entire system nonfunctional. As soon as a mutant cell emerges, its mutation frees it from the metabolic burden of sustaining transgenes, allowing it to outcompete all the remaining cells that are functioning as intended [1]. Within days the population ceases to be what it was engineered to be [2]. Nature defeats the engineer’s attempts at harnessing the vast potential for biological machines to be re-purposed as agents for good. How to Tame Evolution How is it even possible to combat processes as fundamental as mutation and natural selection? The dogma in biology has been that random mutation will strike any gene sequence and initiate a process of selection as a logical consequence of the variations that mutation introduces. But that basic dogma is wrong. As soon as we realize that subtle mistake, the way is opened to bring mutation itself under the synthetic biologist’s control. Decades of genomics and biochemistry research has established that mutation is not truly random. Certain DNA sequences are “hotspots” more prone to mutation than others, while others are resistant against mutagenic damage [3]. Our idea is to rationally modulate the sequence composition of synthetic genes to reduce or eliminate motifs with high mutation risk, substituting them out for mutation-resistant sequences. When combined with gene synthetic technologies, our process becomes a simple and reliable optimization that is universally applicable to genes expressed in any organism An Algorithmic Approach to Control Mutation We have developed a computational algorithm that returns control back into the hands of synthetic biologists. By making synonymous substitutions that preserve gene function, substantial proportions of mutagenic sites can be eliminated from any sequence. Our robust algorithmic strategy for generating mutation-resistant genes has potential for improving the safety and stability of transgenes, which we are demonstrating by performing multiple independent techniques to measure stability at the level of sequences in vitro up to the function of cell populations. To complement our applied research, we are also taking advantage of our new software tools to begin to answer a lingering question in the field: why would a site’s risk of mutation depend so greatly on the base-composition of the nucleotides surrounding it? By synthesizing sequences with tailored patterns of mutation “hotspots”, we may be able to further improve the performance of our own algorithm, and may provide insight into the nature of mutagenesis to advance the field of cancer research. While any single engineered change to reduce mutation may still fail, when our innovative approaches to modulating evolutionary stability are taken in combination, they offer an unprecedented hope for overcoming evolutionary entropy. More than a victory for synthetic biology, we prove that through rational design principles- exactly what mutation most virulently tries to uproot- and with enough clever innovations, it is possible to defend against what seemed like an inevitability of nature.


UNIK_Copenhagen

Our project will be to put into application a newly developed coculturing system combining the properties of microalgae (cyanobacterium) and a bacterium to efficiently harvest sunlight to produce essential compounds like biopharmaceutical, vitamins or plastics for 3D printing. The development of better ways to exploit sunlight in the production of biomaterials can lead to more sustainable and diverse production methods, and to life essential onsite production in remote areas like a Moon or Mars base. To perform lab work for our project, we have been granted permission to work in GMO Class II laboratory allocated at the Department of Plant and Environmental Sciences (PLEN) at the Faculty of Science, Frederiksberg Campus, UCPH. Furthermore, we will be working closely with the Head of Copenhagen Plant Science Center (CPSC) Professor Poul Erik Jensen and Associate Professor Sotirios Kampranis from the Section of Plant Biochemistry. Additionally, to provide extra knowledge within astrobiology and astrophysics, we are collaborating with Master student Christina Toldbo who is specializing in Space exploration at the University of Stuttgärt, Germany and Associate Professor Morten Bo Madsen from the Section of Astrophysics and Planetary Sciences, UCPH. The design and characterization of a coculture system has been done before (1, 2, 3), even in iGEM (4). However, to our knowledge, no one has yet to design a modular coculture system for bioproduction of chemical compounds in space. We will make a proof of concept, by designing such a bioprocessing system and optimizing it for future space mission in the Mars Chamber at the Niels Bohr Institute, University of Copenhagen. We ultimately wish to supply the international space station and future moon or Mars bases with more flexible bioreactors consisting of interchangeable cartridges allowing for onsite production of bioplastics and pharmaceutical compounds all from the same biological system. (1) Bacchus, W and Fussenegger, M. (2012). Engineering of synthetic intercellular communication systems. Metabolic Engineering, 16, March 2013. (2) Zeidan, A. A., Rådström, P., & van Niel, E. W. (2010). Stable coexistence of two Caldicellulosiruptor species in a de novo constructed hydrogenproducing coculture. Microbial Cell Factories , 9 , 102. (3) Goers, L., Freemont, P., & Polizzi, K. M. (2014). Coculture systems and technologies: taking synthetic biology to the next level. Journal of the Royal Society Interface , 11 (96), 20140065. (4) iGEM Amsterdam 2015, [Photosynthetic]Romance, http://2015.igem.org/Team:Amsterdam


UNC-Chapel_Hill

The “What” an “Why”     Outer Membrane Vesicles (henceforth referred to as OMVs) are spherical, double-membrane enclosed structures generated naturally from a variety of both gram-negative and gram-positive bacteria, including E. coli. Typically, they serve to transport a variety of large, unwieldy molecules between cells, including proteins, lipoproteins and phospholipids. For E. coli, they measure 10-300 nm in diameter and possess the ability to fuse to the membranes of other cells, after which their contents may be imported into the cell.     This last feature is especially of relevance, as it shows that OMVs can serve as a sort of natural transport mechanism for proteins. In turn, this allows for cell-cell transport and cell-cell communication beyond traditional methods employed in biologically-oriented sciences, including viral vectors, liposomes and quorum sensing.     Furthermore, if such a system were to be made viable, it would have a few key advantages over other methods. Viruses would not need to be cultured and collected for effective transport between populations, with transport instead occurring naturally as a result of constant OMV production. Design issues regarding liposomes would be irrelevant, as OMVs already retain the capacity to fuse to cell membranes. Protein degradation problems typically experienced by quorum sensing, as well as programming of a receiver cell, need not apply.     Most importantly, OMV manipulation represents a novel system that can allow any part on the registry to effectively be implemented into a fusion protein system and transported between cells within a single round of cloning. If added to the registry, it could be a boon that affects a large amount of projects in the future. Our Research and Current Progress     Although current research has already confirmed the ability of OMVs to incorporate select fusion proteins and transport them to other cells, no iGEM team has ever replicated this feat beyond modeling measures. Our goal, then, is to both design and test a few fusion protein systems in order to allow access to an OMV system for the registry. It can be divided up into four parts: creation of initial fusion protein constructs, assaying of protein levels in select OMVs, production of a final usable part for future registry usage and assaying of protein levels in targeted cells.     Currently, our group has designed and cloned the majority of our fusion proteins and is set to begin OMV assays soon. In accordance with our assays, we will also work to simulate the production of OMVs and incorporation of proteins based on past and current data.


UCLA

Antibiotic resistance is a well-known and pressing global health concern. In more recent times, there has been a stagnation in discovering new classes of antibiotic, particularly for gram-negative bacteria. Throughout the mid-1900s, scientists were rapidly discovering the current major classes of antibiotics using the Waksman platform, which entailed systematically screening soil and fungal microbes for growth inhibition. However, the recurring problem of rediscovery and failure of subsequent high-throughput biochemical assays led many pharmaceutical companies to abandon their antibiotic development programs. Current antibiotics are generally broad-spectrum, acting against symbiotic gut flora in addition to pathogenic invaders. Therefore, specificity has recently become a target in modern antibiotic development in order to bypass challenges of both rediscovery and indiscriminate killing.The core of antibiotic development lies in targeting a molecule or pathway essential for bacterial survival. Bacteria themselves have already developed several mechanisms to both communicate and compete with other bacterial strains occupying similar niches, which can be exploited for the creation of new antibiotic drugs. While some systems rely on secreted signaling molecules, direct cell-to-cell contact is also used to mediate intercellular interactions. Contact-dependent growth inhibition (CDI) is one such system that allows CDI+ bacterial strains to outcompete closely related CDI− siblings by synthesizing and translocating a toxin through the membrane of strains expressing the appropriate receptor. The CDI system is common in many strains of pathogenic gram-negative bacteria, such as Yersinia pseudotuberculosis and uropathogenic strains of Escherichia coli, making it a potentially suitable target for future antibiotics. This type of growth inhibition was first seen in E. coli strain EC93, in which toxin delivery is mediated by the CdiA/CdiB two-partner secretion system and the outer membrane protein BamA, which is a conserved receptor among all strains of E. coli. EC93 is protected from its own toxin, located at the C-terminal region of CdiA (CdiA-CT), by the expression of a CdiI immunity protein that interacts directly with the toxin to neutralize its pore-forming capabilities. The CdiBAI cluster is common throughout most CDI+ strains, significantly varying only in CdiA-CT and CdiI sequences. Our project focuses on the translocation of three different CDI systems from EC93 and Enterobacter aerogenes ATCC 13048 (containing two CDI loci) into one lab strain of E. coli to create a super-soldier organism that is able to selectively inhibit the growth of these strains. A lab strain containing CDIEC93, for instance, would be able to target all bacteria containing the corresponding receptor for CDIEC93, which would in this case be BamAEcoli. In order to target EC93 itself, however, we aim to switch CdiA-CTEC93 with a toxin from ATCC 13048 so that the immunity protein of EC93 does not prevent growth inhibition. It has previously been shown that CdiA-CT regions are modular, and systematically modularizing the toxin region using appropriate restriction sites is another goal of our project. While the CDI system in EC93 targets the BamAEcoli, the relevant receptors in other species of pathogens and even in other strains of E. coli is unknown. An additional facet to our project would be to find the receptors that each CDI system of ATCC 13048 targets by creating a transposon insertion library. Mutants that display a whole or partial CDI immunity phenotype will be sequenced to determine which genes have undergone transposon insertion, providing insight into which receptors may be targeted by ATCC 13048 CDI systems. Protein Cages Higher order self assembling protein assemblies are a commonplace in nature, one common example being ferritin, which carries iron in many single-celled organisms. Due to their encapsulating function and box-like structure, such assemblies are often called protein “cages.” Inspired by these natural sources, much research has been done into creating synthetic cages with new properties such as stability, size, and subunit types. Furthermore, in many cases applications of cages have been suggested, but many have not been tested experimentally. One such application is targeted drug delivery. By specifying the region to which drugs should be delivered, effect can be limited to the areas desired and avoid damaging or affecting other parts of the body. Moreover it ensures the drugs actually affect their desired targets with ideally high efficiency. Since these drugs would likely be inserted into the bloodstream, a function directly connected to that method would be a first step into drug delivery. Thrombosis, when a clot forms inside the blood stream, is associated with widespread diseases including stroke and many heart conditions. Anticoagulants prevent clot formation by interfering with clotting factors and allow a smoother blood flow, restoring normal circulation. However these drugs can have side effects, a main one being problems stopping bleeding from wounds. By localizing and minimizing the amount of drug used, issues such as these would become less serious. A protein cage containing an anticoagulant is well-suited to this. To specify the clot as a target, an associated enzyme or byproduct of clotting could be used. Thrombin is one such enzyme, promoting clotting in most cases. It does, however, cleave a certain amino acid sequence. This sequence, if properly inserted into a protein cage containing the anticoagulant, would result in disassembly of the cage, release of the drug molecule to the targeted area,and destruction of the clot.The goal of our project is to modify a protein cage that can be disassembled using a thrombin protease and to use this protein cage to deliver a drug molecule. We are using two previously created synthetic cages, one composed of 12 subunits forming a tetrahedron cage while the other composed of 24 subunits forming an octahedron cage. For each of these protein cages, we have designed mutants with inserted thrombin cleavage sites and hope to induce disassembly of the cages by treatment with thrombin protease. We will then load anticoagulant drug molecules into our mutant cages and assay for the release the drug molecules when the cage disassembles in the presence of thrombin.


NTHU_Taiwan

Perfluorinated chemicals, PFCs, are hazardous man-made chemicals produced or used in water- resistant clothing (widely known as Gore-TexR) and semiconductor industry, which are harmful to our environment and potential carcinogen human.Due to there was no regulation for banning PFCs usage and emission (even in most countries all over the world nowadays), scientists have discoveredthe liquid and volatile PFCs’ distribution in snow in the mountain, in the air, and even in drinking water.So, it is essential for us to develop an efficient and environmental-friendly method to deal with PFCs disaster before the evolution of the regulation, and most importantly to keep animal and human suffered from PFCs disaster. We want to engineered bacteria with carbon-fluorine bonds breaking enzyme- Fluoroacetate Dehalogenase to be more efficient, more sustainable, and to save our mother nature!


Concordia

Our team is based in Concordia University in Montreal, Canada This year, our iGEM team representing Concordia University aims to design Combat Cells, a novel adaptation of the popular and engaging TV show ‘Robot Wars’. The project concept involves the design and battling of ‘cellular robots,’ providing a new spin on synthetic biology for the scientific community. Our project consists of equipping cells with nanoparticles and having them battle one another in a controllable microfluidic device. Through this, our intention is to create and broadcast a web series through which we can entertain, educate, and inspire the public to participate in synthetic biology, and even create their own Combat Cells. The project encompasses three phases: nanoparticle synthesis, nanoparticle attachment, and analysis of cell survival on a microfluidic chip. Nanoparticle Synthesis To generate nanoparticles, we are harnessing the reductive powers of plants such as garlic, aloe vera and cabbage. Plants possess a variety of biomolecules that are capable of reducing and stabilizing metal ions to form nanoparticles. The sizes and shapes of nanoparticles can be manipulated by varying the amounts of plant extract and metallic solutions used for synthesis. Using a Transmission Electron Microscope (TEM), the nanoparticles synthesized can further be characterized. In this we aim to develop optimized methods for controlling the shapes and sizes of the nanoparticles using plant-mediated synthesis. Furthermore, incorporating this eco-friendly and cost-effective approach to synthesizing nanoparticles will allow our project to reduce the amount of waste we may produce during nanoparticle synthesis. Beyond this, other methods of nanoparticle synthesis are used known as chemical and recombinant synthesis. Martin and Turkevich methods are used for chemical nanoparticle synthesis. Martin uses the strong reducing power of sodium borohydride to reduce gold nuclei into small gold nanoparticles in the 3-6nm diameter range. The gold solution that is being reduced, also contains trisodium citrate whose ions will cap and stabilise the gold nanoparticles. The Turkevich method uses the moderate reducer and strong stabiliser trisodium citrate whose reducing power is increased by heating the solution containing silver nuclei. This reduction of silver nuclei would lead to formation of nanoparticles in the 40-60nm diameter range. The recombinant method will involve the expression of the MelA gene, which will lead to the formation of eumelanin. This protein will in turn reduce the gold nuclei within E. coli cells and will intracellularly form gold nanoparticles. FhuA-GBP, a transmembrane protein linked to a gold-binding peptide, will be expressed in order to induce extracellular display of gold nanoparticles. Nanoparticle Attachment The next step following nanoparticle synthesis is nanoparticle-cell attachment. To do this, our team’s goal is to develop an effective linkage method between the nanoparticles and the cell’s surface, using both model organisms Escherichia coli and Saccharomyces cerevisiae. One of our methods includes the creation of a gold “Nanoshell” made from gold nanoparticles coated with L-cysteine surrounding the outer surface of yeast cells. Another one of our methods involves involves coating silver nanoparticles with polyelectrolytes and attaching these to the surface of both yeast and E. coli cells. We intend to study the relationship between nanoparticle abundance as well as localization on the protective qualities offered to the cell by nanoparticle cell coating. Battle on a Microfluidic Chip Microfluidic chips with varying channel diameters will be designed using AutoCAD and printed onto photomasks which will act to transfer the generated pattern onto the chip. The customized chips will incorporate a battledome where two differently nanoparticle-coated cells will be forced to physically interact and ‘battle’. During this battle, the team will compare the relative protective abilities of the different nanoparticle coatings in order to determine which type of nanoparticle-cell combination is the ultimate winner! In parallel, the nanoparticle-coated cells in the microfluidic chip will be exposed to different physical and chemical “obstacles” such as varied temperatures, salt concentrations, differing pH environments, and so forth, in order to test the protective abilities of the nanoparticles. The potential for colored pigments to travel through the cell membrane as a result of damage from the cell battle will be used to define a winner and a loser. Ultimately, we envision a multi-team Combat Cells league in which every team has a unique nanoparticle synthesis method and attachment strategy that can be demonstrated through a entertaining webseries. It is our team’s hope that individuals of all ages and educational backgrounds will participate under the guidance of experienced coaches to develop novel strategies to design their own Combat Cells using innovative biotechnological approaches.


Edinburgh_OG

Are you using the right chassis? The continuously growing field of industrial biotechnology has incited the replacement of non-renewable processes with more energy-efficient ones. Central to this is the use of genetically modified organisms modified with recombinant DNA technology for a wide variety of applications, ranging from the production of fine chemicals and pharmaceuticals to fuels and bioremediation [1]. These technologies and applications are largely dependent on the use of well-characterised industrial host organisms including Escherichia coli and Sacharomyces cerevisiae. However, such strains are not always the optimal choice for particular processes due to inherent metabolic limitations or a lack of consensus between the engineered components introduced into the host from a heterologous organism for the particular bioprocess. Better Chassis for Better Application While the well-characterised E. coli and S. cerevisiae have a host of molecular biology tools available for engineering them since they have been domesticated (they have been vastly changed from their wild-type and adapted to laboratory conditions), they come with distinct limitations, such as the inability to make the post-translational modifications found in eukaryotic proteins, with a high potential for protein misfolding, aggregation and degradation, besides incomplete translation due to different patterns of codon usage to eukaryotes [2]. Using native producer organisms in biotechnology may lead to higher productivities, but these non-model organisms often lack well-characterised genetic engineering tools, which may present difficulties in optimising and controlling metabolic pathways. This presents a major barrier to the widespread use of these organisms as biofactories. Expand-Ed: Expanding Tools and Gene Editing for Non-Model Organism The Edinburgh Overgraduate iGEM team will address those challenges by domesticating the desired host strains, applying synthetic biology (synbio) genetic engineering standards to the design of protein expression and metabolic engineering systems in a number of non-model organisms and characterising the behaviour of these standardised systems in a number of host strains with high potential for industrial applications. Furthermore, although it has its limitations in bacteria, we will include the CRISPR-Cas9 platform to assess its utility in these organisms as it is a potentially useful tool to have a better control of genomic perturbations and maximise those optimal expression systems and metabolic pathways. Through our project, the path is being paved so that other participants in the synbio community will more easily access these organisms in the laboratory, accelerating the understanding of these organisms and increasing the list of strains that are suitable for the manufacture of relevant products, including those that address global conservation challenges. Our main aim is to open the opportunity of using a number of host chassis in synbio by characterising new DNA parts (e.g. promoters, reporter genes, terminators) that are necessary to produce proteins (through fluorescence observation) as well as the CRISPR-Cas9 technology, all through the modular cloning (MoClo) standard. Synechocystis sp. The first host organism we will be working on is the cyanobacterium Synechocystis sp. PCC 6803. Cyanobacteria could be cell factories for biofuel production since they are able to fix carbon dioxide directly as their primary carbon source by using energy derived from sunlight and have higher growth rates [10]. This approach could help ease the greenhouse gases emissions since, currently, fossil fuels contribute to 98% of them [11] and, because they can be cultivated in non-arable land, they will not compete with food crops [12]. Rhodococcus jostii RHA1 Our second organism is the Gram positive bacterium Rhodococcus jostii. Such bacteria have applications in bioremediation as they are able to degrade polychlorinated biphenyls (PCBs), which are a variety of chlorinated compounds that, even though banned in the United States, they have been found in 500 of the 1,598 National Priorities List sites already identified by the Environmental Protection Agency (EPA) [13] and affect animal and human health by causing skin conditions, liver damage and even cancer [14]. Penicillium roqueforti Our third organism is the filamentous fungus Penicillium roqueforti that is used in the production of blue cheese. As previously mentioned, caution needs to be taken with this type of microorganism because of the production of mycotoxins. Unlocking new chassis: Risk and Safety Because these synbio developments are encouraged to be open-sourced [3], although biosafety/biosecurity measures have been successfully established for managing the model organisms and guidelines such as the Genetically Modified Organisms (Contained Use) Regulations 2014 exist [4], domesticating new strains comes with challenges that, if not addressed properly, they could be dangerous, risking both their function and their surroundings [5]. For instance, filamentous fungi are able to produce a wide array of important secondary metabolites including potential antibiotics and cancer drugs. Nevertheless, they also produce mycotoxins that can cause unwanted health and environmental problems, such as food and silage spoilage [6] and human disease (mycotoxicoses) [7]. Developing a risk assessment tool To enhance the biosafety and biosecurity by making researchers more aware of these potential problems, we are developing a risk assessment tool prototype that will allow researchers to mine the genomes of new species to identify toxic metabolites and genetic elements that might limit their immediate utility as industrial hosts. Based on the antiSMASH program [8], the prototype, having as an input the microorganism’s accession number, will display a list of the related secondary metabolites and their toxicity score/scale. This will enable the user to better assess the strains to be worked on in a more direct manner and will allow to have clearer targets for genome editing, either by knocking-down toxic secondary metabolites or enhancing beneficial ones. Following the previous example, by distinctly showing a filamentous fungus’ secondary metabolites and their toxicity levels, the practitioners would immediately know the potential targets for genome editing. By making this tool accessible – as a website, for example – as a community standard to those involved in the laboratory practice, the risks and benefits related to different strains could be communicated effectively, even across international borders and legal jurisdictions [9]. References [1] Nielsen, J., & Jewett, M. C. (2008). Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Research, 8(1), 122–131. http://doi.org/10.1111/j.1567-1364.2007.00302.x [2] Fakruddin, M., Mohammad Mazumdar, R., Bin Mannan, K. S., Chowdhury, A., & Hossain, M. N. (2013). Critical Factors Affecting the Success of Cloning, Expression, and Mass Production of Enzymes by Recombinant E. coli. ISRN Biotechnology, 2013(3), 1–7. http://doi.org/10.5402/2013/590587 [3] Evans, N. G., & Selgelid, M. J. (2014). Biosecurity and Open-Source Biology: The Promise and Peril of Distributed Synthetic Biological Technologies. Science and Engineering Ethics, 1065–1083. http://doi.org/10.1007/s11948-014-9591-3 [4] HSE. (2014). The Genetically Modified Organisms (Contained Use) Regulations 2014. Health and Safety Executive, 2002, 1–78. Retrieved from http://www.hse.gov.uk/pubns/books/l29.htm [5] Dana, G. V, Kuiken, T., Rejeski, D., & Snow, A. a. (2012). Four steps to avoid a Assess the ecological risks of synthetic microbes before they escape the lab ,. Nature, 483(1-March), 2012. [6] Filtenborg, O., Frisvad, J. C., & Thrane, U. (1996). Moulds in food spoilage. International Journal of Food Microbiology, 33(1), 85–102. http://doi.org/10.1016/0168-1605(96)01153-1 [7] Peraica, M., Radić, B., Lucić, A., & Pavlović, M. (1999). Toxic effects of mycotoxins in humans. Bulletin of the World Health Organization, 77(9), 754–766. [8] Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., … Medema, M. H. (2015). antiSMASH 3.0--a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research, 43(May), 1–7. http://doi.org/10.1093/nar/gkv437 [9] Marles-Wright, J. (2016). Better by Design, Safer through Practice. Synbio LEAP Strategic Action Plan, (January), 1–5. [10] Dismukes, G. C., Carrieri, D., Bennette, N., Ananyev, G. M., & Posewitz, M. C. (2008). Aquatic phototrophs: efficient alternatives to land-based crops for biofuels. Current Opinion in Biotechnology, 19(3), 235–240. http://doi.org/10.1016/j.copbio.2008.05.007 [11] Demirbas, A. (2009). Biofuels. Securing the Planet’s Future Energy Needs. [12] Dragone, G., Fernandes, B., Vicente, A. A., & Teixeira, J. A. (2010). Third generation biofuels from microalgae, 1355–1366. [13] Spaeth, K. (2011). Polychlorinated Biphenyls, 126(4), 217–218. http://doi.org/10.17226/19865 [14] Recio-Vega, R., Velazco-Rodriguez, V., Ocampo-G??mez, G., Hernandez-Gonzalez, S., Ruiz-Flores, P., & Lopez-Marquez, F. (2011). Serum levels of polychlorinated biphenyls in Mexican women and breast cancer risk. Journal of Applied Toxicology, 31(3), 270–278. http://doi.org/10.1002/jat.1672


UCL

Due to the enthusiasm of the team members, we came up with a variety of interesting ideas during our brainstorming sessions. A few of our discontinued favourites included: a how to survive on mars concept and a means to control the weather (in true British style). At first we found it challenging to narrow our ideas down to one project idea. However, once we explored the potential of each topic in context of the BioBrick components and how we could integrate Human Practices within the idea it became easier. This enabled us to focus upon feasible ideas, with room for creativity, whilst eliminating those which were not suitable. Next, we looked at existing BioBricks created previously by iGEM teams, and consequently how we could contribute to enlarging the registry and broadening the application of synthetic biology. We found that the whole team really felt that ageing was a great topic to explore within iGEM and has a huge potential to make both social, cultural and economic impact. BioSynthAge: Do not go gentle into that good night We envision a time in which the human population lives a healthier life, for longer. We will use synthetic biology to ensure the ageing world population can both maintain their quality of life and extend their lifespan - increasing their ‘healthspan’. The health challenges currently posed by ageing are many and complex so we propose a suite of synthetic biology solutions to tackle these challenges. Our synthetic biology solutions will include, but not be limited to, the following: Oxidative stress - the root problem Oxidative stress underlies many of the health problems of ageing so we will develop a number of free radical mopping devices. These devices will include therapeutic bacterial chassis triggered by oxidative-stress to deliver free-radical mopping compounds. To lay a conceptual foundation for genetic tools that address ageing within human cells, we will also use gene-editing tools to map the relationship between telomerase expression and cellular robustness to oxidative stress. False teeth - a thing of the past Increasing tooth loss remains a feature of old age in humans throughout the world. We will harness synthetic biology to improve the dental health of the ageing population by designing bacteria that do not cause decay but actually prevent it. These biofilm-fillings will provide a regenerative internal environment for the tooth whilst fighting off the surface bacteria that cause dental plaques. Grey love - it does not have to be dangerous You may be surprised to know that sexually transmitted diseases are particularly prevalent in elderly populations. By embedding living biosensors into lubricant gels we will simplify the process of screening potential partners for sexually transmitted infections – as the gel will glow in the night on contact with organisms such as Neisseria gonorrhoeae.


TU-Eindhoven

In the emerging field of synthetic biology, many new innovations arise. To use them as efficient and safe as possible, regulation is the key. Therefore, iGEM TU Eindhoven is developing new kinds of scaffold proteins, based on the T14-3-3 protein. These scaffold proteins have a wide range of applications in regulating systems in synthetic biology. 14-3-3 proteins are a protein family which are highly conserved and are expressed in all eukaryotic cells. We are working with 14-3-3 proteins from the Nicotiana plumbaginifolia (Tobacco) plant (T14-3-3). T14-3-3 proteins dimerize to form a functional scaffold. A T14-3-3 scaffold is known to interact with the last 52 C-terminal amino acids of the regulatory domain of tobacco H+-ATPase (CT52)1. It is also known that this interaction is greatly stabilized by the natural product Fusicoccin2. Thus under influence of FC two CT52 protein can bind to the T14-3-3 scaffold. The first scaffold protein that we will make is a heterodimeric variant of the T14-3-3 protein. A second orthogonal binding interaction between T14-3-3 and CT52 compared to the wildtype needs to be found to create a heterodimer. This possible new binding interaction was found through computational design, using the Rosetta software package. With this New scaffold protein, one could bring two different proteins in close proximity of each other. One of the possible applications of this protein is regulating the CRISPR/Cas9 system. In a recent study from Zetsche, Volz, & Zhang3, the authors successfully split the Cas9 protein into two inactive fragments which can assemble into active Cas9 when in close proximity of each other. When each of these two sCas9 fragments is linked to the CT52 protein, they could be assembled on our scaffold protein under the influence of fusicoccin, creating a novel switchable CRISPR/Cas9 system that can be regulated with fusicoccin. The second protein that will be made by our team is a tetrameric variant of the T14-3-3 protein. This will be accomplished by linking four 14-3-3 monomers to each other. It is expected this protein will have a stronger response with respect to the naturally occurring dimeric variant of T14-3-3, because a larger amount of CT52 can bind in comparison with the dimeric variant. An application of this protein is a kill switch. To make a functional kill switch, caspase 9 is used, a protein which induces apoptosis when brought in close proximity of each other. By linking caspase 9 to CT52, apoptosis can be induced dependent on the presence of fusicoccin, thus a kill switch is created. This kill switch can be implemented in genetically modified cells as an extra safety mechanism. An example of implementation of the kill switch is T cell therapy. This is an emerging possible cancer treatment in which human T cells are extracted from the body, then they are genetically modified to detect and exterminate cancer cells more efficient when placed back in the body of the patient.4 Our kill switch might be valuable to ensure the safety of this treatment. This is not expected to happen on short term, it is just one example of the possibilities our kill switch might have in the future.


Hong_Kong_HKU

Cancer has always been a devastating disease. In 2012, there were 14.1 million new cancer cases worldwide.[1] Early diagnosis of cancer may help to reduce the mortality rate and extend the life expectancy of patients. For instance, in the U. K., nearly 90% of patients diagnosed with stage I lung cancer lived for more than a year while only 19% of patients diagnosed at stage IV do so.[2] Early diagnosis of cancer is also believed to be vital for successful treatment and recovery. Significant gene mutations might indicate the possibility of development of cancers. Although recent research has diagnosed cancers by analyzing individual genetic mutation profiles[3],[4], such diagnostic method takes up considerable amount of time to obtain accurate results. As conventional diagnostic methods involve complicated procedures, DNA nanostructures have been introduced to detect cancer biomarkers to facilitate simple diagnosis. DNA has emerged as a promising material that allows researchers to construct novel designs as its structure could be predicted easily and accurately.[5] Examples of DNA nanostructures include nano-tweezers to detect norovirus and a DNA ‘Nano-Claw’ to detect membrane markers of cancer cells.[6],[7] DNA Boolean logic gates have been constructed to produce signals in the presence of multiple targets, such as OR-gate and AND-gate DNA tetrahedra that generate fluorescence resonance energy transfer (FRET) signal when multiple inputs hybridize with the probe.[8] As for the targets to be detected, different microRNAs (miRNAs) have been identified to be associated with cancers. For example, miR-15b-5p, miR-338-5p, and miR-764 found in plasma are potential biomarkers for detecting hepatocellular carcinoma cancer (HCC), a common type of liver cancer.[9] It has already been reported that it is promising to use these biomarkers - miRNAs to detect cancers.[10] Our aim is to design a novel DNA nanostructure that can detect multiple miRNA targets simultaneously. We hope that our design can discriminate a single base mutation of the target miRNAs. Hence, it can be highly specific to our targets and avoid false positives. Our goal is clear - we aim to design a tool which can possibly detect a combination of biomarkers and enhance the sensitivity of detecting a particular type of cancer. Recently, in vitro applications of DNA nanostructure have already achieved point-of-care (POC) diagnosis[11]. Therefore, we hope to move from in vitro to in vivo by developing a self-assembled DNA nanostructure that can potentially target miRNAs in vivo. Detecting serum miRNA can be challenging because of the low serum miRNA level, so methods such as quantitative polymerase chain reaction are used to amplify the target miRNAs before detecting them.[12] We hope that our DNA nanostructure, which is synthesized and assembled in vivo, can potentially eliminate the need of target amplification. In addition, our design has an advantage over the current designs of molecular beacon. Molecular beacon makes use of fluorophores and quenchers[13], which cannot be synthesized in vivo. Our design does not require the use of fluorophore and quencher and thus can work well inside cells. In addition, our DNA nanostructure can be produced at a lower cost as fluorophore and quencher are not used. Our design is a 3-dimensional structure that can be self-assembled from oligonucleotides. Our aim is to construct a nanostructure that is able to detect multiple miRNA biomarkers such that it can reach a higher accuracy for diagnosis. For the selection of biomarkers, we are looking for a combination of miRNAs that are specific to a certain type of disease including cancers. At current stage, we are testing different designs in vitro to see if they can produce desired signals. After proving our designs can work in vitro, we will attempt to test them in vivo. Finally, we will design a mechanism such that E. coli can synthesize the required oligonucleotides to form the specified nanostructure. In the past decade, functional DNA nanostructures have been used in similar in vitro approaches to detect various cancer biomarkers.[14][15]It is noted that most of those designs were applied in vitro. Recently, 1D and 2D DNA structures were successfully expressed and assembled in vivo,[16] while several novel 3D DNA structures were synthesized to produce signals in vivo.[17],[18] Given these advancements, our ultimate goal is to enable our functional DNA nanostructure to be synthesized and self-assembled in E. coli, that can function inside the disease cells. This, if successful and with further refinement, could be a great replacement to colour coded surgery in the surgical field.[19] Last but not least, the cost and quality of production, efficiency and accuracy of our intracellularly-synthesized 3D structure will be compared to current diagnostic methods.


Paris_Bettencourt

Project description Dry cleaning is a process used to clean delicate fabrics which cannot withstand conventional detergents, physical forces and temperatures inside a washing machine. Despite being useful, dry cleaning can pose a threat to human health and the environment, since throughout the process different hazardous solvents are used to remove the stains from the fabric. Among the most widely used chemicals are tetrachloroethylene and perchloroethylene (also called "perc" by the industry). “Perc” is a volatile organic compound, hence it generates fumes that allow it to spread through the air from the clothes after the dry-cleaning process. Furthermore, “perc” is listed as "reasonably anticipated to be a human carcinogen" in the Thirteenth Report on Carcinogens published by the National Toxicology Program, because long-term exposure to perchloroethylene has been linked to different types of cancer. Luckily, the French government has begun, in the light of the Horizon 2020, the process of banning the use of “perc”, and promoting eco-friendly alternatives in all establishments close to the inhabited areas. This is where our iGEM project starts. We interviewed several dry cleaning facilities in Paris to get a better insight about their needs, and what problems they might be facing. Not surprisingly, they told us that wine stains are one of the most difficult stains to remove from clothes, and thus we decided to have them as our main focus. Wine, in general, is a complex mixture of alcohol, sugars, water and different secondary metabolites, such as anthocyanins, flavonoids, tannins, amongst many more. Our project is based on finding and improving enzymes, and processes, to degrade pigment molecules from wine stains. We are going to design and implement a series of assays in order to identify different enzymes and microbes from environmental samples. In addition, our project will develop a library of various binding domains with affinity for different fabrics, such as cotton, wool, silk, nylon or polyester. Some of these domains already exist in nature, and some are available in the iGEM registry. By adding these domains to our enzymes, we expect to improve cleaning efficiency and localization to the stain. We are also planning to focus on other important issues concerning our project, such as enzyme robustness, extraction and secretion, preserving the fabric quality, growth conditions and medias. Also, we will explore other interesting aspects of clothes industries like denim bleaching. And, of course, every successfully developed product will be forever perpetuated in the BioBrick format. This project was selected from a pool of ideas generated in a series of discussions, brainstorming sessions and votings. Our selection process has included constant deducting and adding new ideas, up until final voting which resulted in the Frank‘n’Stain project. To achieve the best results on this year's iGEM competition, we have assembled a team based on our motivation, ambition, interdisciplinarity, creativity and scientific background. Together, with a little help from our advisors: Ariel Lindner, Jake Wintermute, Jason Bland and Nadine Bongaerts, we are going to work hard and rid the world of the nasty (although very French) wine stains! Sources: https://toxtown.nlm.nih.gov/text_version/chemicals.php?id=22 http://ntp.niehs.nih.gov/ntp/roc/content/listed_substances_508.pdf http://www.developpement-durable.gouv.fr/Le-perchloroethylene-interdit-dans.html


ATOMS_Turkiye

The extraordinary physical and functional properties of DNA and RNA have led to extensive investigation into their suitability for use in many fields including therapeutics, diagnostics, chemistry, nanotechnology, and molecular computation. This year ATOMS_Turkiye team has decided to describe some properties and applications of nucleic acid enzymes. We think that our project will show a different side of applications of nucleic acid enzymes. We plan to introduce new nucleic acid-based sensors that in future can become fast, user-friendly and inexpensive.


DTU-Denmark

We are DTU BioBuilders, the iGEM team of the Technical University of Denmark. We study biotechnolgy, bioinformatics, mathematical modelling, environmental engineering and biomedical engineering. Our team consists of 13 graduates and 3 undergraduates. In addition, we have 3 highschool students assisting us in the lab. Our team members come from Denmark, Germany, the Netherlands, Greece, China and Poland. This year we tackle substrate utilization in cell factories and this is our wiki:We tried to identify a project that meets the following criteria: In Denmark today, less than half the waste produced is recycled, which means that more than 3.5 million tons get burned off each year.We have abundant waste streams from the industry such as glycerol from biodiesel production, byproducts from rapeseed production, used cooking oil and ordinary household waste.Cell factories are becoming an increasing factor in the industry today, where different microorganisms are utilized to produce various compounds from therapeutics to food additives. Currently however, the sustainability of these industrial processes is limited by the narrow substrate range of the organisms used. The most common feeds in use are simple carbohydrates such as glucose produced by enzymatic hydrolysis from edible plants such as maize, rice and wheat.This project aims to develop the chassis for a versatile and efficient cell factory that can transform abundant waste streams into valuable products using Yarrowia lipolytica and state of the art genetic editing techniques.The reason why Y. lipolytica has not been implemented in industry yet is the current lack of tools for genetic engineering. In our project, we develop and test tools for Y. lipolytica. This set will standardized and based on CRISPR/Cas9-mediated genome editing. Y. lipolytica naturally comes with a high potential for biotechnological applications. By using our toolbox, anyone will be able to easily customize the genome to their needs.


Toulouse_France

Paleobtilis "Back to the origins..." A shield for the Lascaux cave The Lascaux cave is in danger ! The Lascaux cave has been home to parietal paintings for more than 18 000 years. It has been discovered in 1940, and opened to the public a few years later. It gained success right away, and hundreds of people visited the cave, which first caused algal contamination. The cave was subsequently closed in 1963 to the public. It is currently infested by bacteria and fungi that cause black and white spots on the paintings. Diverse treatments have been tested (antibiotics, antifungals, chemicals, manual scratching...), but no long term solution was found. Worse, the ecosystem was disturbed... We are offering a biological solution that consists in creating a bacteria with a predation system that will be able to use the bacteria responsible for the development of fungi as a nutritive source (such as Pseudomonas fluorescens). Moreover, our bacteria will have the ability to sense the presence of fungi (like sp. Ochroconis), and get rid of it. We have divided our project in 3 modules: 1) Predation module We will create a Bacillus subtilis strain that possesses a skf operon under the control of a constitutive promoter Pveg. This will enable the bacteria to use Pseudomonas fluorescens as a nutritive source, and thus deprive fungi from their prime support. 2) Antifungal module The modified Bacillus subtilis will be able to sense fungi's presence with a specific recognition of N-acetylglucosamine (thanks to the inducible promoter PnagP). That would trigger the production of an antifungal cocktail. 3) Confinement module The double system toxin/antitoxin avoids the propagation of the genetic material in the environment. Also, a third plasmid contains a gene coding for a subunit of the RNA polymerase (we will knock out the strain for it) and for the RepU gene (which controls plasmid replication) under the control of a repressed promoter. With this system, we can control our bacteria lifetime. It is also spo- to prevent Bacillus subtilis sporulation. Why did we choose this subject? After months of intense brainstorming, we finally decided to work on the conservation of the Lascaux cave. We wanted to choose a project that was personal and original. We first thought of a solution for damaged paintings that were attacked by fungi and bacteria. The Lascaux cave then imposed itself. It is part of the French heritage, and was added to the UNESCO World Heritage Sites list. It has been threatened of destruction since decades now, and organizations from all around the world have gathered to solve the Lascaux cave crisis, unfortunately without success. The Lascaux cave is what traces us back to our humanity. The first men lived there and the first pieces of art ever were created. Combining art and science was an interesting idea, but we wanted a system that could be used in other disciplines as well, like public health. As you know, there is always a high risk of fungal infection in health institutions, where the situation is similar to the one in the Lascaux cave. Thus, a biofilm of bacteria is a nutritive source for fungi and our solution, if it was to be improved, could be used to solve the problem locally and for a selected period of time.


Northeastern

Northeastern’s brainstorming this year evolved around two proposals: E. coli that maintain anoxic conditions and E. coli that deliver pathogen-disabling CRISPR-cas9 constructs to pathogen bacteria. While the two ideas were dissimilar, we discovered an area that we believe could make use of both projects: microbial electrochemical technologies. Microbial electrochemical technologies take advantage of bacterial oxidation of food sources by the production of electrical current. Microbial electrolysis cells, which are a subset of microbial electrochemical technologies, use the electrical current generated by bacteria breaking down substrate as a subsidy for the evolution of valuable chemicals on the cathode side of the cell. Hydrogen, which would normally require around 0.41V from acetate, for example, can be produced in an MEC at around 0.2V since the bacteria themselves provide some of the current. Oxygen in an MEC will hinder hydrogen generation since oxygen will readily reduce at the cathode, therefore, maintaining an oxygen-free environment, by the engineering of partner E coli, may prove advantageous for MEC’s. We believe that conjugation of CRISPR-cas9 plasmids to pathogenic bacteria also makes sense in the context of MECs. The reason for this is that MECs show the greatest potential for use in wastewater treatment facilities, where there are large unused quantities of reduced organic material. An additional but unaddressed need within wastewater treatment is the ability to detect the presence of pathogens; discovering pathogens in wastewater may predict the emergence of disease. In this pursuit, existing technologies fall short. PCR is difficult to apply in this situation, given the sheer number of circulating pathogens, and microarrays are not robust enough for the application. If it were possible to use the partner bacteria in MECs to also conjugate CRISPR plasmids into pathogenic bacteria, detecting pathogens if they are present in the wastewater, we believe that it would represent a reliable solution to the existing problem. Therefore, our project is centered around investigating these two problems, both of which could be addressed the treatment of wastewater.


UNSW_Australia

When project discussions began, we immediately decided to centre our ideas around a key theme: to broaden the toolkit of synthetic biology, rather than simply applying existing tech. Put simply, we wanted to leave a legacy that would make future research and industry projects brighter and more powerful. And so we brainstormed a few novel tools, including building upon UNSW's 2015 team via pseudoknot characterisation, or creating the first voltage-sensitive promoter in bacteria. We then split up into groups to flesh out and give substance to our thoughts, eventually coming together for a debate. Unanimously we decided on our current project: to standardise outer membrane vesicles (OMVs) for use in synthetic biology projects. So what’s an OMV? They’re secreted by some species of gram-negative bacteria, when their outer membranes pinches in and buds off; the result is a nanoscale lipid bubble being released into the environment, decorated on the outside with outer-membrane proteins, and encapsulating some periplasmic contents. Given this, OMVs can be tailored to a variety of functions, by targeting proteins either to the periplasm or outer membrane. In nature, they've been co-opted for the export of signalling messages or virulence factors, but, in contrast, synthetic biology has been slow to explore their potential. One recent paper showed that scaffolding an enzymatic cascade on and in an OMV could increase the reaction rate 23-fold, relative to the same enzymes in solution; evidently, the biotech applications of OMVs may potentially be enormous, but little research is going into them. The barrier to applying OMVs, we feel, is that there is currently no standardised, well-characterised system for making bacteria produce and customise them. While a variety of genetic variants are known to help overproduce vesicles, their relative or even absolute production rates are not known – but to best apply OMVs to an issue, isn’t it first critical that you have an optimised system for producing them? Thus, the project of UNSW Australia is to compare and contrast the effectiveness with which different genetic factors induce OMV formation, and, in doing so, provide future researchers with an effective platform to apply them from. - To develop a simple assay to score OMV formation, e.g. on OMV size, stability, and rate of production - To use the assay to compare a range of genetic variants, both on their own and in combination, with regards to OMV formation - To use the above data to produce a strain of E. coli optimised for protein and OMV production, suitable for use in future synthetic biology projects - And, if all works out, to demonstrate some simple applications for OMVs in solving environmental or medical issues In doing so, we hope to make OMVs a viable tool for use in years to come by all synthetic biologists. We’re looking forward to a productive year!


UNebraska-Lincoln

We wanted our project to address a problem of significance on both global and local levels. Because Nebraska’s economy relies heavily on agriculture, a project devoted to an aspect of this industry was the obvious choice. Our objective is to reduce the nitrate levels in the waterways around Nebraska. Runoff from land treated with nitrate-containing fertilizers causes the accumulation of these compounds in waterways, where they are carried to the Gulf of Mexico. According to the National Oceanic and Atmospheric Administration, the Gulf of Mexico is the second-largest dead zone in the world, measuring approximately 5,500-6,500 square miles.A dead zone is a hypoxic area in a body of water where little marine life can survive. The excess nutrients in the water from fertilizers cause algal blooms at the surface. Because algae is not a good food source for other organisms in the ecosystem, it sinks and decomposes when it dies. The process of decomposition uses oxygen dissolved in the water, making the area uninhabitable for many species.We want to fix this problem by reducing nitrate levels in local rivers, addressing the problem at its source. We aim to engineer E. Coli to convert nitrate ions back into elemental nitrogen, a process called denitrification. Engineering E. coli to denitrify waters will involve introducing a nitrate-responsive promoter, corresponding bacterial ‘termination sequences’, and safety steps to ensure that the process can be controlled to the cells.


NYU_Shanghai

Vibrio harveyi, a bacterium non-pathogenic to humans, is a primary pathogen for marine animals, including shrimps, lobsters, seahorses, sharks, and sea bass. It can cause eye-lesions, gastro-enteritis, vasculitis, and luminous vibriosis in these animals and in particular, has been a great threat to the shrimp industry. The main goal of our project is to detect the pathogenic bacterium Vibrio harveyi and design a potential antimicrobial agent for it. To do so, we are going to engineer E.coli to manufacture nitric oxide (NO) which is known to have certain antimicrobial effects. As a first step, we are going to engineer E. coli to detect the presence of the pathogenic bacterium Vibrio harveyi. This means that we are going to use a mutant E. coli strain with a silenced LuxS gene so that this E. coli cannot synthesize its own quorum sensing molecule Autoinducer-2 (AI-2) but is still capable of detecting the AI-2 secreted by the marine pathogen Vibrio harveyi. We will then further engineer E. coli so that it has a pathway for synthesizing NO by inserting a bacterial Nitric Oxide Synthase (bNOS) gene from Bacillus subtilis into a vector that is then to be transformed into the E. coli. The expression of this gene will be regulated by T7 promoter which is in turn regulated by T7RPol, which is under the control of lsr promoter. Lsr genes in E. coli are induced once the repressor LsrR is de-repressed. The signalling molecules AI-2, once phosphorylated, de-represses the LsrR repressor. Thus, this means that when the E. coli detects AI-2 from V. harveyi, there is an uptake of AI-2 molecules that are then phosphorylated to phospho-AI-2. These then activate the lsr promoter, which then initiates the synthesis of T7RPol. T7RPol activates the T7 promoter and this initiates the transcription of bNOS. Once transcribed and translated into NOS, NO, an antimicrobial agent for Vibrio harveyi, will be produced.


NTNU_Trondheim

Our story Our early brainstorming sessions were very effective and resulted in countless ideas regarding our project idea and scope. After several meetings and debates we narrowed it down to 3 main topics: pathogenic bacteria detecting sensor for food, possible upgrade for probiotic bacteria or using CRISPR to introduce information to bacteria genome as a binary code. From those, the CRISPR project was the one we initially chose. However, during the research phase, we found an issue that can not be solved within a reasonable timeframe and we had to develop a new idea. That is how our current project came into fruition. Our goal In a world where computers are getting increasingly life-like, it is our goal to introduce computational logic in living organisms. As NTNU’s contribution to the 2016 international iGEM competition, we will make a system for introducing logic gates in living cells. Computers work by moving information between computational units, called gates. Each of these gates exhibits a simple logical statement (AND, OR, NOT...). The implementation of these logic gates is the foundation for all of the life-changing applications computer technology has provided. Our goal is to bring the great potential of computer technology, such as developing a new generation of biosensors, improving the process of industrial fermentations, or advancing cancer research to the field of biological engineering. In order to achieve this, we are making a system for engineering in vivo logic gates. We are planning to introduce XOR logic gate into E.Coli genetic code.


Evry

280 million tons: it’s the average plastic amount product each year worldwide (what means 8,880 kilograms per second)! 1,000 years: it’s the average duration of a plastic bottle! Up to 450 years: it’s the time needed for the degradation of a plastic bag in the environment. For these reasons, our team thought about working on a biological alternative to the plastic: the PLA!PLA, or polylactic acid, is a totally biodegradable polymer and a thermoplastic. It’s currently used as food packaging but also in other applications such as, for example, the sutures in surgery.PLA has a lot of advantages. Indeed, around 80 days are estimated to be sufficient instead of 1000 years for the degradation of a bottle. Moreover, it has a high rigidity, very good optic properties in terms of transparence and brilliance, good properties of protection against fats, oils and gases (O2 and CO2) allowing it to be intermediate to different mass market polymers and an alternative to the current plastics.Our objective for iGEM 2016, is to produce a significant amount of PLA solely by biological way by using distinct species of bacteria. This will enable an ecological and inexpensive synthesis, just from simple sugars.Thanks to its advantages, the PLA may have to replace all fossil plastics. It is possible to make bottles or other PLA cutlery, but its properties also make it perfect for 3D printers or biomedicine.Indeed, we may also consider using our PLA synthesized to create vesicles for the transport and release of molecules such as drugs in the human body. The PLA is not hazardous to our health, it would be a new application for this compound!Thereby, this process could allow a decrease of the PLA import in France, which would reduce its cost and would give a biodegradable alternative to the use of plastics. Our team project has an economic interest (reduction of importation and costs) but also an ecologic one (biodegradable plastic reducing the plastic pollution).Considering the devastating effects of petroleum-based plastics in the lands, seas and their wild lives, and the fact that their production is increasing, we need sustainable alternatives to maintain our lifestyles without further deteriorate our environment.The bacteria chosen for the bio-production of PLA is pseudomonas putida. Indeed, Pseudomonas putida produce naturally lactate, then we will engineered it for production of lactyl-CoA, and polymerization into PLA. To do that, we will add two enzyme in the pseudomonas plasmid, the first one, is Propionate coA-transferase and the second one is PHA synthase.To follow the bio-production, we are going to use 4 steps fermentation, in the first steps, we will optimize the growth of our bacteria. Then, we will induce the transformation of the lactate into lactyl-coA, after that, we will induce the polymerization and at the last steps, the lysis for the release of PLA.


WPI_Worcester

We are using CRISPR/dCas9-based RNA targeting and dCAS9 fusions to two different RNA editing enzymes, APOBEC and ADARs1, to make C->U or A->I (G) edits in an RNA target. Our technology will be reversible and tunable, and will increase the variety, efficiency and safety of gene editing technologies. We hope to be able to apply this technology through RNA therapeutics to cure diseases caused by nonsense and substitution mutations.Greetings all interested visitors, we are working on our project but are still in the preparatory stages. Because of this, we have not yet started on filling out our site. We will be sure to add more to our website in the near future. Check out our Facebook!


UChicago

The KaiABC system consists of three core proteins that comprise the 24-hour circadian clock endogenous to the cyanobacterium Synechocococcus elongatus. Oscillations are driven by the kinase activity of KaiC and its interactions with KaiA and KaiB which catalyze the cyclic auto-phosphorylation and auto-dephosphorylation of KaiC, respectively. The establishment of a modular circadian oscillator would be a useful tool for synthetic biology. The Kai oscillator can be reconstituted in vitro with purified protein, motivating a previous study to transplant the Kai system into E.coli (Chen et al, 2014). Our aim is to expand this line of research and transplant the Kai system into Saccharomyces cerevisiae, demonstrating this system in eukaryotes for the first time.We first aim to express the Kai system in yeast with an appropriate protein stoichiometry. Once the oscillator has been properly established, reporter constructs utilizing a LexA-SasA fusion protein will be introduced which respond to phosphorylated and dephosphorylated KaiC, respectively, with the production of two different fluorescent markers. This will allow oscillations to be viewed in real time as varying concentrations of these fluorophores. It will also serve as proof-of-concept for a system with the ability to synthesize two temporally separated protein products generated during alternating 12-hour time spans, a tool with potential downstream applications in basic research and medicine. It also serves as a first step towards introducing the KaiABC system into higher eukaryotic organisms such as Drosophila and human cell lines.


CCA_SanDiego

Substances such as drinking water, groundwater, runoff, and other chemically exposed areas have sustained much damage to both their quality and purity. Common pollutants include alcohols, esters, and other organic substances that pose harm to organisms when ingested in large quantities. Current methods of purification involve exposing the toxic substrates to more chemicals, which, while are effective, also lead to a mixture of more chemical substances in the original substrate. The issues in detoxification lie within inapplicable delivery systems and a lack of absorbance and efficiency. However, detoxification has proven to be an effective way to minimize amount of chemicals used for maximum efficiency. We aim to solve this issue by engineering a multi-functional plasmid to be implanted in E. Coli bacteria for detoxification of contaminated groundwater. Our plasmid will achieve three main aims: 1. The plasmid will contain 2 genes: the first being CYP2E1, and the second being adhE. CYP2E1 serves to break down harmful substances including acetone and ethanol, whilst adhE breaks down additional alcohols. 2. These genes will recognize substances of interest and be effective in breaking down the toxins into simpler, safer compounds. 3. The plasmid will be purified and isolated for possible implantation into a variety of biological systems. We honed in on these two genes due to their already biologically proven abilities to process alcohols and other toxic organic substances. Because the CYP2E1 gene is more commonly found in mammalian organisms, and is not found in E. Coli, we aim to utilize the metabolism encoded for in this gene in conjunction with the already found aldehyde dehydrogenase gene in E. Coli to enhance its detoxification abilities. Our hope is that this multifunctional plasmid, or the E. Coli platform itself, will be able to be applied to a wide range of detoxification processes involving these organic compounds. In the meantime, we work to develop a filtration system using indirect exposure to the secreted proteins as a method of purifying the water.


SCU-China

This year, we designed an innovative insole called "Comfootable" to prevent foot odor and foot infection of microorganisms by two strains of engineered E.coli, after our project brainstorming in January 2016. Two engineered strains E.coli both involve VHb gene to promote the growth ability in tough environment and some genes in two strains are knocked out to keep the strains themselves odorless. In strain 1, CecropinXJ, an antimicrobial peptide, is supposed to express in a fussion protein form to attack other microorganisms including fungi by foot temperature induced cell lysis. In strain 2, liv operon / polyleucine protein and aarC are expected to remove the odor in shoes. The insole has a specialized shape and inner structure design to make sure the successful diffusion of substrate, availability of microorganism growth and biosafety. Two strains are mixed together in the insole system to grow. We did a lot of modeling work, and we hope to spread the knowledge of foot odor and human microbiome through a series of attractive human practice projects. Sichuan University Architect Competition of Microorganism Application: Human Microbiome, for example, which attracted more than 200 students to attend in Sichuan University and Sichuan Agricultural University


Stanford-Brown

The Stanford-Brown 2016 iGEM team is building biologically produced membranes and sensors for space exploration. Biological materials have a variety of advantages over traditional building materials; most significant for our purposes, they are light and self-replicating. These characteristics make biomaterials ideally suited for space exploration. One possible application for these materials would be a biosensing balloon, which could be sent up into both terrestrial and extraterrestrial atmospheres to detect both temperature and molecules of interest. Furthermore, biomembranes and biosensors have many additional applications both on here on Earth and in space.


TecCEM_HS

TecCEM_HS 2016 team, initially recruited on March 2016, determined that the early detection of sexually transmitted diseases was of major importance given the broad range of consequences they have on public health. After some weeks of research and incidence analysis, the Human Papilloma Virus (HPV) was selected because of the concern it has raised throughout Mexico. Nowadays, HPV is the most common cause of cervix cancer within the country. The virus has been characterised and documented at the genetic and proteomic levels, but given its pathophysiology during infection, diagnosis at early stages is somewhat complicated and unusual, particularly because of the absence of symptoms. Moreover, it is of crucial importance as some HPV strains have been shown to correlate with oncogenic outcomes. TecCEM_HS has decided to dedicate 2016 project to the development of a rapid test method by using the novelties of riboswitch technology. With careful and appropriate design, bacteria could serve as a signal provider that may give insight into the viral presence by means of fluorescence. The device would thereby provide a money-wise, quick, and reliable way of concluding upon Papilloma's infection, serving as an alert for further physician assessment.


JNFLS_China

Alzheimer is a disease prevailed in olds around the world and currently there hasn't have any effective treatment and the early diagnosis is hard to accomplish. Current research has already found that the fold change of specific kinds of microRNA has correlations with Alzheimer's development. To improve the method we can use widely to detect the disease,we are going to develop a rapid and simple diagnosis for Alzheimer disease using the different expression of microRNA between patients and healthy controls. A reporter carrier containing a repressed promoter is hoped to be constructed, which opening is controlled by microRNA degrading or inhibiting mRNA. The accuracy of the system will be increased by the synergistic effect of repressor proteins. Combined with reporter gene, a couple of microRNA would also be used to construct different plasmids to get efficient system which may can offer prototype for massive detection accurately and fast in a massive scale.


USP_UNIFESP-Brazil

We are a multidisciplinary team from São Paulo, Brasil, with students of architecture, biology, biomedical sciences, social sciences and more,from the universities USP, UNESP and UNIFESP. The team originated from the synthetic biology club (SynBio Brasil), which is a independent club that works promoting synbio and open science awereness and education. Since 2012, different members of the club have organized themselves to take part in iGEM competition .This year, our project is based on the heterologous expression of spider silk protein in Chlamydomonas reinhardtii . The project started when we looked at the problem of growing antibiotic resistance and started to think in ways to tackle it. We specially focused on injury related infections, for example in the case of burn victms. We devised the creation of an antibiotic patch, combining the physical properties of spider silk with antibiotic enzymes (enzybiotics). We intend to express both the spider silk and chimeric enzybiotic proteins with spider silk motifs in Chlamydomonas and polymerize then together to form the product of interest. We hope to acomplish, besides the final goal of patch development, improvement of Chlamydomonas as a synbio chassis and analysis of its capability of producing enzybiotics and monomers of spider silk. Moreover, the team is envolved with open hardware developement and promotion and synthetic biology popularization, helping to promote the synthetic biology culture in Brazil, raising awareness and engaging the public.


Manchester

We are a team of 11 undergraduate students all studying at the University of Manchester based in the Manchester Institute of Biotechnology under the supervision of Professor Rainer Breitling and Professor Eriko Takano. Science Behind AlcoPatch Controlling alcohol consumption can be difficult, especially amongst students in the UK. An alcohol patch that generates a visible colour change according to blood alcohol concentration could be used to monitor the level of intoxication in a person. Having an indicator to show how intoxicated a person is could help reduce undesired consequences of being too drunk Our Project Plan It is known that the ethanol concentration in sweat is linearly related to the blood alcohol concentration. Based on this, we aim to develop an ethanol biosensor by using synthetic biology with two separate methods to measure intoxication levels. The first mechanism involves the usage of alcohol oxidase (AOX) in a cell-free system to oxidise ethanol to acetaldehyde that produces hydrogen peroxide ($H_2O_2$) as a by-product. $H_2O_2$ is used as an oxidising agent by horseradish peroxidase (HRP) to convert ABTS to produce luminescence. The second mechanism involves activation of ethanol sensitive alcR in engineered Escherichia Coli (E.Coli). The activated transcription factor then activates the promoter alcA leading to the expression of chromoprotein.


TCU_Taiwan

To achieve our goal we incorporated antimicrobial peptides (AMPs) into our medical dressing. AMPs, are stable peptide that have extensive ability in bactericidal effects. Unlike antibiotics, AMPs can puncture the cell membrane to kill the bacteria therefore bypassing bacterial antibiotic drug resistance mechanisms. [1] Besides, the peptides also have ability to help skin recovered. [2] After reading numerous of research articles, we selected two kinds of AMPs: Signiferin and Epinecidin-1 as our reagents. Signiferin is a peptide came from the skin mucus of Crinia signifera. It demonstrated effectiveness in killing Methicillin-Resistant Staphylococcus aureus (MRSA), and has already been demonstrated by the TU-Delft 2013 iGEM team. [3] Epinecidin-1 is a peptide came from the skin mucus of Epinephelus coioides. It has ability to help wound healing and has been proven by animal studies, and was selected as an additional reagent. [4] By combining these two properties, we believe that can develop a wound dressing that may be useful in trauma patients without the additional risk of developing drug-resistance. To control the AMPs expression and secretion, the Lac operon was used and treated signal peptide into our system. Helping peptides secret into culture medium. [5, 6] After purification of the peptide we will be testing the effectiveness of our synthetic AMPs. We will test macro-dilution of S. aureus and in vitro wound healing assay for epithelial cells line (HaCaT). Out goal is to create a wound dressing that is effective in inhibiting bacterial growth and assisting wound healing process.


SCUT-China_A

As we know, oil is one of the most important energy in the world, however, burning the oil has done great harm to the environment. Especially the sulfur element, which causes the acid rain, has caused serious damage to the buildings, plants, and animals and so on. To avoid these harm, people have done a lot in industry, but the traditional desulfurization has shown its evident shortcomings. Therefore, we put forward the bio-desulfurization to improve this matter. In the process of bio-desulfurization, we choose the thiophenes DBT as substrate, and desulfurize in a 4s pathway. By now, we have succeeded building the gene pathway of the enzymes Dsz A ,B, C, D in E.coli, which are used in the 4s pathway, and they have expressed. In the same time, we suppose to introduce a MexAB-OprM efflux system in E.coli so that the product HBP can be removed from the bacteria, preventing the bacteria from harming. In the preliminary experiments, we have proved that the engineering bacteria are able to turn DBT into HBP, this is what we call bio-desulfurization. In the future, we will optimize the system and improve the efficiency of desulfurization. When we are modeling, we have found that when Enzyme concentration meet Dsz B>DszC>DszA, we get the highest efficiency. So in the next stage, we will adjust the biocircuit and the ratio of oil and water, in order to find the best model. With regard to human practice, parts of work are in progress, including questionnaire, discussion with Guangzhou environmental monitoring and petrochemical works, and searching for relevant laws and regulations. In addition, we will contact the Environmental Protection Bureau, jointly develop a new standard of sulfur emission, and promote the bio-desulfurization to public.


Cardiff_Wales

Our project is focused on healthcare - from the initial meetings we played with multiple threads, which shared a common theme of using a novel biosensor, CRISPR/Cas9. Eventually the focus turned to sexual health, and the speed and methods of testing used.From here, the idea of a bioluminescent DNA assay, for improved and near immediate point of care testing of disease, came about. This would be via a CRISPR/Cas9 and split luciferase. Not only do we hope to achieve proof of concept (i.e that the luciferase can successfully recombine to noticably fluoresce), via our outreach contacts we aim to improve the public knowledge of GMO, and to inspire younger generations.


Linkoping_Sweden

What is our project about? The 2016 iGEM team representing Linköping University, Sweden, will focus on allowing the usage of CRISPR/Cas9 in the unicellular model algae Chlamydomonas reinhardtii. This organism has shown great potential as a future source for production of biofuels. There are several advantages of growing algae for this purpose as they offer high productivity and production of biomass, which avoids competition with other productive land uses. These properties are not utilized on a large scale, partly due to the relatively low lipid content of today’s algae. Therefore, many attempts have been made to modify them for promotion of lipid synthesis, and to optimize them for production of biofuels. Our goal with this project is to create new BioBricks consisting of an inducible promoter, and to couple it with a CRISPR/Cas9 system in C. reinhardtii. The reason why an inducible promoter is used, is to avoid complications such as the toxicity of a constitutively active Cas9. Our solution to this problem is to cause cultures of algae to undergo genetic modification in response to high intensity light when a sufficient amount of algae have been accumulated. A variety of genes can be targeted with this approach in order to upregulate synthesis of lipids in algae. Why did we choose this project? As a result of global warming due to excessive use of fossil fuels the LiU iGEM 2016 team decided to contribute in the search of alternative green energy sources. As previously mentioned, C.reinhardtii have shown beneficial properties in conservation of energy but also for applications in synthetic biology by reason of its unicellularity and sequenced genome. The discovery of the problem with the inefficient lipid production in C.reinhardtii led to the idea of using a controllable CRISPR/Cas9 system for optimization of the metabolism. What do we hope to accomplish with our project? The aim of this year’s project is to verify that an inducible promotor can be used with CRISPR/Cas9 in the C.reinhardtii model algae. This will allow further modification of metabolic genes in the near future. A more distant future prospect is to make algae the most efficient source for biofuel production and to make a contribution for the well-being of our planet.


SMS_Shenzhen

As high school students, we want to something meaningful which can change the world. We gathered after school brainstorming our ideas, including the aspect of environment, health care, and food safety-of all the subjects. Seeking an advancing method which potentially deals with people’s recent problems in lives, our team has experienced a long discussion throughout March. We had searched for mounts of paper on the website while still in school. A late article published in April on NCBI give us light. It characterized SDF1α-elastin-like-peptide nanoparticles, which can highly accelerate wound closure. After perusing the paper and further investigating into the topic in the reality, we agreed that we would set our topic as wound healing.However, we want our final products not only to promote wound closure, but also prevent infection, which is another important aspect of wound helaing. Therefore, we choose LL-37 and DCD-1L as the two antimicrobial peptides reach this purpose.SDF1 is a human growth factor which supports re-epithelialization. When fused with ELP(elastic like peptide), a peptide with repeated sequence of a pentapeptide, it can better fix on the skin, since ELP will aggregate into nanoparticles after being expressed at the temperature of 40 Celsius. LL-37 and DCD-1L both can prevent growth of a wide range of bacteria including Gram-positive and Gram-negative bacteria. We designed the device that can be used by every family. The device includes temperature control since the temperature can induce the aggregation of ELP. We plan to design an APP as well to instruct users.At the same time, we design and plan our Human Practice. In summer vacation, we will carry on the activities, cooperation with companies and experiments we planned.


OLS_Canmore

We are the "Our Lady of The Snows Catholic Academy - OLS" team from Canmore, Alberta, Canada. Our project aims to break down hair in wastewater treatment facilities, and to break down feather waste in the poultry industry. It is from 'Keratinase' and 'keratin degradation' that we chose our name (BreaKERs) and our motto, that we are KER-ate chopping the keratin waste.After much brainstorming, we chose our project topic because our small community of Canmore is struggling to deal with hair build-up in our wastewater treatment facilities. These buildups have caused equipment failure, clogging, and increased maintenance costs for our town. Currently, these blockages are only dealt with by manually removing the accumulated hair. We thought there must be a better way, using synthetic biology, to solve this problem. Through our research we also found that keratin waste is a huge issue in the poultry processing industry, as feathers are also made up of the protein keratin. Billions of tonnes of feather waste accumulates, with limited options for disposal. At the moment, feathers are often disposed of in environmentally harmful ways. One method is incineration, which leads to the release of many pollutants, foul odours, and harmful runoff contaminating livestock and plants in the surrounding area. Burying the waste is another common disposal method, which leads to harmful leachates. As keratin is protein-rich, there is an opportunity of turning keratin waste into products such as animal feed or fertilizer; however this process is extremely expensive, time consuming, and often yields products of low quality. The goal is for our project to provide an inexpensive and efficient method to more completely break down keratin in both hair and feathers, providing a step towards solving the issue of keratin waste treatment.Our plan is to genetically engineer E.coli K12 to express Keratinase—an enzyme that breaks down the protein keratin, found in feathers and hair. We will use two different genes—Keratinase A (kerA) and Keratinase US (kerUS)—both of which are found naturally in the Bacillus genera. The kerA and kerUS sequences have been optimized for expression in E.coli and synthesized into plasmid rings, then will be ligated into a standard biobrick backbone for submission to the iGEM parts registry. Further plans characterizing these parts and constructing a prototype bioreactor to demonstrate a possible implementation strategy for our project. You can also view other team wiki pages for inspiration! Here are some examples:


Rice

The photoacoustic effect describes the conversion of electromagnetic energy to mechanical energy, namely, that an object absorbing non-ionizing laser pulses experiences local thermal expansions, and vibrates with frequencies in the ultrasonic range which may be detected. Imaging based on this effect yields high contrast from the optical component, and high resolution from the acoustic component (1). For biomedical purposes, users of this technique take advantage of endogenous and exogenous contrast agents to obtain physiological information from the biological tissue, endogenous examples including oxy- and deoxy-hemoglobin to determine blood flow speed (2). The bacterial pigment Violacein (Vio) has been reported to be an effective contrast agent under this technique (3). Furthermore, previous iGEM teams have developed and optimized a biosynthesis pathway for this pigment (4, 5). This team seeks to build upon, and move forward from, these past investigations and develop a biosensor in E. coli to produce Violacein in the presence of significant concentrations of biomarkers for disease; naturally, the team’s search for potential biomarkers will be for those which may pass through an animal’s or human’s gastrointestinal tract. This team considers the additional design aspect of logic gates to modulate the specificity for our system. Alongside Violacein, this team will experiment with similar genetic circuits using the fluorescent protein iRFP. For the purposes of testing the resultant system(s), this team has made an arrangement with a group at MD Anderson who can introduce our bacteria into mice, and who have photoacoustic imaging equipment to image the bacteria within the gastrointestinal tracts of the mice. References Jun X, Junjia Y, and Lihong VW. “Photoacoustic Tomography: Principles and Advances.” Progress in Electromagnetics Research 147:1-22, 2014. Fang H, Maslov K, and Wang LV. “Photoacoustic Doppler Effect from Flowing Small Light-Absorbing Particles.” Physical Review Letters 99:184501, 2007. Yuanyuan J, et al. “Violacein as a Genetically-Controlled, Enzymatically Amplified and Photobleaching-Resistance Chromophore for Optoacoustic Bacterial Imaging.” Nature.com. Nature Publishing Group. 19 June 2015. Web. 18 May 2016. E. Chromi. 2009. (18 May 2016; http://2009.igem.org/Team:Cambridge) USCF iGEM 2012. 2012. (18 May 2016; http://2012.igem.org/Team:UCSF)


UPO-Sevilla

Bacteria are an amazing field to work on. They can develop a wide variety of functionalities and properties in a very short time, being easy to work with and extremely versatile. On this basis, we wanted to take advantage of one of the most remarkable characteristics of the bacteria we were working with, Pseudomonas putida – the ability to form biofilms. These structures are composed of communities of bacteria that find themselves integrated in an extracellular polysaccharide-made matrix that protects them from several kind of stress. In addition, they have an increased metabolism, a feature that is often required in industrial production. Therefore, we thought that it would be a good application to try and do some bioremediation with these well-protected high-metabolic bacteria. In first place, we thought about glyphosate, an herbicide that has been demonstrated to be toxic to human. But due to technical difficulties, we could not continue with that idea. Instead, we looked for another substance that was an environmental problem, and found out about glycerol. It is being overproduced in the biofuel industry, and it is starting to become an environmental problem. So we started to model how our bacteria would eat that glycerol, and developed an attack strategy to combine that with biofilm. But what could we do with our grown bacteria? We decided that there could be a product we could produce with these biological reactors, and this product was propionate. It is widely used in a large variety of fields, easy to excrete from our bacteria and, according to the model, easy to produce. Let’s get started, don’t we?


Hong_Kong_HKUST

Tri-stable switch is a biological device that could perform three discrete, but alternating, steady states driven by three different repressible promoters. The presence of a transient pulse of inducer allows effective state shifting, while signal interference is prevented. In order to enhance the specificities towards inducers, improvements were made based on the Brown’s tri-stable switch model in 2006. This year, three well-characterized repressible promoters are used: phlFp, tetp, and lacp. The whole construct is divided into three parts, and each contains one functional system with two protein coding sequences(CDS), creating an interconnected tri-stable toggle switch. Moreover, mathematical modelling is applied to predict and verify the consistency of the experimental results. At present, it is by far possible and practical to apply the switch in biosensing which could be achieved by developing a combinatorial circuit of promoters and CDS. With its advantageous characteristics, it is foreseeable that the switch could be applied in a wider spectrum of fields in the near future, for example, biocomputational system and diseases diagnostic.


Melbourne

Our team is working to build upon the work of the 2014 Melbourne iGEM team, who worked on in vivo production of star-like peptides in E. coli. Our goal this year is to redesign the star-like peptides from the past project to allow easy cross-linking of individual subunits with each other as well as with various enzymes, with the use of inteins. This “StarScaffold” system has various potential applications, primarily as a highly customisable hydrogel and as a method of of improving reaction kinetics via enzyme co-localisation. We hope it will also act as a platform technology, with applications in industrial and medical science as well as other synthetic biology systems. During the months we were setting up our laboratory, being inducted and organising sponsorship, our team spent several months brainstorming and discussing ideas at our weekly meetings. During the orientation and training of team members in the laboratory we continued with the 2014 Melbourne University’s project as a way of practicing common laboratory procedures. During this time the potential of the star peptide became clear to the team and we decided to continue and expand upon this exciting project, using the basic concepts from 2014 but designing our own, improved DNA constructs and expanding the applications of the star peptide.


British_Columbia

Petroleum-derived chemicals are used as building blocks to create a variety of products we take for granted in our day to day lives. And while these molecules have proven to be critical for modern society, their overuse has had significant negative environmental and societal impacts. Microbial biocatalysts play a prominent role in the future of renewable biomass degradation into bio-equivalent chemicals that can be used directly in established industrial processes. However, there is high cost to process raw biomass into a usable form which has remained a major obstacle in successfully implementing these techniques in industry.During our brainstorming process we came up with the initial idea of using an engineered microbial community to effectively transform biomass into useful products. We were inspired by new research at our university on the expression of functional enzymes onto the S-Layer of certain strains of bacteria. We aim to use these new techniques together with traditional bacterial bio-catalytic pathways to make the processing and utilization of renewable biomass feedstocks cheaper and more efficient. To accomplish this task, we are designing a two-part microbial community. One half will be responsible for transforming biomass feeds stalks such as lignin and cellulose into useful growth substrates. While the other half will focus on using these growth substrates for the production of useful products. To create our biomass transforming bacterium, we will use the robust surface expression system in the bacterium Caulobacter crescentus to display biomass transforming enzymes, mimicking the cellulosomes and laccases found in natural biomass degrading bacteria. To create our production bacterium, we will engineer Escherichia coli, to produce violacein. Violacein is a high-value natural product with interesting pharmacological properties. It also has the benefit of being easily detected and quantified, allowing for the validation of our approach. When combined, these bacterial strains will be able to work together to degrade and valorize biomass. So far our team has been working to characterize a bio-bricked β-carotene construct in E. coli in order to do an initial proof of concept, we have also been working on the violacein construct. Simultaneously we have been cloning several laccases and celluloses into the s-layer protein of C. crescentus. We hope to get functional expression of our enzymes onto the s-layer and characterize the enzymatic activity to build and active model for our system which we can test by growing the two bacteria together in minimal media with restricted carbon sources.


UNH_Durham

Polychlorinated biphenyls (PCB’s) were infamous in the past, and they are still a threat today. PCB’s are organic compounds that were used extensively in various electrical industries in the past, specifically as a coolant. However, the production and usage was banned in the United States of America in 1979, and in the Stockholm Convention on Persistent Organic Pollutants in 2001. This action was in response to the discovery that PCB’s are non-biodegradable and cause serious neurological, reproductive and immune disorders in both humans and animals. PCB’s are still present in many water sources around the world, and they may cause problems through bioaccumulation. The EPA set the standard that more than 0.0005ppm of PCB is bad for the environment and human health. Clean water is becoming one of the most important and dwindling resources globally. Hence, the UNH iGEM Team aims to build a sensitive PCB biosensor that detects the base biphenyl structure in water sources. Bacteria like Pseudomonas pseuoalcaligenes, Acidovorax sp., Burkholderia, Luteibacter, Williamsia, etc. can degrade PCB’s, and the enzymes that do so are coded by the bph operon. We want to build a system based on the bph operon, such that production of an intermediate of the PCB degradation pathway will give a fluorescent output. Previous iGem teams have attempted to design similar biosensors based on the bph operon, but have struggled to obtain positive results. Teams such as Evry and Paris-Saclay had been unable to achieve positive results, and the current testing methods are unable to detect to the EPA’s standards for PCB. Our team aims to develop a more accurate and precise biosensing tool using bacterium to identify lower concentrations of PCB than are presently available.


SYSU-CHINA

How to trace cells generation by generation has confused scientists both in fundamental research and translational medicine, especially in stem cell therapy. Now, SYSU-CHINA intends to develop a system that can define the number of the cell cycle after a specific phase(eg. tracing the homing of modified stem cells). /


Harvard_BioDesign

The Harvard iGEM team began our brainstorming sessions during the late spring. We had a massive brainstorming session where we generated topics to investigate, and in the following weeks, scoured the internet for previous research relating to these topics. We met a few more times to discuss what we had found. After narrowing our search down to 4 projects, we wrote mini proposals to present each idea to the rest of the team. At the beginning of the summer, we continued our project planning with one project: Breaking PET. In Breaking PET, we hope to engineer a biological system that breaks down PET, a molecule which makes up one sixth of plastic products. Our project is grounded in research done by the Oda group at Kyoto Institute of Technology. In the paper “A bacteria that degrades and assimilates poly(ethylene terephthalate)”, they describe a bacteria found at a bottle recycling plant that has the ability to metabolize PET. From this paper, we found enzyme sequences for the two enzymes thought responsible for PET degradation: PETase and MHETase. PETase breaks down PET into the compound MHET, or mono(2-hydroxylethyl)terephthalic acid. MHETase further breaks down MHET into terephthalic acid and ethylene glycol. The discovery of these two enzymes is exciting because, unlike other PET degrading enzymes, PETase and MHETase are dedicated to the role of PET degradation. Additionally, PETase has been shown to have a degrading efficiency 120 times greater than alternative enzymes. Our project aims to use E Coli transformed with PETase and MHETase to break down PET and generate electricity. We will create BioBricks for PETase and MHETase and characterize these parts against enzymes used in previous PET degrading iGEM projects. Additionally, we hope to engineer a secretion system for these enzymes. We will also attempt to make a bioreactor/microbial fuel cell to generate electricity from the products of the PET degradation process.


NUS_Singapore

Conventional drug delivery systems are plagued by problems such as non-specific targeting and low bioavailability. Bacterial-based drug delivery systems have gained much interest due to their ability to overcome the issue of non-specific delivery of drugs. This is achieved by engineering bacteria to sense and respond to specific stimuli present in the microenvironment of these pathogenic cells. In this project, we propose the development of a dual-sensor bacteria which can only survive, and release therapeutics, within the targeted part of the human body (i.e., spatially specific). As our proof of concept, we will be engineering the Escherichia coli bacterium to target cancer tumors with high environmental lactate — see Warburg effect. To ensure that the bacterium will only affect cancer cells, the bacterium is engineered to detect, and adhere to a cancer specific surface marker. Upon detection, a quorum sensing system and the production of invasin and listeriolysin O is triggered. The invasin and listeriolysin O then allows the bacteria to deliver its payload directly into the cytoplasm of the cancer cell. Since the production of invasin and listeriolysin O cannot occur in the absence of the said marker, this delivery system will only target cancer cells, concentrating drug payload at the intended site. Our team has been working on cloning our desired biobrick parts and modelling our gene circuit. We hope to be able to characterise and optimise our parts, and demonstrate a functional spatially-specific drug delivery system, as well as complement our wet lab efforts with our model.


Wageningen_UR

Introduction Bees are the most important pollinators on earth and may account for a substantial proportion of the food we eat and therefore also for our quality of life [1, 2]. Their importance for the abundance and variety of our diet makes it all the more disturbing that honeybee mortality has been increasing in almost all western countries for at least 30 years [3, 4]. Sometimes even whole bee colonies die in one winter, a phenomenon that has been termed Colony Collapse Disorder (CCD). The most important cause of CCD is the parasitic mite Varroa destructor. Current treatments In the Netherlands, the Varroa mite is now combatted by a year-round treatment with organic compounds that include Thymol, Formic acid and Oxalic acid. However, these compounds have to be applied strictly according to the provided instructions. Thymol, for instance, has a small concentration margin between killing the mites and harming bees. The hobbyist character of beekeeping has to be considered in the context of these treatments. Beekeepers might not have the time and resources to apply the treatments in the intended manner. Synthetic Biological Treatment We aim to create a new and better solution for the Varroa problem using synthetic biology. Our project would yield a product harmless to both humans and bees because we intend to use a Bacillus thuringiensis protein toxin to target Varroa. B. thuringiensis is known for the production of very specific insecticidal protein endotoxins. Multiple Bacillus strains have now been identified that target the Varroa mite. We will employ the toxins from these strains to relieve bee colonies from this most harmful parasite. In addition to the B. thuringiensis toxin, our synthetic biological system will contain systems to provide efficient production and release of the toxin and to provide users with a high level of control.


Glasgow

Vitamin deficiencies are a major problem across the globe, especially in developing countries. Hypovitaminosis A (deficiency in Vitamin A) is the primary cause of preventable blindness in children, whereas folate deficiency is linked to an increased rate of spina bifida. We hope to target these ailments by manipulating yogurt bacteria to produce beta-carotene and produce more higher levels of folate. Our final goal is to introduce three genes in the beta-carotene synthesis pathway and upregulate the production of folate in a strain of lactic acid bacteria e.g. Streptococcus thermophilus. The yogurt produced from the bacteria would be rich in both beta-carotene (which is converted by the body into Vitamin A) and folate. Alongside this, we also aim to characterise lactic acid bacteria in various ways in order to increase understanding and ability to work with these potentially useful organisms. Additionally, we aim to make an accessible solar water bath incubator that could be used in developing countries to pasteurise milk and make yogurt. cessible solar water bath incubator that could be used in developing countries to pasteurise milk and make yogurt.


USP-EEL-Brazil

We started our project in the "Clube de Biologia Sintética EEL" (Synthetic Biology Club from Lorena Engineering School of the University of Sao Paulo), a place where many discussions come to place since 2014 and where a group of really dedicated students decided to take part in iGEM. This is our first year participating in iGEM competition and we plan on producing alkanes with a modified E. coli, resistant to fatty acids. We started our brainstorming for the project last year on September and on November we've decided that we would work with biodiesel, considering our campus infrastructure and research themes. From this, we looked for previous iGEM teams and articles and we wrote our project. It is based specially on Washington 2011 and LaVerne-Leos 2015 projects and the article "Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli." (HOWARD, TP; 2013). Writing our project was essential for start looking for sponsors to pay for our team inscription on iGEM. We are focusing on the idea of a drop-in biodiesel that could fit to regular diesel combustion engine, without any of the corrosion or malfunctioning that the transesterified fuel normally causes. Our E. coli would be like a catalyst transforming plant oils that are already used for the production of biodiesel into a fuel with better qualities. Our plan is to use the lux operon (consisting on luxC, luxD and luxE) and aldehyde descarbonilase (NpAD) and enhance the resistance of the E. coli membrane to fatty acids using the tocopherol pathway. Thus, a large scale production of biodiesel with E. coli would be possible. Our team consists on engineering undergraduate students and industrial biotech graduate students. Besides the project, we are visiting schools and promoting ethical discussions with the public regarding biotechnology and synthetic biology and we plan on making these kinds of technology more reachable and popular.


SJTU-Software

When discussing SynBiology, one usually starts from parts to devices. And this time, we think from devices to parts. While studying on a device, a biologist may encounter new parts the functions of which are still unknowable. Based on a database of enough parts including their sequences and functions, the software can automatically find out existing parts the sequences of which highly tally with the new parts’. Following that the software will analyze the functions of these parts and draw the common ground. Thus, the functions of new parts will be knowable to us. Through this way we can constantly extend the base of parts and that will definitely contribute to the development of SynBiology.SJTU-Software 2015 developed a web-based tool to search, evaluate and visualize biobricks at part, devise and system levels. This year, we make it as a part of our software. Knowing the function of every part, the software will provide various permutations of different parts, which form devices. The software evaluates devices and draws them into a database of viable devices. After inputting requirements, the software offers the most viable device. So a biologist may directly put it into experiments, which shortens the time dramatically.


Dundee_Schools

Every month running from February 2016 our team attended monthly meetings to discuss our project and brainstorm ideas, allowing us to talk about what we would like to work on throughout the summer. During these meetings we all came up with various ideas and eventually managed to narrow it down to the idea of targeting water-borne bacterial infections affecting developing countries. Two of the main bacterial infections caught in these countries are shigellosis and cholera; shigellosis is an infection caused by the bacterium Shigella and cholera by Vibrio cholerae. Both are usually caught by ingesting water or food contaminated with the respective bacteria and both conditions also have similar symptoms; 163 million cases of Shigellosis are recorded annually in third-world countries, 1 million of which proving fatal. In addition, cholera causes around 100 000 deaths in these countries per year. We have decided to combat these infections by using RNA interference; this will hopefully be a cheaper, faster and more accessible solution than current cures. Since beginning our project full-time in June, the dry team have contacted various individuals and charities to get a range of opinions on our proposed method and have started developing the wiki; meanwhile, the wet team have begun work in the lab.


Shenzhen_SFLS

Inspired by Olivia Hallisey’s invention in 2015--Detection of Ebola via a Silk-Derived Lateral-Flow System and Mr. Keith Pardee’s article about Paper-Based Synthetic Gene Networks, initially, we had the idea of designing a test paper to contribute to virus detection via the method of synthetic biology. We’ve made research on several viruses, including Ebola, Zika and HIV, however, when later confronted with statistics revealing the high mortality rate of HCV and the great magnitude of its spreading, China included, we shifted our attention to the relatively neglected virus. Later, Mr. Keith Pardee and his lab published an article about the detection of Zika virus which was an extension of their previous program (Keith Pardee, 2016). The article has motivated us to apply Nucleic Acid Sequence Based Amplification (NASBA) to our project.


Gaston_Day

Gaston Day School is a non-sectarian, college preparatory school for grades Pre-K through 12 where nearly 100% of graduating students attend a four-year college. Located in Gastonia, North Carolina and founded 1967, the school provides education to students from Gaston, Mecklenburg, Lincoln, Cleveland, and York counties, in addition to international exchange students from various countries such as China and Germany. Accredited by the Southern Association of Colleges and Schools, Gaston Day is a member of the National Association of Independent Schools, the Southern Association of Independent Schools, and the North Carolina Association of Independent schools and approved by the North Carolina Department of Education. Within the research community, lab safety standards are designed to contain microorganisms; however, bacteria are often engineered for use in the open environment. In particular, many iGEM projects, especially in the environmental track, are designed for use in remote or less developed parts of the world. Additionally, many bacteria are now engineered using multiple antibiotic-resistance elements. Should antibiotic resistance spread, untreatable diseases would become more prevalent. A “superbug” resistant to most antibiotics, only seen outside the US, has now found its way into the United States. This form of E. coli is resistant to the last resort antibiotic Colistin as well as multiple other antibiotics(Centers for Disease Control, 2016; Christensen, J., & Goldschmidt, D., 2016). Chloramphenicol, an antibiotic commonly used in Africa because of its low cost and relatively long shelf-life, is the required antibiotic for part submission as a BioBrick. Also, Cillins and Cyclins are commonly used in United States medical facilities as well as in synthetic biology labs. While the K-12 strain of E. coli typically used in labs is not usually pathogenic itself, it is known to exhibit lateral transfer to other, potentially pathogenic, species of bacteria (Smelt, et al., 2015; Hamada, K., Oshima, K., & Tsuji, H., 2003).Measures must be taken to prevent both the proliferation of genetically engineered bacteria and the lateral transfer of antibiotic resistance in the environment. Our 2016 iGem team’s goal is to build a killswitch, so that when bacteria escape the lab environment and are separated from the growth medium, it will die. We have designed a passive killswitch using the arabinose-repressible pBAD promoter driving the production of a TetR repressor. TetR will prevent the transcription of colicin. When the concentration of arabinose drops, the colicin will no longer be repressed and will kill the cell, preventing proliferation.


Mingdao

It all begins with a news we saw on TV.The news is about an old man who had a conflict with a police. At night, driving a car, the old man was stopped by a police and he asked the old man to pull over and have an alcohol examination. However, the old man refused to take the test and started shouting at the police. It occurred to us that the testing method used these days seems to contain a few problems and wasn’t that reliable to the public. Therefore, we started to aim at finding a better way to proceed the alcohol test. Here’s how our project was born. First, we did quite a lot of research about how alcohol tests work and tried to find out the way alcohol reacts with the proteins and chemicals in our bodies. After few weeks of working and a long discussion, we came up with the idea of using the method that blood glucose meters equipped. We decided to oxidize alcohol and produce hydrogen peroxide to cause exchanging of electrons then detect it by blood glucose meters. Then, we conducted a survey of whether people will be more willing to take alcohol tests if the results are more accurate, and the results support our project.Thus, we believe the way will finally work out and can reflect the alcohol content in our bodies better.


Ryerson_Toronto

Cyanobacteria represent one of the most ecophysiologically diverse phyla, inhabiting a range of environments and exhibiting an array of biogeochemical specific processes. Cyanobacteria are unique in that they are the only prokaryotes that are able to use sunlight as energy, water as an electron donor, and air as a carbon source. Furthermore, some strains are even capable of fixing nitrogen, making them extremely important for converting atmospheric nitrogen to ammonia, which can be used by organisms. In addition, cyanobacteria also produce a number of tetrapyrrolic dye molecules such as heme, chlorophyll, and phycocyanobilin (PCB). BODIPY is an organic dye that is a dipyrrin-containing derivative. This tetrapyrrolic dye and its derivatives are used in many applications; either for dye-sensitized solar cell (DSSC) applications or towards the design of fluorescent molecules as organic light-emitting diodes (OLEDs). However, the synthesis of these organic dyes can be time consuming and expensive. Molecules such as heme, chlorophyll, and PCB are very similar to dyes such as BODIPY. As such, the tetrapyrrolic dyes produced by cyanobacteria could be extremely useful for photovoltaic applications as these organisms use enzymes and molecules found in their environment rather than expensive catalysts. The ability to genetically direct the bacterial synthetic machinery would be significantly beneficial to carbon dioxide sequestration, nitrogen fixation, as well as the production of low-cost dyes. The biosynthesis of heme and its subsequent product PCB represent an attractive pathway to develop novel dyes. Therefore, by combining genomics, bioinformatics, as well as synthetic biology, the Ryerson team aims to genetically engineer cyanobacteria to efficiently produce novel dyes. Thus far, the Ryerson iGEM team has been working on developing its project and finding the appropriate resources. By the end of the summer, iGEM Ryerson aims to have created novel biobricks that can be added to the registry while also obtaining the target molecule in our model organism.


METU_HS_Ankara

Colon cancer is a widespread disease which is the forth most common cancer throughout the world. It is the third most commonly diagnosed cancer and the second leading cause of cancer death in men and women combined in the United States. Furthermore, in Turkey 7 in 100,000 is suffering from colon cancer and each year 3200 people die. In colon cancer, polyp formation is observerd. They are the growth tissues in colon’s inner surface. Polyps are benign (non-cancerous) growths, but cancer can start in some types of them; like Adenomatous polyps. They are the only type of polyp that can turn in to a colorectal cancer cell. We searched about some tumor suppressor genes and proteins. We saw that their arrangements are too long to use in E.coli. At that point, we found that butric acid is more appropriate for us. We researched again and found a substance called butyrate. Butyrate is a short chain fatty acid which is formed by bacterial fermentation of carbohydrates. Considering it’s positive effects on colon cancer, we decided to choose butyrate as our remedy for colon cancer. After, our bacteria sticks to the cancerous cells in colon flora, it will secrete butyrate which induces apoptosis and differentiation and also inhibits proliferation. We use RPMrel and FimH in order to provide our bacteria to stick to cancer cells with the help of its pili. Last year, Team Harvard 2015 developed a pathway for E.coli to bind to cancerous cells in colon. They used a pathogenic E.coli. Pathogenic E.coli has a structure called “pilli”. They are attached two adapter proteins FimF and FimG, and FimH adhesin at the and of the pillus. Then, they inserted a binding peptide called RPMrel into the FimH protein to achieve specificity. This year, we will take their project to the next step; treatment. Our E.coli will bind to the cancerous cell and after binding it will start producing butyrate, which will induce apoptosis in the cancerous cell


Austin_UTexas

Our team has been pursuing several different research avenues this summer. We are working with a variety of organisms- including microbial communities- in an attempt to engineer a system that may be useful to the world in some way. Currently, we are discovering and attempting to engineer the organisms that make up the SCOBY in Kombucha tea, various cyanobacteria, and other organisms that are more commonly used in the lab. Though this may seem to cover a very broad range, UT’s iGEM team is united under one front- we aim to improve something in the world through genetic engineering. Thus far, each sub-project has accomplished something different, but we are all ultimately experiencing successes and failures. One of our sub-teams is developing a process by which gellan gum (a substitute for agar) can be made at home for novice biochemists, but there have been several issues with the process. Similarly, a sub-team whose goal is to create an organism that can detect GMOs is having to work and rework the system they are using, and they are having to troubleshoot just like many other sub-teams. Additionally, through weeks of trial and error, many teams have become very familiar with non-model organisms that the lab has never before worked with. Furthermore, we are very proud of a partnership that we are developing in the Kombucha industry, as this will be an invaluable resource as we proceed in this area. In the coming weeks, many of our projects will need to adjust and improve our Golden Gate Assembly system because the whole lab has been having problems in that respect. Furthermore, many projects will need to create a process to transform their organisms as these organisms have either not been used in our lab previously or are new isolates from the environment. A few of our sub-teams have shown successful conjugation, though. Finally, it is clear that we will need to consolidate our sub-projects to bring to the iGEM Jamboree. While each of our aims is valuable and interesting, not all will be ready to present and only some will yield results of a quality that we are proud of.


SYSU-Software

Synthetic biology has been developed for decades and many useful as well as mature principle in engineer disciplines are applied in designing, building and testing synthetic parts, devices or systems. However, it still remains difficulty and complexity in experiments validating the newly designed function. As same system might perform differently in different chassis and incorrect operation plus contamination might lead to entirely fail, an experiment should be repeated times to obtaining our ideal results. Our project aims at realizing the potential of computer function in guiding experiment after the design of synthetic biology. On one hand, our software can help the user choose existing synthetic devices more conveniently, or provide a platform for them to design their own parts, assembling their own synthetic system. On the other hand, based on selected synthetic systems, in order to decrease the mistakes, our software can supply a standard protocol, guiding the steps proceeding the validating experiment.


Queens_Canada

The majority of drugs on the market have a biosynthetic origin. A significant portion of these biosynthetic drugs are produced by nonribosomal peptide synthetases (NRPS), large multi-modular enzymes found in various bacterial and fungal species. NRPS synthesize structurally and functionally diverse biologically active peptides that often have unique modifications (such as cyclization, oxidation, methylations, etc.), and are a source of antibacterial, antifungal, and anticancer drugs (examples include cyclosporine A and vancomycin). Their products are highly specific and can contain non-standard or synthetic amino acids, but are also difficult to create and optimize through synthetic chemistry. Queen’s iGEM aims to accomplish three goals: improve tagging of NRPS products for high-throughput screening to assess biochemical activity, append functional groups such as halogens to NRPS products by incorporating cis tailoring domains via homologous recombination, and performing in silico mutagenesis of NRPS domains to alter their substrate specificity for incorporation of non-standard amino acids.


UI-Indonesia

HIV is one of the biggest health issues the world has ever faced, and although antiretroviral therapy (ART) has made it possible to prevent mortality in HIV patients, it has several limitations, including the logistic and economic burden that arises from the need for lifelong treatment. To end HIV, we still need a cure. Today, the best hope for a cure is DNA vaccines, which are DNA molecules that harbour a gene encoding an antigen. When administered, cells will take up these molecules and produce the antigen. Dendritic cells will take this antigen to lymph nodes and present them to T cells, activating them and licensing them to hunt and kill infected cells. In theory, this would allow for the elimination of viral reservoir in the body. In reality, however, DNA vaccination for HIV hasn’t worked in humans. Although the key component of a DNA vaccine is the antigen-encoding gene, the vaccine backbone, as the name implies, accounts for most of its mass and governs its activity. So, we wondered, can we design a better vaccine backbone? We have designed genetic elements that, when put together, will hopefully achieve improved transgene expression (promoter, intron, polyadenylation sequence and barrier element) and immune stimulation (immunostimulatory DNA motif and RNA gene as well as coding sequences for peptides that direct antigen processing) with respect to existing vaccine backbones. We’re having the parts synthesized and assembling them soon. We hope that this new vaccine backbone will give rise to new, safer and more potent DNA vaccines for HIV—maybe even a cure.


Austin_UTexas_LASA

Organophosphates are a class of chemical compounds commonly used as pesticides that have also been used as chemical warfare agents (CWAs). Common organophosphate pesticides include glyphosate, a controversial pesticide that the Agency for Research on Cancer declared “a probable human carcinogen." Our team is currently working on creating a bacteria that will assist in the degradation of organophosphates, a class of chemical compounds used in many chemical weapons and insecticides. Organophosphates are not only highly dangerous to humans as nerve agents but their prevalent use in insecticides is also a threat to the environment due to many adverse effects and a very slow degradation rate. Common organophosphate pesticides include glyphosate, a controversial pesticide that the Agency for Research on Cancer declared “a probable human carcinogen.” We believe that in our project we can create a bacteria that will help in creating a safer environment for us and our loved ones and the life around us as well. So far, we have found pathways that can degrade many organophosphates, including sarin, glyphosate and paraoxon, into a product, para-nitrophenol (PNP) that we can then use to go into the Beta-Kap pathway. The Beta-Ketoadipate pathway is useful in converting aromatic compounds into food sources for bacteria. The Beta-Kap pathway will be useful in degrading the PNP resultant from our bacteria’s initial degradation of organophosphates.


SUSTech_Shenzhen

We are not satisfied to use the traditional ways to regulate gene expression, but to choose auodiogenetics and optogenetics to establish a high-efficiency regulation platform. Compared to the chemogenetics, sound and light are precise and nontoxic to our objects. Furthermore, the signals are easy to input into the system without delay.
 We try to use a membrane mechanosensitive channel- transient receptor potential channel (TRPC5) to transform the audio wave energy as the input into cho-k1 cell. To select the cells which are sensitive to the specific wavelength, we mutate TRPC5 by molecular engineering and use calcium indicator(R-GECO) to quantify the intracellular calcium. Finally, we use the YFP as the downstream output signal to quantitatively analysis the regulatory ability of audiogenetics. At the same time, we attempt to use opsin chrimson and coch-R expressed in C.elegans neurons, exploring a new way to study the neuronal response and learning process of worms. We choose a pair of sensor neurons AWA\AWB which are respectably and directly related to attractive and repulsive odorants. By using light-ray instead of chemicals, we can manufacture the alternative and consistent neuronal stimulus and observe its neuronal pathway in vivo. Microfluidics is an important tool used in our experiments. Cells or C.elegans are seeded in the channels of microfluidics undergoing shear force controlled by microfluidics apparatus. We utilize shear stress as mechanical wave to impose pressure on cell membrane by changing the velocity of liquid flow in channels of microfluidics. Another technology used is directed evolution. Here, we apply random PCR to acquire a large library of mutants of mechanosensitive channels which are then screened and selected based on the downstream pathways we design to meet our needs.


SYSU-MEDICINE

Background Mesenchymal stem cells (MSCs) are promising candidates for cell-based therapy to treat several diseases. Up to now, MSCs are used in over 600 ongoing clinical trials (June, 2016) like treating IBD, diabetes, encephalitis, etc. MSCs in current clinical use are isolated from bone marrow, adipose tissue and the umbilical cord. Different from the embryonic stem cells, MSCs have been shown to be highly immunosuppressive. In many studies, MSCs were found to suppress adaptive immune system as well as inherent immune system in multiple inflammatory diseases, which make MSCs a promising tool in treating inflammatory disease. Despite significant advantages, clinical trials of MSCs have produced mixed results which may significantly impede the advancement of MSC-based therapies. One of the most important reasons is for the inefficient homing ability of MSC that only a few MSC can indeed arrived the inflamed tissue after systematic administration and exert their immunomodulatory function. Current Design This summer, next generation of MSCs are coming. We intend to construct a circuit of three plasmids that will be able to reinforce the locating function of MSCs. Previous studies have demonstrated that immune cells depend on chemokine receptors to accomplish directional moving. In our project, we are going to empower MSCs with chemokine receptors in order to ensure its effective homing. At the same time, with the purpose of locating in vivo MSC and assuring their arrival at the inflamed tissue, we will introduce several kinds of positioning system into our system and detect them by various methods.


SDU-Denmark

SDU’s iGEM project is the production of a bactericidal band-aid. There are 4 subgoals we will try to accomplish: (a) Production of biodegradable plastic (b) Production of an antibiotic (c) Production of spidersilk (d) Combine the production of antibiotics with the production of the hybrid-silk. We have chosen to split into 3 teams, that will focus on one goal each and combine it in the end. One group will focus on trying to make an E.coli bacteria produce a desired antibiotic compound. Another group will try to produce hybrid spidersilk, where the silk has bindingsites to the antimicrobial. Using spidersilk has many beneficial properties - it has been the center of interest in the medical world for a while now. And for good reason, it has been shown that our immune system doesn’t react towards this product and has extremely good flexibility as a material but also for eventual genetic manipulation. Our first goal will be trying to produce the spider silk with properties we choose to give it. Polyetylentereftalat, also called PET, will be used as primary substrate for the group focusing on plastic. We recycle under 10% of the plastic in our world - therefore, this could be beneficial for solving the major pollution issues we are facing. Plastic does not degrade naturally, but it merely fragmentizes. Animals can’t tell the difference between a foodsource and a non-degradable product. Consequently, animals in all size ranges have been shown to feed on plastic, which clogs their system and eventually kills them. Hydroxyalkanoat will be used as ground stone for different polyesters. We will probably use polyestren poly--hydroxybutyrat (PHB) due to our knowledge of its pathway. Others poly-hydroxyalcanoates can be synthetised, their properties depends on the size of the monomer. As supreme goal, we would like to combine the bactericidal subproject with the silk part of the project. We would end up with a combined product consisting of silk and antibiotics produced by an E.coli. We would like to be standing with a full functional band-aid in Boston in October.


Kent

What is our project? We aim to create magnetite crystals in Escherichia coli. Magnetite is an iron oxide that is formed by organelles called magnetosomes. Magnetosomes are found inside of some species of magnetotactic bacteria (MTB) such as Magnetospirillum gryphiswaldense. Magnetotactic bacteria use magnetite to orientate themselves; by following magnetic fields MTB can move towards anaerobic environments at the bottom of a body of water. However, the applications of growing magnetite crystals in Escherichia coli are far greater. Synthetic biology allows us to create unique constructs and for our team means that Nano-crystals of magnetite could be produced in different shapes and sizes that allow for a variety of applications. Why is it important? There are many novel applications for magnetite that could be explored. Our main areas of interest are heavy metal removal from water, as well as data storage in the form of crystals with different levels of magnetism. The use of magnetite in MRI scans and drug delivery are currently being explored. Magnetite crystals have already proven useful in catalysing the synthesis of ammonia at an industrial scale and were also used in early audio recording. If magnetite can be grown in Escherichia coli it could potentially produce a sustainable source of magnetite thereby eliminating the need for mining the mineral. How are we going to do it? Team UKC will express genes associated with magnetite formation in Escherichia coli by growing the bacteria with a plasmid that contains both these genes and a gene for resistance to an antibiotic. Should the expression of a single gene not yield magnetite, we aim to express multiple genes to determine what construct is necessary for magnetite particles to form. We will then grow our modified Escherichia coli in the presence of iron. Alternatively, we will lyse the cells to test our expressed proteins in an iron rich environment, thereby eliminating the constraints that being cell bound poses. If successful, our magnetic crystals should be visible under an electron microscope.


HSiTAIWAN

Background: Chinese Medicine has been among our ancestors and still remains today with us since its discovery around 5000 years ago. Chinese Medicine is not just a mixture of herbs and seeds that can cure people, but represents a crucial culture of Asians. However, as technology advances, people begin to take artificial drugs with more scientific proof of curing. But what really prevents people from taking Chinese Medicine is the poison in it. Yes, Chinese Medicine has been found to carry large amounts of poison. Whether it is the preservation or producing process, Chinese Medicine has a much higher contamination chance than artificial drugs due to its natural source. If this risk of poisoning remains, people will no longer take Chinese Medicine. And sadly, this distinctive culture will be forever gone. Solution: We decided to create a series of E. coli biosensor. When the bacteria detect certain poison in the environment, they will produce fluorescence protein. That way, we can detect the poison inside the Chinese Medicine by just examining the fluorescence intensity. Also, to make our project more efficient and standardized, we developed a biosensor kit. With the suitable pH level, temperature, E. coli living environment, we can provide a more accurate and faster result.


UAM_Poznan

Production of recombinant proteins in Escherichia coli systems is very attractive and popular due to its rapidity, low cost and well-characterized genetics. The most popular is pET (Merck, Novagen) lactose/IPTG induced T7 RNA polymerase dependent expression system, however this system leaks and introduces more mistakes in transcribed sequence comparing to E.coli RNA polymerase. That’s why we are looking for tightly regulated promoters, which can be induced independently of each other in one cell by sugars: arabinose, rhamnose, xylose or melibiose. We are trying to reduce their size to obtain minimal but fully functional promoters. Natural 5’UTRs of promoters that play role in translation initiation are substituted by other sequences. The modifications include better RBS positioning, introducing translation enhancers and removal of potential inhibitory secondary structures, which could interfere with translational machinery and decrease protein expression. To further evaluate translational efficiency, we also focused on codon optimization since it is believed that the frequency of particular codons in the gene of interest can cause expression problems because of rarely occurring tRNAs. According to bioinformatics analysis of codon frequency in E. coli we created two ORFs variants of sfGFP and sfRFP that are composed exclusively of the most frequently codons or the rarest ones.


Freiburg

'cause spore is more! After a ton of ideas and a lot of brainstorming, we decided to work with bacteria and spores this summer. More specifically, we are focusing on the organism Bacillus subtilis. B. subtilis is a gram-positive, aerobically growing bacterium, which is easy, safe and cheap to handle in the laboratory. Under nutrient deficient circumstances, they form so-called endospores. These are highly resistant to heat, cold, radiation and enzymatic attacks. Our goal is to unlock the hidden potential of the spores and to engineer them for the display of binding proteins and functional enzymes on their surfaces directed against structures of our choice. Those binding properties can be used to specifically target disease-associated cells and undesirable bacteria.


Sydney_Australia

Have you ever packed a banana for lunch but forgotten about it, later finding that it has coated your bag with a sticky, mushy mess? Have you ever ventured into the supermarket to seek out that perfect avocado, squeezing countless candidates but finding none that make the cut?Ethylene is the major hormone involved in plant ripening, and this has led to it's regulation being crucial to the agricultural industry. Premature ripening has resulted in large losses in the agricultural industry. However, it is currently difficult to efficiently and cost-effectively measure the levels of this elusive gaseous hormone. This year, the University of Sydney iGEM team will develop a portable, convenient and cost-effective biosensor to measure ethylene concentrations in all sorts of situations. Current ethylene detection methods for regulating ripening rates include gas chromatography, electrochemical or optical sensors, or simply dispensing a set volume of ethylene gas into a sealed fruit room. Alternatively, ripeness is monitored by inspecting colour or firmness of the fruit. These existing methods are generally expensive, inconvenient, or involve direct contact with the fruit. By creating a cell-based biosensor, iGEM Sydney aims to create the foundation for a safe, reliable method of ethylene detection which will minimize global losses due to fruit spoilage. This can potentially be translated to a cell-free, paper based biosensor which can take the form of a fruit sticker, immediately displaying the ripeness of the fruit.


UIUC_Illinois

Promoters can be used to control the gene expression of whichever gene they are placed upstream of. Most promoters which are currently in the iGEM registry can be separated into one of two categories. There are constitutive, or “always on,” promoters of various strengths. There are also inducible promoters, which activate transcription based environmental factors such as light, pH, or the presence of any number of molecules. For our project, UIUC_Illinois is characterizing a promoter library that will give users more control over gene expression, without the need for inducers. We are currently working to isolate a set of e. coli promoters that turn on and off according to the host’s growth phase. For example, one promoter may become active during exponential growth but shut off once stationary phase is reached. Another promoter may be active only during the initial lag phase before shutting off for the rest of the growth curve. It is our hope that these promoters will be useful tools for any teams wishing to time protein production in vivo, whether the intended applications are metabolic engineering, probiotics, or any number of related topics.


Nanjing-China

Considering superb conversion efficiency, environmental friendliness, and high energy capacity of hydrogen(H2), H2 has become a promising substitute for fossil fuels. Currently, H2 production is mainly rely on steam reformation which derive from hydrocarbons, coal gasification, and nuclear-powered water electrolysis. What has mentioned above, however, is not environmentally-friendly or unsustainable enough. When it comes to the biological method of H2 production, the original resources, sunlight energy, is inexhaustible and renewable. We focus our attention on Chlorella, a green algae, which can photolyze water to produce H2 using hydrogenase under anaerobic condition. However, this process only occurs within a transient time, last for a few minutes during dark–light transition. Owing to the fact that the certain hydrogenase would lose its function when exposed to oxygen, cellular creates anaerobic conditions via respiration in darkness that can activate hydrogenase. Another material that we take consideration into is the capsid from the bacteriophage P22. The P22 capsid is a particularly powerful platform that encapsulate of various products such as enzymes. It can create discrete spaces to localize certain chemical processes such as biohydrogen production by hydrogenase.


UESTC-China

BACKGROUND Since the 21st century, the urgency of environmental problems and energy crisis looming large. At the same time, bioenergy began to emerge for its biodegradable, renewable, no harm of environment and other advantages. Among them, bio-diesel is considered as an ideal alternative energy for its sustainable regeneration, highly biodegradable, low pollution, high environmental protection and other characteristics. ADVANTAGES OF MATERIAL Microalgae as a third-generation biodiesel, it solves the previous two problems of the first two generations of biodiesel. The problems are scrambling for human land resource, the limited sources and low efficiency of raw materials. Microalgae also has some advantages other green oil plant do not have: 1. Cultivation of microalgae does not require a lot of arable land and microalgae can be grown in a variety of water environment like sea, waste water without being provided special water. 2. Microalgae is easy to be cultured and strong adaptability to the environment. It has fast growth speed and short growth cycle, which provides a reliable guarantee for the supply of biodiesel. 3. The photosynthetic efficiency of microalgae is high, it can fix CO2 effectively. Microalgae also can absorb N, P and other nutrients in the water in the process of growth to purify eutrophic water. 4. Comparing with conventional oil-producing crops, microalgae’s oil content is higher. It is more suitable for biodiesel production as a raw material. DETERMINATION It is an urgent problem to be solved of how to enhance microalgae oil content and soar oil production at the time of industrialization. To this end, our predecessors have tried by overexpression of the relevant genes to increase oil production in microalgae, but they are limited to operating only a few genes. Therefore we want to over-expression of multiple genes at the same time to significantly improve microalgae oil production. Through a lot of literature to read, we initially identified as a material for itself with a higher lipid content and its stable conversion performance. In the subsequent study of algae oil metabolic pathways, we locked closely related to algae oil production with ten genes: ME, DGAT, GPAT, GPDH, LPAAT, PAP, PDAT, TGL1, PEPC, U3P. So our main job is to over-expression of the first seven genes, knockdown the latter three genes in phaeodactylum tricornutum to significantly increase the accumulation of lipid(TAG)


Ain_Shams-Egypt

Liver cancer in adult men is the fifth most frequently diagnosed cancer worldwide, and is the second leading cause of cancer-related death in the world. In adult women, it is the seventh most commonly diagnosed cancer and the sixth leading cause of cancer death. The burden has been increasing in Egypt with a doubling in incidence rates in the last 10 years, Egypt has a one of the highest incidence of in hepatocellular carcinoma (HCC) in the world. Treatment options for HCC are limited and often inefficient. Anti-cancer therapy faces major challenges, particularly in terms of specificity of treatment. The ideal therapy would eradicate tumor cells selectively with minimum side effects on normal tissue. So as a team that believes in synthetic biology we searched how could we help our community regarding this problem & we found that it’s been shown that circular RNA (circ.RNA) is associated with human cancers, & some studies have been reported in HCC. Circular RNA will be delivered as it is a new area of research with around 130 circular RNA sequence detected in HCC only less than 10% of these has been investigated and characterized through previous studies. Circular RNA is a type of RNA which, that forms a covalently closed continuous loop. This feature confers numerous properties to circular RNAs, many of which have only recently been identified. Circular RNAs have recently shown potential as gene regulators. Like many other alternative noncoding isoforms, the biological function of most circular RNAs are unclear, circular RNAs do not have 5' or 3' ends so they are resistant to exonuclease-mediated degradation and more stable than most linear RNAs in cells. We are using mammalian cells to see the expression of the circular RNA in the deregulated micro RNA environment of the cancer cells in tissue cultures, prove their role and detect if they can serve as a biomarker in HCC, Detect the relation between its expression levels and rate of progression and the possibility of using it as a potential novel target for the treatment of HCC.


Lubbock_TTU

In 2010, it was estimated that 6.5 million people in the United States alone suffered from chronic wounds, accruing an annual cost of about $2.5 billion. Furthermore, experts predict that the burden of chronic wounds will increase rapidly in the near future due to increasing medical costs, an aging population, and the emergence of antibiotic resistant bacteria.A chronic wound is considered a wound that does not heal in an orderly set of stages or within a time period of about three months. The etiology of chronic wounds is very diverse. One of the most prevalent reasons patients have persistent chronic wounds is that their bodies produce too many proteases at the wound site. In turn, these proteases degrade the extracellular matrix of the wound site which acts as a scaffold for new cells to migrate and grow. Proteases have also been shown to decrease healing rates by degrading growth factors that are needed for recruiting wound healing cells and inducing cellular proliferation.Wound healing progresses through three successive stages known as inflammation, proliferation, and remodeling. Ultimately, the degradation of the extracellular matrix and growth factor cause the wound to remain stuck in the inflammation phase, thus unable to heal. We will use synthetic biology principles to help treat chronic wounds by targeting the overproduction of wound site protease. - For Aim 1 we will genetically engineer E. coli to produce a protease inhibitor and platelet derived growth factor. - For Aim 2 we will purify the protease inhibitor and platelet derived growth factor in a bioreactor. - For Aim 3 we will design a collagen bandage that mimics the human extracellular matrix, and infuse it with purified protease inhibitor and platelet derived growth factor. Our approach is two-fold. By infusing the collagen extracellular matrix with platelet derived growth factor and protease inhibitor, chronic wounds should be able to progress past the inflammation phase and begin healing once again.


William_and_Mary

WM iGEM 2016 Presents: The Circuit Control Toolbox.Genetic circuits can be described according to their input-output relation by using a Transfer Function, which plots the concentration of output protein with respect to concentrations of input molecule. Such functions are well-modeled by Hill Functions, and as such have three parameters: the hill coefficient n, the half-max concentration K, and the saturation level V. These mathematical parameters correspond to the physical circuit properties of response steepness, input sensitivity, and maximal response level, respectively, in addition to the emergent properties which arise from their combinatorial modification.We present a toolbox of BioBrick parts that will allow for the modification of the Transfer Functions of arbitrary circuits via the incorporation of these parts into the final steps of the circuit. These parts include Decoy Binding Arrays, which buffer the sensitivity of the circuit to low levels of input concentration, promoters driven by synthetic enhancers to allow the circuit to reach up to four levels of discrete output levels, and a suite of ribosome binding sites to modulate the circuit's total output level. Our parts are all buffered by the inclusion of characterized ribozymes downstream of the promoter, in order to insulate the specific circuit component's transfer function from the choice of expressed protein, allowing for greater orthogonality and modularity in our toolbox components.In addition to creating, characterizing, and submitting these Toolbox parts to the Registry, we will also create a Circuit Toolbox Calculator which experimenters can use to navigate the high-dimensional space of possible Transfer Function modifications. Experimenters who have built a genetic circuit will input two transfer functions: their empirical observations of the circuit's response at different input molecule concentrations, and a desired transfer function for their modified circuit. The calculator then finds the optimal match to the target function by iterating through the possible modifications to the empirical transfer function through the parts in our Toolbox, returning to the user a list of Toolbox parts and small-molecule inducer concentrations that will replicate this best-match function in vitro. These calculations will be based on both theoretical and observational insights from mechanistic models and kinetic simulations of the interactions between our Toolbox components and arbitrary genetic circuits.


UCSC

A large amount of food processed for human consumption leaves behind agricultural co-products that we hope to utilize. Currently these co-products are shuffled to cattle feed or plowed under. We propose to use synthetic biology to make use of this excess biomass. Our team will capitalize on recent findings in synthetic biology to build a novel conversion platform that can be used by teams worldwide. These global partners will then be able to expand this and create innovative solutions for transforming our agricultural waste into high-value products. As a pilot project of this platform we will synthesize erythritol, a sugar alternative, using a custom made bioreactor. Estimates suggest that we will beat the market price tenfold. While a lower erythritol production cost may disrupt a 2 billion dollar sugar alcohol market, we anticipate our true success will be in the possibilities unlocked by our platform. Erythritol presents a considerable means of returning the value of our agricultural waste back to society, but more importantly we look forward to the advances that other scientists across the globe will make using this new technology.


NUDT_CHINA

Since we had a great summer last year working on a project about the new application of the genome editing technique TALEN. This year, in our brainstorming process, we decided to stick to this strategy and to discover the brand-new application of genome editing techniques on other purposes of usage. In our literature research, we found out that Small non-coding RNAs (sncRNAs, invluding microRNAs, piRNAs etc.), as a family of non-coding RNAs with the length no larger than 200nt, has now been reported relevant with the tumorigenesis, development and metastasis of several different cancers. Some also reported sncRNAs as promising bio-markers for the early detection of several specific cancers. However, the rapid and low-cost detection of sncRNAs remains problematic, thus limits the further implementation of sncRNAs in the early detection of cancers. Meanwhile, the lack of valid tools for the real-time and in vivo detection of sncRNAs in living cells also limits the further development of cancer research. In our project this year, we intend to use the rapid-developing CRISPR/Cas9 technique in combination with other genome-editing tools such as Zinc Finger Protein to develop a new method for the detection of sncRNAs by using the nucleic acid binding ability of such tools. The split-GFP, split-luciferase, and solit-HRP systems will be the candidate manners for generation of reporting signal in our study. We have now conducted in vitro Cas9 cutting experiments for the primary test of our design, and to select the sncRNA for our prototype. Our primary results turned out positively. Also, we constructed and compared two different split-GFP systems, to select the best one for our further study. The split-HRP and split-Luciferase system are also being tested.


Slovenia

In the past years of iGEM and synthetic biology a lot of projects have been devoted to the development of synthetic genetic circuits and logic gates. Most of those were based on transcription regulation, however this mechanism is relatively slow and the final output can be detected only after several hours or days. This year team Slovenia has decided to tackle the problem of the design of fast logic circuits. We plan to introduce new protein-based sensors that will allow cells to quickly respond to input signals such as light stimulation or chemical dimerizers and produce outputs that could potentially be used for therapeutic treatment.


Aachen

The following text shall inform you about what we will try to achieve this year and give you a little insight about how and why we chose the topic we will work on. In our brainstorming phase, the initial idea that met with broad approval in the team, included reversible inhibition of an enzyme to improve a lab method. So we dived into research about enzyme inhibition and came up with several possibilities and approaches. Especially "Photocaging", a method using photoliable molecules to reversibly inactivate all kinds of compounds and reactivate them with light, really awakened interest in all of us. Along with knowledge about inhibition, more and more application possibilities occurred and gained shape as we talked to several supporters in academics as well as in industry. In the end, the project that suits the iGEM spirit most and offers a highly educational and interesting experience for us, was the inhibition of a protease for washing detergents. So far, proteases in washing detergents are being inhibited by boric acid and tons of it are needed every year. Its handling in this scale is complicated and additionally, the ECHA (European Chemicals Agency) classified this chemical as a substance of very high concern. If we can make our idea work, the protease in the washing detergents would be produced inactive and could be activated with a small, inexpensive device that can be used with any normal washing machine. Thus, the amount of chemical needed could be reduced by a great deal, as only one molecule per enzyme is necessary for inhibition. That would make a difference, especially for chemical workers, who have to handle tons of boric acid, but also for every household and sewage disposal. As a side project to the development of the “uncaging” device for the washing machine, our engineers will also work on an affordable “Dark Bench” that will make sterile handling of light-sensitive chemicals, needed for our work, more easy.


NJU-China

According to the latest report carried out by WHO in 2012, 15% of worldwide death came from cancer, ranking the second leading cause of death (following cardiovascular diseases) and causing more than AIDS, tuberculosis, and malaria combined. Traditional treatments vary from surgery, radiation, to chemotherapy. While surgeries have low prognosis, patients treated by radiation and/or chemotherapy show fragile health since these treatments damaged normal cells in their body, also leading to the weaken for immune system. Nowadays, clinical trials broaden their way to immune therapy, hormone therapy, and targeted therapy. Since they're general treatments for the whole body, the first two therapies get their obstacles on side effects. Thus, a drug targeting a specific molecule that functions in cancer growth or metastasis can be an ideal choice for further exploration. Inspired by these facts, our project aims at building a simple transplantable drug system based on targeted cancer treating.By packing gene-specific drugs into modified exosomes, we can deliver them into a certain part of our body without interfering any irrelevant tissues. And by including small interfering RNAs (siRNAs) to exosomes, targeted gene expression will be decreased or eradicated in the transcription level. Based on work published in 2010, systemic injection of iRGD, a previously characterized tumor-penetrating peptide, showed great help on drug treatments of mouse tumor, regardless of compositions of drugs. To build the drug-treating system, we modified our exosomes with iRGD, which acted as a targeting tool, and for the oncogene-silencing part, we took EGFR as a target gene for siRNAs’ function verification. Validation goes into two parts – one for the targeting and the other for the silencing, and for each part, both in vivo and in vitro sections are carried out. By chasing fluorescence signals from exosomes and siRNA in vitro, we demonstrated that iRGD-modified exosomes loading with EGFR-specific siRNAs (siRNA-iRGD-exosomes) efficiently got into the tumor cells, compared with other normal ones. Also, in vivo imaging showed specific distribution of dyes in mice, indicated our siRNA-iRGD-exosomes traveled and finally reached the mice tumor tissues. Through experiments analyzing the expression level of EGFR and index of apoptosis, significant changes after siRNA-iRGD-exosomes treatment are expected.


Newcastle

Electronic engineering has given us the television and the mobile phone, while genetic engineering has afforded us mass-scale antimalarial drugs, biofuels and an enormous range of biosensors. More than a decade ago, Tom Knight and colleagues envisioned using 'BioBricks' to standardise synthetic biological parts. Here at Newcastle we want to return to iGEM's humble origins and come full circle. We are currently working on replacing traditional electronic components with biological alternatives. Building a series of new compatible bacterial components, we can mix and match to create electro-biological components within a breadboard. This merging of biology and computer science holds fantastic opportunities for education, and we are looking forward to working with school children to develop and incrementally improve our project.


MIT

This year, the MIT iGEM team is creating a circuit constructed of five plasmids that will be able to sense the presence of endometriosis in affected women. Endometriosis is a disease caused by cells from the endometrial lining of the uterus growing elsewhere in the body, usually on the ovaries, which causes significnt and chronic pain as well as infertility. The circuit will function through a double-check, two "latch" system, checking the cells' miRNA profiles in both the estrogen-high proliferative phase and the estrogen-low secretory phase of the menstrual cycle. While the team is still unsure if the circuit will function as a diagnostic tool, a treatment, or some combination of the two, the design of the circuit upstream of the output has been completed. Current Design The circuit will first rely on endogenous estrogen receptors (ERa) to report the presence of estrogen to the circuit through an ERa binding region called ERE in a synthetic promoter. In the estrogen high phase-reactive half of the circuit, this interaction, combined with the correct miRNA conditions, will activate the expression of a recombinase that will flip the first latch before the output. The wrong miRNA conditions will result in the degradation of the recombinase genes's mRNA, and the lack of a small molecule drug will result in the degredation of the protein if by chance the recombinase mRNA reaches a ribosome before it is degraded by the miRNA complex. This is because the recombinase will be synthetically combined with a degradation tag, DDd, that is stabilized by that small molecule drug. In the estrogen low phase-reactive half of the circuit, the binding of ERa to the synthetic promoter region activates expression of a repressor protein that prevents the expression of the second recombinase. This way, when there is very little estrogen, the repressor is not expressed in significant amounts and the constitutive promoter before the recombinase can activate its expression. As before, the miRNA profile of the cell in the estrogen low phase is used to degrade mRNA of the repressor at that point, and degrades the mRNA of the recombinase during the estrogen high phase. The second recombinase is also controlled by a degradation tag and small molecule drug. Through this system of repressors, the team hopes that the second recombinase will only be expressed in the estrogen low phase. The first possible output would be the apoptosis of cells identified by the circuit as endometriotic. This is a risky option as there is a chance for leaky expression of the recombinases despite the number of repressors. The second possible output would be a fluorescence gene, so the disease cells can be more easily identified during surgery, allowing for better complete removal of the lesions. This is a less ideal option because through the circuit, the team hopes to decrease the need for women with endometriosis to undergo surgery, and while this output may decrease the number of surgeries required, it would not provide an alternative to surgery. The third possible output would be the production of a biomarker that can be sensed through blood or urine testing as a diagnostic, an alternative to laparoscopic surgery that is the sole diagnostic tool at this time. This option would remove the need for one surgery, but would not be able to actually provide a treatment. It's also possible to do a combination of these outputs.


Tianjin

This March our team paid much attention to an article ‘A bacterium that degrades and assimilates poly (ethylene terephthalate)’published in Science in the same month. A new kind of bacteria that can decompose PET was found and studied in detail. We plan to express its unique genes in some commonly used mode organisms such as yeasts and E.colis to enhance its activities of decomposition significantly since they are relatively low at present. Background: This March our team paid much attention to an article ‘A bacterium that degrades and assimilates poly (ethylene terephthalate)’published in Science in the same month. A new kind of bacteria that can decompose PET was found and studied in detail. We plan to express its unique genes in some commonly used mode organisms such as yeasts and E.colis to enhance its activities of decomposition significantly since they are relatively low at present. Current situation: We have synthesized the gene sequences of the PETase and MHETase based on the supplementary materials of the original paper after several months’ literature reviewing. And we began several preliminary experiments to figure out if those exogenous genes could be well expressed in the host cells. We decide to enhance the activities of these two enzymes via surface display, protein scaffold and fusion expression. Another way to enhance the rate of reactions is to put the first (hydrolysis of PET) and the second step (hydrolysis of MHET) together by cascade catalysis. Vision: We hope to construct a system that can efficiently express and secrete (or display) these two enzymes. The system will be able to hydrolyze PET with a much higher rate than the Ideonella sakaiensis reported in the thesis.


Dundee

Hello! We are the FBI (Fighting Bacterial Infections) team of Dundee and we are ready to present you our mission.The mission’s brainstorming process came from monthly meetings in which the team has come together and looked into previous projects and discussed potential products in the area of health, hygiene, pollution and farming. The choice of the final project came from a mutual agreement in which this project was identified as the most interesting and feasible, our iGEM team wanted to accept a challenging project which is achievable and thus will result in a good amount of data which can be modelled and displayed. Our project choice also has a wide public outreach option which is something other projects in the brainstorming sessions were lacking.Colicins are toxins released by bacteria which inhibit the growth of surrounding bacteria of the same or similar strains, enabling them to minimise their competition. We plan to harness this innate ability, targeting four different bacteria which can result in bacterial infections within the human gastro intestinal tract. This will include common causes of food poisoning such as E.coli, salmonella and shigella as well as helicobacter pylori which causes chronic inflammation of the stomach, potentially leading to ulcer formation and thus increased risk of stomach cancer.We plan to pinpoint the most specific bacteriocins for each of these bacteria and ligate them into E.coli, along with transcription promoting machinery which is activated at a low pH, so that production is only stimulated when the engineered E.coli reaches the stomach. This way target specificity can be achieved thus protecting the stomach microbes which are important for a healthy gut. With antibiotic resistance becoming a growing strain on public health, alternative treatment to bacterial infection is of increasing importance. This method could improve specificity of treatment while limiting the overuse of antibiotics. So far we have designed the colicins which we want to use and had them synthesised. Colicins have 3 domains, a receptor, translocation and toxic domain or warhead. We plan to alternate the toxic domains of the colicins to minimise the chance of resistance. We have identified alternative warheads for the colicins, picked promoters and selected some additional parts for our construct.Our iGEM team is aiming to create a universal biobrick useful for multiple applications. An alternative solution to relieve antibiotic over-usage. Fighting bacterial infections through harnessing bacteria’s innate ability to eliminate their competition. The vision is a marketable powdered product suitable for travel or home usage and useful for combatting bacterial infections of the human GI tract. Dundee’s FBI (Fighting Bacterial Infections) team are ready for action!


Marburg

The iGEM team Marburg 2016 has decided to overcome the issue of landgrabbing by producing desired substrates through fermentation. This is achieved by establishing a modular system of artificial co-culture between different model organisms. Our novel approach allows us to engineer a system that benefits from the strengths of each strain to full extend. Therefore, bottlenecks in high-value substrate production can be overcome easily such that landgrabbing is replaced by fermentation methods. Currently we are engineering dependencies to stabilize the cell-cell-interactions well as implementing production pathways for our desired products. Our Human Practices project aims to establish multidirectional communication channels between society, academia and industry as our advanced fermentation project has a high impact on all these fields. In order to draw industrial interests, we define our project’s main aspects in terms of economy and ecology. Also we want to find out how the public feels about products that have been produced by fermentation, which is also of high interest for industry as well as academia. But as the public may not always be familiar with the terms and the subject of fermentation and Synthetic Biology, we are additionally working on an easily accessible platform that provides knowledge, information and material to get an insight into the field of Synthetic Biology and Metabolic Engineering. Following up on the killswitch statistics from the iGEM Team Marburg 2015, we want to extend the database by providing fully characterized kill switches to the iGEM community. This subproject will be carried out in collaboration with the iGEM Team Lethbridge. While we will provide modelling approaches they will implement and characterize identified killswitchs in the lab.


UC_Davis

We’ve come to expect vivid colors in our food, however, with the current push against synthetic food dyes, some of the bright colors we’ve all learned to love may soon start to disappear. These changes stem from uncertainty about the safety of synthetic food colors in relation to human health, both short term and long term. Although some of the controversy pertaining synthetic food colorings and health is not conclusive, the FDA and an overwhelming amount of consumers are placing increasing pressure on corporations to rid their products of artificial colors. Recently, large corporations such as Mars, Kraft, General Mills, and Nestle USA have promised to use all natural food coloring by 2020. However, switching this market to natural food colorings has provided numerous issues. The current market of natural food colorings is limited in both the cultivation, vibrancy, and color range. For example, the spice turmeric is commonly used to replace yellow dyes. Not only does turmeric cultivation require arable land, since it is such a small market it is subject to dramatic market fluctuations – between late 2009 and 2011 the price of turmeric rose about $100 per kilogram. The natural alternative to red dyes is carmine, which is the ground scales of certain Porphyrophora species which clearly provides consumer concerns because the dye is not Halal or vegan. Grass organisms, like Spirulina provided a promising alternative; however, the lack of color vibrancy is significantly inhibiting it’s use. Color is an intrinsic aspect of our lives and essential to how we perceive food and our goal is to keep this standard for generations to come. Here, we seek to use synthetic biology to remove the use of arable land for synthetic dye production, lessen consumer concerns, and bring market stability to a multi-billion dollar industry. Our plan involves harvesting the color capabilities of cyanobacteria to provide a viable alternative to synthetic dyes. In our project, we aimed to optimize production of our colored proteins and expand the available spectrum to match current industry standards.


Pittsburgh

We are developing a cell-free sensor that conditionally expresses a chromoprotein only in the presence of thallium. The metal ion detection is based on a DNAzyme that is cleaved in the presence of thallium. The released DNA strand activates a toehold switch regulated by the T7 promoter system, which will promote transcription of T3 and T7 RNA polymerases. The transcription of additional T7 RNA polymerase will amplify the signal from thallium. The T3 RNA polymerase will activate the expression of a chromoprotein. Our circuit will also incorporate a differential amplifier to remove noise from other heavy metals such as mercury. For the differential amplifier, a second DNAzyme with a greater affinity for other metals will be cleaved and produce a DNA strand complementary to that from the thallium DNAzyme. This will remove noise from other heavy metals that may also cleave the thallium DNAzyme.Early in the brainstorming process, our team wanted to develop a biosensor, since previous projects that hijacked glucometers and pregnancy tests sparked our interest. In deciding what to detect, we looked for analytes that were less widely studied and eventually decided upon thallium. Thallium, like lead and mercury, its neighbors on the periodic table, is toxic to humans. Because it has a similar atomic radius as potassium, thallium follows potassium pathways in the body. Thallium poisoning in low dosages results in hair loss and damage to the peripheral nervous system. In high doses, thallium is lethal. Thus, detection of thallium is important, especially in areas with industries that use thallium.We are also looking for collaborators. If you are interested, please contact us at pitt.igem.2016@gmail.com. We look forward to an exciting summer!


TU_Delft

Biolasers Imaging cells is essential for understanding life at the smallest scale and fighting cellular diseases like cancer. Imaging often relies on fluorescence, but fluorescent proteins have some drawbacks, such as their wide spectrum and low intensity. Our biolasers will provide an accurate, safe and biological way to improve this. Fluorescence is the ability of a molecule to take up the energy of a photon and release it again, which makes the molecule light up. Lasing works with the same principle as fluorescence, but now the light source is put between mirrors. The photons keep ‘bouncing’, increasing the energy of the system. When the light gets a certain power, the photons can escape in the form of a laser beam.A biolaser is achieved by trapping fluorescent proteins inside a reflective agent. We have chosen two reflective agents: bioglass (polysilicate) and bioplastic (PHB). By covering a cell with polysilicate, the photons can resonate inside the cell, making a whole-cell laser. The polysilicate is synthesized by an enzyme called silicatein, which is expressed on the cell wall by fusion to membrane proteins. By filling a cell with PHB, which forms intracellular granules, the photons can resonate inside a part of the cell, making an intracellular laser. The PHB is synthesized after expressing the pha-operon. By fusing the GFP to the PHB synthase, the GFP is relocated into the PHB granules. Biolenses Microlenses are an emerging field in technology and have a ton of applications, including high-tech cameras, chips, solar panels and research & imaging techniques. However, they are expensive, hard to fabricate and the production uses heavy chemicals and high temperatures, so it is bad for the environment. Our biological microlens will be cheap, easy to make and environmentally friendly.When we cover a cell with polysilicate, using the enzyme silicatein, we are able to make a biological microlens. By overexpressing either the transcriptional regulator bolA or the cell division inhibitor sulA we can play with cell morphology and investigate optical properties. These enlarged cells can also be used in the lasing experiments. The single cell will be able to diffract light as a single microlens. When we make a grid of lenses, a microlens array, we can use the lens for a coating for solar panels, thin lightweight cameras with high resolution or 3D screens.


IIT-Madras

When we started to ideate for iGEM 2016, our goals were to tackle two of the fundamental issues being faced in synthetic biology today - non-modular nature of RBSs and variations in the protein expression levels, designing an efficient measurement device. We have also designed efficient ribo switches and been using them for several potential applications like inhibition of HGT, pre-screening of desired clones of Cas9-gRNA treated cells. Our final project will consist of 3 modules - RIBOS riboregulatory switches, efficient measurement device, and characterizing widely used RBSs for their modularity.RIBOS(RNA Inducible Boolean like Output Switches) is a riboregulatory system in which presence or absence of mRNA molecules of one gene can modulate the expression of other genes. RIBOS devices are triggered by sequence specific RNA molecules and give output in the form of activation or repression of translation of specific mRNA molecules. We have designed RIBOS for scalability, orthogonality and composability. We wish to characterize RIBOS for tunability and highly precise outputs. It can be game changing in the field of synthetic biology, it's applications range from detection and quantification of mRNA molecules to the design of extensive independent and modular genetic circuits using forward engineering.Measuring GFP, RFP and other fluorescent signals to characterize biobricks, biological devices are one of the most important part of iGEM team projects. It is well known that these measurements are rarely reproducible due to several factors including the intrinsic noise of the part or device and the extrinsic noise like variations in bacterial cell count, plasmid copy number, instrumental error and human error. We are making an efficient measurement device, which can be used to measure GFP signals while eliminating the variations in the bacterial cell count and plasmid copy number. Promoter and RBS parts provide the driving force for protein production. Ideally, a combination of promoter and RBS should give similar expression level with different proteins. Recent research papers have shown high amount of variability in the expression levels. We are designing a model and validating it with the available data to predict the variations in the expression level. Also, we are characterizing widely used RBS parts to estimate their modularity


ZJU-China

This idea is proposed on the basis of our interests in Biometric Encryption. During the information age, data encryption is very important. We wonder whether we could construct a confidential gene circuits in order to encrypt the information with the help of the diversity and complexity of biological mechanisms. This question enlightened us.We hope to simulate a matrix composed by 0 and 1, and then part of these elements are encrypted by reversing. Using this method, we could get several different gene circuits, making the mixed group of E.coli realize the encryption process at different times and locations. We hope to use short range coupling of the technology of microfluidics, realizing cyclical change of the two quorum sensing materials at each location in the matrix. And then do reversing or not based on different wavelengths of light signals representing 0 and 1, using the corresponding fluorescent proteins to express. Seeing from the appearance, it is just an irregular matrix. In order to get the original information, the decoder have to know the unknown code and the time when correct information appears. Also, biometric encryption doesn’t rely on computers, and therefore, it couldn't be deciphered by conventional methods. If the overall dimension of this device can be reduced a step further, it can become a substitution of the traditional mechanical code case.


UESTC-software

We are the software team from the University of Electronic Science and Technology of China. Combined with the characteristics of electronic information, we have an interest in the two aspects: biological computing and biological information storage. In the promising field of biology, we used our professional strengths to make a research and discuss the selection of project. In the DNA information storage area, we understood that the existing software applications about DNA information storage were still very small, and had not reached the real utility yet. Some features such as low synthesis accuracy, slow speed, high cost and so on, make us want to improve and standardize the DNA information storage software. At present, there are a variety of algorithms about DNA information storage, we think of sorting out them to develop a DNA information storage platform -Bio101. It can realize the existing computer file coding and decoding, solve the problem of storage format standardization. Furthermore, we will try to complete random DNA information storage function.In terms of biological computing, we mainly focus on the design of genetic transcription circuit based on living cell in biological computing. The research of gene regulatory network needs to study in living creatures, and the function of plasmid transcription is affected by various conditions in the experiment. Inspired by the cello software, we plan to achieve an interactive genetic transcription circuit design platform -Bio1024. It owns visual interface and produce genetic circuit sequence through drag the modular components. Users can set parameters of each component of the circuit. Eventually, software gives the function prediction of the circuit performance. This platform has strong practicability. It makes the abstract concept presented in the practical function.Besides these designs, we developed a game software named Bio2048. It‘s an Android game based on the Grabriele Cirulli’s “2048”, a popular sliding block puzzle game. Instead of the numbers, the blocks are labeled with some common biological patterns, such as gene and protein. All the patterns form a biological ladder by their spatial scale. If two patterns with the same biological terms collide while moving, they will merge into a pattern with a new biological term which moves up by one on the biological ladder. This design aims to promote the biological knowledge among youngsters.


WLC-Milwaukee

In recent decades the issue of coral reef decline has become a global issue; from the coasts of the Florida Keys to the Great Barrier reef in Australia to the Andaman Sea reefs off the coast of India. Some of this decline is due to Serratia marcescens, a gram-negative bacterium that has contributed to the loss of Acropora palmata which is commonly known as Caribbean Elkhorn coral. Bacteriophage therapy, the focus of WLC-Milwaukee, is not a recent innovation but it could be the key to stopping the decline of coral reefs from this pathogen. Building on methods and research done by the 2015 WLC-Milwaukee iGEM team, we are hoping to find bacteriophages that destroy or incapacitate this pathogen using specific bacterial protein receptors. Using Escherichia coli as a surrogate to express Serratia proteins, we can isolate Serratia-specific phages using a simple lab strain of E. coli. Looking ahead, we would like to increase phage specificity for S. marcescens as well as improve phage enrichment techniques that were previously developed.


NorthernBC

Hey everyone! This is our first year competing in IGEM and are very excited to be joining the community. We're a small university of 4000 students hidden away in the wilderness of northern British Columbia. Our project was inspired by the high levels of Copper in our water systems and the Mt. Polly mining disaster that released a large amount of copper and other metals into the environment. Because of these issues we're working on a water remediation project. We're hoping to use copper binding proteins to reduce the amount of copper in water. This summer 12 students are working in a class like format to accomplish our goals. So far we've transformed a few of our desired parts into e.coli but are still waiting for a couple in the mail. Once all of our parts arrive we can start ligating them together. We're hoping that we can get the copper binding protein to attach to the outside of e. coli, by joining the sequences for the copper binder and a trans membrane anchor. Our team is ambitious, we hope that we can raise enough money to send all twelve of us to IGEM 2016. We're constantly working events and fundraising activities. We're very lucky to be Partnered with the Spirit of the North Health Care foundation who have helped us to reach out to the community and raise additional funds.


OUC-China

It has been proved that in Clostridium cellulolyticum, there is a kind of post-transcriptional regulation called selective RNA processing and stabilization (SRPS), which describes how stem-loops make a difference to mRNA level in a polycistron. As we all know, stem-loops which have lower folding free energy (∆G) than most oligonucleotides. And mRNA with stem-loops on 3’ or 5’ end often more stable than those without stem-loops. In some extent, the lower (∆G) of stem-loop is, the more stable corresponding mRNA is. Our team would like to design a series of stem-loops followed by a putative RNase E site and put them in intergenic region of a polycistron. We hope to decouple the expression level of upstream and downstream genes by this design though they are under the control of the same one promoter. And finally we would give a series of pithy regulation parts for others so that they can have another more choice.


Exeter

Biosafety is an important issue in synthetic biology. Awareness needs to be raised in the population so as to increase the confidence in this new technology and its applications. A lack of quantitative data in the area of Kill Switches is a major barrier to this. Our team have decided to extensively test the viability of kill switches, especially those currently available from the iGEM registry, to try to improve the robustness of bio-containment systems. The core of our project will be based around using simple kill switches from the registry. We are proposing to perform a continuous culture of the transformed E.coli to determine the length of time until functional loss of the kill switch gene. As the project moves further we are interested to test whether two kill switches implemented in a system provide a fail safe. We aim to test KillerRed and a new part KillerOrange, a homologue of KillerRed excited by a different wavelength of light, in isolation and together in the hope of improving the stability. In addition to this we aim to test if the stability of kill switches is improved by integration into the genome vs expression on a plasmid. Ultimately we would like to develop a new kill switch which aims to address the problems associated with them in a new way. In our discussions about the topic of our iGEM project it became apparent that our ideas fell into two categories. The first being food security with a focus on fighting plant pathogens, the second focused on measurement. Lots of research was done into anti-fungal proteins and a delivery system by which we could attach E.coli to the fungus using a novel prokaryote-eukaryote bridge. We looked into using a viral vector to introduce a kill switch into fungal pathogen and have it spread sexually through the population. These presented what we decided were insurmountable issues for an iGEM project.


Leicester

For the past few years, space travel has become a frequent topic in the news and of interest to the scientific community, especially since Mars has now become a viable option for manned exploration. Within the next decade, we are set to see the launch of a vast number of human missions to Mars. Bone weakening in astronauts who experience extended spaceflight has been discovered to cause serious side effects, a recent study found that astronauts lose on average 1-2% of their bone mass each month and some astronauts have been found to lose 20% bone mass throughout their lower extremities (NASA, 2016). Many researchers have attributed the bone loss to prolonged weightlessness, because the stress on the bone, due to gravity, is greatly reduced resulting in astronauts experiencing osteoporosis. In spaceflight the parathyroid hormone inhibits the action of osteoblasts (increases bone density) and stimulates the action of osteoclasts (degrade bone mass). However, the hormone calcitonin inhibits osteoclast function and decreases calcium levels inducing osteoblast activity. We hope to tackle Osteoporosis in astronauts using gene-targeted therapy through CRISPR/Cas9 technology to upregulate calcitonin secretion. We will upregulate calcitonin by targeting the promoter of the calcitonin gene using CRISPR/Cas9. We will begin by using E-coli plasmids as our models and monitor the products produced by using GFP-tagged sequences. Although there are means of obtaining calcitonin via pills, injections and nasal sprays; they do not work as effective therapies for astronauts in space and are extremely inconvenient for space travel. Using CRISPR/Cas9 our project hopes to create a more potent form of calcitonin causing a reduction of bone loss in astronauts, as well as provide a new and innovative method for transporting space medicine.


FAFU-CHINA

Chlamydomonas reinhardtii has been used to explore the potential to use it as an inexpensive and easily scalable system for the production of proteins. As the most widely used insect-resistant gene all around the world, the cry gene from B.thuringiensis(Bt) is one of the most efficient gene encodes a insecticidal crystal protein (ICP) with strong specific activity against only one or a few insect species. Based on the recent research in our school, we have been cloning a series of genes which could control the larvae of mosquito from natural B.thuringiensis(Bt).Considering the difficulties of colonization in the natural environment, especially around water, for traditional chassis biont,such as E.Coli and yeast, constructing genetic engineering Chlamydomonas reinhardtii with cry and cyt gene is a good way to keep the effect of toxic protein in natural environment.


TecCEM

Fractos: Endolysin-powered antimicrobial system for selective lysis of Acinetobacter baumannii iGEM TecCEM 2016 team, first gathered on 5th of December 2015, decided that a quite important problem affecting hospital throughout the world was the uprising antibiotic resistance. While carefully analysing statistics on the metropolitan area within and surrounding Mexico City, Acinetobacter baumannii was chosen as the prime target of our project development. Acinetobacter baumannii is a pathogenic and opportunistic bacterium responsible for infections in hospital environments, mainly amongst patients at ICUs. Nowadays, it has drawn major attention given its ability to acquire resistance to commonly used antimicrobial agents. Due to the widely spread resistant mechanisms among microorganisms, antibiotics have lost their efficiency at annihilating pathogens, up to the point of being non-efficient at all in the treatment of certain infections. After several weeks of research concerning the bacterium, its genetic and microbiological properties, and the pathophysiology it follows for infecting humans, we decided to aim the development of 2016 project into generating a novel mechanism for its elimination from hospital environments. This year iGEM TecCEM 2016 team is developing a novel and specific method to avoid Acinetobacter baumannii proliferation onto nonliving surfaces, through cell wall lysis, as an alternative to currently used antimicrobials that promote the development of antimicrobial resistance. The use of endolysins ensures the elimination of the pathogen of interest, as specificity for Acinetobacter baumannii increases its efficiency. The purpose of formulating a disinfectant driven by such endolysins is the sanitization of surgery and nursery equipment as well as room furnishing, and other objects that are potential transmission vectors for Acinetobacter baumannii.


TU_Darmstadt

The critical evaluation of the project’s safety is required from each iGEM Team participating in the competition. Therefore the iGEM HQ created an entire subpage on their website where the teams can find all the necessary information, such as risk levels or general safety requirements. Unfortunately there is no chance to look up complete, working safety approaches from previous teams. It should be easy for teams to choose a well characterized safety approach which is suitable for their own project out of a catalog and directly see how to easily incorporate it. Our project is supposed to lead the way into that direction. In our 2016 project we focus on easily enabling teams to work safely with E.coli. By integrating genetic circuits into the E.coli genome we ensure that genetically modified bacteria cannot survive outside of the required lab with the particular conditions they need. The genetic circuit is based on the availability of an unnatural amino acid (UAA) and is regulated within two steps: 1. When the concentration of the unnatural amino acid is low a reporter protein is expressed which signalizes the low level of UAA. 2. When the UAA concentration reaches zero (which is also the case if bacteria get out of the lab) the expression of colicin is induced which then kills the bacteria. Additionally we hope to facilitate and accelerate the molecular cloning process of DNA through a new standard based on the RFC10 standard. We use riboswitches to show a successful ligation without additional testing procedures. Project brainstorming Like every year we started our weekly team meetings in january and thought about possible projects. This year it took us a bit longer to find a project but around the end of march we were closing in on a safety project around colicin. By mid march we had our project overview and started dividing into several lab groups that focused on their individual pathways. By now the first cloning procedures have been succesful and we are looking forward to conduct first measurements.


Uppsala

We are developing a method to make CRISPR and microfluidics more available to iGEM teams and researchers. The technique will be used to fuse a fluorescent protein called UnaG to a genomic protein in both prokaryotes and eukaryotes. We are including state of the art research involving the CRISPR associated protein CPF1 and microfluidic methods. UnaG is a fluorescent protein that needs bilirubin as a co-factor in order to fluoresce. Bilirubin binds non-covalently, which facilitates the possibility of creating inducible fluorescent switches from UnaG. Bilirubin occurs naturally in higher vertebrate cells, making it suitable as a biosensor for research on vertebrates. It is therefore convenient to use UnaG together with CRISPR systems, such as CRISPR/CPF1. CPF1 cuts downstream of the PAM sites and leaves 5’ overhangs. By providing UnaG with the complementary overhangs, we could insert this fluorescent protein in the genome of our host. In order to increase the chances of correct insertion, we aim to engineer UnaG with homology arms, which enables cells to insert UnaG by means of homologous recombination in the exact position where the genome has been cut. To facilitate the insertion of the genomic material we will design a microfluidic chip capable of transformation. This will be done through soft lithography by 3D printing a mold and baking a PDMS chip on it. A microfluidic chip will reduce the amount of reagents needed to perform a transformation, which could potentially reduce the cost and workload of a conventional transformation. The chip methods are not size-dependent, therefore it will be possible to do any given plasmid insertion with the same device. By using this chip, cell transformation becomes simpler and cheaper to do for other iGEM teams and small laboratories. In our project we will use it along with CRISPR to fuse UnaG with a genomic protein in yeast, but a microfluidic chip could potentially be used for any transformation technique.


CU-Boulder

Bacterial microcompartments (BMC’s) occur in nature to encapsulate enzymatic and metabolic processes in organisms such as E.coli. This capsulizing system can also be utilized to efficiently deliver drugs to targeted regions. Our goal is to engineer the reversible assembly and disassembly of an ethanolimine utilization compartment (EUT), by introducing a non-natural amino acid into the outer shell protein. The EutS gene codes for a protein that forms the hexameric tiles which make up the EUT compartment shell and can associate with EutC tagged proteins. Azo-benzene, the non-natural amino acid we will be using, undergoes a conformational change when exposed to specific wavelengths of light and will be used to disrupt the EutS structure. The formation of compartments will be visualized through EutC tagged eGFP localization within the Euts compartments and the destruction of the compartments will be indicated by EutC-eGFP dispersion throughout the cell. Previous research has shown successful changes in chaperonin conformation by crosslinking cysteine residues with a light activated azobenzene - dimaleimide. At 450 nm azo-benzene will primarily be in its longer trans state but when exposed to 365 nm light, azo-benzene has a pinched cis conformation. We will be replacing amino acids within the EutS structure with azo-benzene to create steric hindrance caused by cis to trans isomerization rather than crosslinking. If placed correctly in the EutS protein azo-benzene may control the formation of the BMCs. Successful microscopy has confirmed the viability of EutS and EutC-eGFP in E.Coli, but the laser used to excite eGFP may also cause conformational change of azo-benzene. Instead Neptune, another light activated protein that is excited at a much longer wavelength, will be used to visualize the formation and destruction of EutS microcompartments. Future work will focus on the implementation of a multiconstruct system with EutS, EuC-Neptune, and a third construct that creates tRNA’s to integrate azo-benzene into the EutS at locations we expect to see significant steric hinderance.


UGA-Georgia

The goal of the University of Georgia’s iGEM team is develop tools and methods to further the utility of Archaea in the field of synthetic biology. Previously, we have established an mCherry reporter system. In a fruitful Interlab collaboration with eight other iGEM teams, we have quantified the mCherry fluorescence for a library of ribosomal binding sites or RBS with single-base pair nucleotide substitutions in Methanococcus maripaludis, a model organism for Archaea. As a continuation of last year’s project, this year the our team plans to 1) measure more RBS mutants from last year’s library, and 2) expand our project by determining the effect of the spacer region on the strength of RBS. The spacer region is defined as an oligonucleotide region consisting of adenine and thiamine nucleotides located between the RBS and start codon. Presumably, the strength of mCherry fluorescence would change when varying the length of the spacer region. In addition to measuring the fluorescence, we also wanted to learn how the position of the RBS would change in the mRNA secondary structure in our spacer experiment, by modeling the secondary structure with the Vienna RNA Package 2. Furthermore, we hope to expand our Interlab study to the use of both plate reader and flow cytometer.


Northwestern

Our team is investigating the utility of outer membrane vesicles (OMVs) in the delivery of Cas9 in vivo. All Gram-negative bacteria produce OMVs and use them to deliver toxins, communicate with other bacteria, mediate membrane composition, and extract materials such as metal ions from their environment. OMVs have been successfully engineered to carry heterologous proteins,1 which makes them an attractive candidate for systems that require the delivery of a functional protein or complex to recipient cells. One such system is the application of CRISPR-Cas9 to treating antibiotic-resistant bacterial infections. At the moment the most effective methods of delivering Cas9 to target cells are either limited to DNA delivery (bacteriophage delivery2 and hydrodynamic injection3) or require extensive vector engineering in order to facilitate controlled delivery and uptake (lipid-mediated tranfection4). We hope to use signal peptides and protein fusions to direct Cas9 protein into OMVs so that the functional complex can be delivered to and act on the resistance genes in antibiotic-resistant bacteria without extensive lipid modification to facilitate uptake.


IvyTech_SouthBend_IN

Project Proposal (Draft): This year Team Ivy Tech is investigating environmental endocrine disruptors in the local water shed and the food supply. We intend to build a new biosensor for estrogen and test for activity in the St. Joseph River Valley watershed and in Lake Michigan and screen for the constituents of soy that effect breast cancer proliferation. For biological read-out we will use estrogen-sensitive cells lines like the human breast cancer cell line MCF-7. In addition, the most commonly prescribed drug is 17-beta estradiol and it is prevalent in human sewage and may be the largest contributing factor to the observed feminization of aquatic vertebrate species in the environment. One approach to the inactivation of estrogen is the irradiation of sewage. With our biosensor and estrogen-sensitive cell lines we will screen for the loss of estrogenic activity and/or the formation of unknown anti-estrogenic compounds. Finally, the number and types of genes that are under the control of estrogen is uncertain. We plan to use CRISPR to insert a RFP-generator cassette in genes under the control of an ERE in one of the two homologous chromosomes. Gene-edited cells that respond to 17-beta estradiol or estrogenic/anti-estrogenic compounds that we isolate from the environment will cloned using our "Bio-CNC machine" (a modified 3D printer) with the eventual purpose of identifying the genes that are activated.


USTC-Software

We had a long-time brainstorm and find an appropriate project for the team. Although there're many aspects that can be solved by computing, things that can be done perfectly by us seem restricted. Before we finally decide which project to work on, we used to investigate those projects: 1. GRN (genetic regulatory networks) research 2. Software for NgAgo 3. CNN application in protein picture analysis 4. Biopano further development (Biopano 2.0) 5. Aptamer analysis Finally, we discussed with our primary PI Haiyan Liu, and reached an agreement that Biopano has a better prospect than other alternatives. Moreover, a developed Biopano platform can be friendly to users who need to analyze genetic networks, which is part of project 1. After months of surveying, discussing, and brainstorming, our team selected Biopano 2.0 as the ultimate project.Biopano is an open source software based on visual editor servicing for editing large-scale gene networks. It helps in group work as well. Target gene can be licked to the existed network form the public database easily with the searching functions built in the software. The software also supports external plug-in, which allows users adding features they need. News in the second generation are: 1. Real-time simulation for the expression of the gene network. To design the prototype gene lines with the truth table. To imply the gene network according to the result of the expression. To export into other software formats


HZAU-China

The biological pattern formation is a important research field in Systems Biology. In the past 50 years, there were several major breakthroughs on finding the mechanisms of biological pattern formation. Many classical theories have been proposed, for instance, The Turing Model (A.M.TURING et al, 1952) and The Clock And Wavefront Model (Cooke, J, 1976), etc. With the emergence of Synthetic Biology, many research teams are trying to understand and verify these theoretical models with the ideology of Synthetic Biology and some developments have been made (Liu Chenli et al, 2013). However, the understanding to the mechanisms of biological pattern formation is far from mature. For this year, we are aiming at developing a system in which computers are used to guide the biological pattern formation. In this project, the easy operability and strong control ability of computers are exploited to monitor and regulate the growth process of bacterial community in real time to achieve the shape we want. Our system can also be extended to eukaryotic cell community which will be useful in aiding the development of biological tissues and the regeneration of organs.


Jilin_China

Tumor cells compete with normal cells for all kinds of nutrition, and therefore can be considered as harmful mutants in the ecosystem in vivo. To effectively eliminate tumor cells, we propose to utilize microorganisms that share high ecological niche with tumor cells to deliver tumor-killing drugs to the tumor tissues. Through extensive literature search and correspondence with leading specialists, we decide to use Bifidobacterium Long, which has been proved to be non-immunogenic to human body and has the ability to preferentially settle in hypoxic regions, such as tissues with solid tumors. We plan to inject Bifidobacterium into tumor-bearing mice, and simulate the distribution and association of Bifido-bacterium with tumor cells using ecological competition models. We decide to use apoptin as the tumor-killing drug. Apoptin is a small molecular protein that induces apoptosis only in tumor cells but not in normal cells. To deliver apoptin, we will construct a recombinant plasmid, which consists of DNA replication origins and related genes from pMB-1, a bifidobacterial plasmid, and DNA replication origins from pUC18, a plasmid commonly used in E.coil. As a result, the plasmid can be amplified both in E.coil. and Bifidobacterium. Furthermore, we will clone HU, a Bifidobacterium promoter, and apoptin gene into this recombinant plasmid. After the tumor-killing ability of this recombinant plasmid is proven, we will focus on enhancing the biosafety of our system through regulating the expression of apoptin gene and applying a conditional lethal mechanism to restrict the proliferation of Bifidobacteriun.


UPF-CRG_Barcelona

The past October 2015 the World Health Organization publicly announced that the consumption of processed meats could, in a long term, increase the probabilities of developing cancer. According to many underlying studies, the polyamines, a group of natural and essential molecules for growth and cell development, were found to be responsible for this carcinogenic activity when they are in high concentrations. Our main idea is to develop a supplementary probiotic that, used in a regular and preventive way, can reduce the amount of polyamines that our body absorbs, so as to maintain their concentrations within a healthy level. This probiotic will consist on a mix of different modified bacteria that will simply process the exceeding part of polyamines from the digestion and eliminate them using a set of natural enzymes also found in our bodies. This probiotic will be consumed as an oral capsule, and the bacteria composing it will exclusively be extracted from the intestinal human microflora, which are also found in many products nowadays, such as cheese, yogurt, milk, etc. Additionally, we have planned to develop a cancer risk detector by engineering a bacterial cell. The principle behind this idea is that an acetylated version of polyamines are exported to the blood and later to urine. This molecules have been targeted in previous studies with a high success in both sensibility and specificity of cancer risk detection. The problem of those studies is that the methodology is costly (it is expensive and takes weeks), and it is very far from being implemented in hospitals. For this reason, we are planning to develop a much easier system, that can test the risk of having a growing tumour in less than four hours. This system will consist in a set of modified bacteria, freezed dried in a strip, that will produce a reporter protein, a specific color, in the presence of the acetylated polyamines in urine.


AHUT_China

Our team has chosen to continue our 2014 project of BIO-COMPASS after discussing its meaning and feasibility as well as comparing with other projects. Firstly, we firmly believe that the project of 2014 was quite potential and could be further researched and developed so as to bring more real benefits to human beings. Besides, our initial plan of using paclitaxel to cure diseases like cancer is not practical enough, thus needs to be further improved. Finally, our team is always ready for delving into a wonderful subject and pursuing the better or perfection, and continuing our 2014 project of BIO-COMPASS serves as a great option to achieve this purpose.Our project aims to build a new available bio-navigational system in which the map information will be coded in DNA strands with correlative biochemical reactions. The bio-navigational database builds up the relationship between biochemical operation instructions and traditional navigation instructions. In order to improve work efficiency, BIO-COMPASS 2.0 is designed to screen out and optimize the conditions of reaction according to road conditional filtering. Therefore, we attempt to renew the system based on our project in 2014 to adapt to the more complex path plans. As for this point, based on our previous pathway planning which includes design of sites and lines, we have further conducted deeper coding to lines. Also, the lines are used not only to complement corresponding nodes, but also encompass the information of length, node and specific identification. Through BIO-COMPASS 2.0, the shortest way to achieve the purpose of navigation will be obtained by using a variety of detection methods (such as electrophoresis , sequencing, etc).


Peking

Uranium, a heavy metal element, is weakly radioactive and poses a threat to both the environment and human health. A person can be exposed to uranium by inhaling dust in the air or by ingesting contaminated water and food. Long-term exposure to uranium increases the risk of various diseases and health issues including cancer, kidney problems and immune system damage. Uranium has become more commonplace due to nuclear accidents (the Chernobyl Accident,the Fukushima Daiichi nuclear power plant Explosion), uranium mining and the development of depleted uranium weapons.To alleviate these problems, the Peking iGEM team aims to construct a novel functional biological material, which can absorb uranyl ion with the employment of a specific uranium-binding protein. This novel material has numerous promising characteristics such as high specificity, high efficiency, self-assembly and self-reproduction. With some modification, the design can be applied to deal with uranyl ion in polluted water and soil, demonstrating its impressive potential. We believe that the material can effectively solve the increasingly serious uranium pollution in the near future.


XMU-China

The bacteria is one of the pathogen of humans. For many years, overusing of antibiotic contributes to antibiotic resistance of many bacteria. At present, drug-resistant bacteria are becoming a huge threaten to human's life health, the development of new antibiotics can't catch its demanding. Focusing on this, our team uses the way of synthetic biology to detect and kill the drug-resistant bacteria.On gram-positive bacterium, we choose the MRSA to study. We make use of the quorum-sensing system of gram-positive bacterium and a genetic switch based on cI and lacI genes, then we design a genetic circuit to detect MRSA and then kill it by producing a toxin, and we put our genetic circuit into the E.coli to produce a new E.coli that can detect MRSA specifically and then kill it. In our experiment, we use MSSA to study because MRSA is a second-level pathogenic bacteria. Now, our present work is connecting the plasmids.In terms of gram-negative bacterium,E. coli was selected and the engineering bacteria was designed to resist antibiotic resistance E. coli. After the engineering bacteria detects the group sense signal molecules of pathogen, siRNA which will silence the gene allowing a bacterium to be resistant to antibiotics is released. Meanwhile, special enzyme is emitted from the engineering bacteria to destroy the biofilm. At this stage we designed and synthesized siRNA, and the next step is to carry out the in vitro transcription experiment of siRNA.


Bilkent-UNAMBG

Cancer is one of the most common and lethal disease in the world and it is always highlighted that early diagnosis is crucial in terms of cancer treatment. It is often invasive and painful to diagnose cancer with the existing methods. At this point, breath test appears as a promising non-invasive and real-time technique which allows the monitoring of metabolic status. Volatile organic compounds(VOCs) in the exhaled breath provide in vitro detection, classification and discrimination of diseases and microorganisms. Concentration of specific VOCs in the exhaled breath can either increase or decrease depending on the type of diseases and microorganisms. In this project, our goal is to produce a prototype which can detect and discriminate four most common cancer types: lung, breast, colorectal and prostate. In order to achieve this, we will engineer an artificial plasmid including promoter and reporter genes that are specific to a particular VOC. It is expected that when that particular VOC is given into the environment, bacteria will express reporter gene hence we will get some signal. After achieving getting the signal for a particular VOC, we aim to construct logical gates and circuits by using CRISPRi system on plasmids to create well accoutred bacteria which will be able to differentiate these four cancer types. Our future goal is to transform our prototype into a kit. So that, diagnosis of cancer will be simpler and non-invasive.


Tokyo_Tech

Our Team Tokyo_Tech is currently working on the following four projects:Ⅰ. Representing fashion show and Othello with the interaction among E.Coli. Ⅱ. Engineering the E.Coli which can secrete and absorb protein. Ⅲ. Engineering the E.Coli which can increase the efficiency to allocate phosphorus fertilizer and synthesize a variety of plant hormones. Ⅳ. Representing the famous fairy tale, Snow White with the interaction among E.Coli. Ⅰ. We have developed the mechanism about coating the surface of E.Coli , and run the fashion show of E.Coli with various kinds of fluorescence. It is expected that the development of proteins which bind with specific antibody or cell targeted would be applied to determining the location of the target, establishing the system to control the motion of the target and also microbe sensor for the specific substance. This system will be applied in various fields such as Biology and Medicine. In our opinion, the control of multiple motions among E.Coli will be used as a device of microbe sensor by combinating E.Coli and hardware. Ⅱ. We aim to develop the system of E.Coli which can secrete a large amount of target protein. because in order to synthesize and collect target protein, we have to break down the whole E.Coli, It‘s a time-consuming process to get the purified target protein. However, if the system secreting the target protein efficiently can be established, we’ll be able to produce the target protein without killing E.Coli and reduce the cost of production. Ⅲ. We are trying to produce phosphoric acid from phosphate in E. Coli which is hardly soluble and not absorbed by plants. Through this process,it will be able to increase the efficiency of phosphorus fertilizer’s allocation and to alleviate the depletion of phosphate rock. In addition, we aim to grow vegetables in a short term by synthesizing plant hormone by E.Coli. Ⅳ. We plan to apply AHL-degrading enzyme and toxin used for representing Snow White by E.Coli in the practice. AHL-degrading enzyme can be applied to preventing the generation of biofilm. In our opinion, the death of malignant cells can be induced by inducing the expression of toxin gene. According to the mathematical modeling about competition and balance of bacteria, we are still studying about the analysis of the competition among bacteria populations in vivo, river and soil.


Hannover

TAL (Transcription Activator Like) –effector proteins are a new possibility for genetic engineering. Due to a special, repeating sequence of amino acids, a so-called repeat domain, TAL-effectors can easily bind to a certain DNA sequence and perform various functions. Originally, those proteins were discovered in Xanthomonas. Those bacteria use TAL-effectors to specifically regulate host genes. After decoding the amino-acid-code of TAL-effectors, genetic changes can be generated. In this way, DNA-fragments can be replaced and precisely cut or foreign DNA can be inserted. TAL-effector proteins offer a significant advantage compared to usual procedures e.g. with restriction enzymes: Trough an easy change of the amino acid sequence, the protein can be customized to any DNA sequence. The function of TAL-effectors could be proven in vivo in cell cultures and also in animals. However, they show a high instability outside living organisms. This instability leads to the problem that the purification of TAL-effectors as well as the in-vitro application in the lab is difficult to perform. For this reason, TAL-effector proteins are excluded from a huge field of application, because a lot of genetic work usually takes place “in test tubes”. Our aim is to develop a circular TAL-effector with the help of a linker in order to stabilize the protein. Thereby, TAL-effectors could be utilized on a daily basis and enable new techniques of genetic engineering in the lab.


UT-Tokyo

We aim to create a genetic circuit functional in E.coli which allows the gene expressed to change after each cell division. Specifically, the E. coli will be expressing GFP, RFP, and CFP after subsequent cell divisions and will loop back to expressing GFP again. This will be achieved by the use of the Pnrd promoter to sense to cell division, sigma factor/anti-sigma pairs control transcription, and a toehold switch to create an AND gate required in the circuit . Our project would be able to exhibit, in E. coli, that despite carrying the same genetic information, different phenotypes can be expressed across generations. Much like the phenomenon seen in epigenetics. Moreover, this technology could potentially be applied in field to carry out certain tasks automatically without the need of external input eg. to make engineered cells automatically carry programmed cell death after a certain number of divisions.


Technion_Israel

We, the Technion iGEM team of 2016, are developing FlashLab - a user-friendly chip for rapid detection of various substances such as hormones and heavy metals. The detection relies on the E. coli chemotaxis system, which allows bacteria to move away from or towards target materials. In comparison to existing biosensors, this system is expected to combine simplicity, speed and universality - offering the ability to detect diverse materials using the same method without the need for expensive lab equipment. The idea is to use a bacterial chemoreceptor and exchange its ligand-binding domain (LBD) with a small library of various LBDs. This library will be based on (1) natural bacterial chemoreceptors and (2) novel LBDs; designed using the RosettaCommons software suite. Moreover, to expand the repertoire of LBDs we plan to use an innovative approach to introduce self-splicing inteins as triggers for chemotactic activity. To observe the bacteria, which co-express both the redesigned chemoreceptor and a color protein, several different designs of microchips will be tested. The bacteria will be confined to a microchannel and chemotactic movement, induced by the target material, will lead to the formation of clusters that are visible to the naked eye. Given the simplicity of the design, the chip is expected to work much like a home pregnancy test – just insert a sample and wait for the answer!


Hamburg

This year the iGEM Team Hamburg is determined to construct a biosensor against Chlamydia trachomatis, a pathogenic bacterium that is transmitted sexually and has an adverse health effect in developing countries. There the problem is less the treatment, which can be easily done by broadband antibiotics, but the diagnostic identification of the exact bacterial strain. And these diagnostic methods are costly, since they mostly rely on immunologic methods like antibody-staining, ranging between 30 to 150 Dollars. This is fine in industrial nations, but for many people in developing countries living close to the poverty line (1.25$ per day) this is far from affordable. Noteworthy is also the widespread incidence of chlamydial infections, as well as the severity with which the disease can progress. Estimated 89 million people worldwide are affected by Chlamydia trachomatis, 4 million of which have lost their eyesight due to the namegiving trachoma that forms when the bacterium infects the conjunctiva of the eye, leading to cicatrization. To combat this, the iGEM Team Hamburg is developing a fusionprotein-biosensor, used in diagnostic bacteria, to offer an inexpensive alternative to present diagnostic methods for medical doctors in developing nations. is constructing a fusionprotein with signaling pathway to function as a biosensor in prokaryotes. EnvZ-NOD1 fusionprotein, activating transcription factor OmpR, after sensing an unincorporated building block protein of the peptidoglycane membrane of Chlamydia trachomatis. The fusionprotein is then to be used in diagnostic bacteria, which - for biosafety purposes - are locked in an inexpensive microfluidic device.During the last wintersemester our P.I. and patron Prof. Dr. Zoya Ignatova has been inviting guest speakers for lectures about synthetic biology, and we have been gathering ideas for the project of this years competition. In March 2016 we had decided and started collecting sponsors to finance the project. Over the last few months we started constructing different reporter systems, based on fluorescence, bioluminescence and other methods of signalling. We also optimized the EnvZ/NOD1 fusion protein for the host organism's code bias and constructed our fusionprotein in way that allows simple restriction and insertion of other periplasmic sensing domains. The nanoscientists of our iGEM Team are in the process of testing alginate incapsulation for additional biosafety in our microfluidic device, and the first results are looking good.


CGU_Taiwan

Photodynamic therapy (PDT), also called photochemotherapy, involves three key components: photosensitizers (PS), a light source, and tissue oxygen. In the presence of tissue oxygen and appropriate wavelength of the light source, photosensitizers will generate cytolytic reactive oxygen species (ROS) to destruct PS-accumulated cells/tissues. More importantly, ROS will attack multiple cellular targets, preventing it from being selected for resistance which is a universal problem nowadays in radiotherapy and chemotherapy of all diseases. In the present study, a novel PDT is exploited by the unusual mechanism of Leishmania parasite. When these trypanosomatid protozoa infect mammalian hosts, they will find their way to specifically parasitize in macrophages and other antigen-presenting cells (APCs). Moreover, a transgenic Leishmania, which are deficient in heme biosynthesis, undergo photolysis when illuminated by specific wavelength of light. Accordingly, it is a useful drug or vaccine carrier. To develop a new way of vaccination, we would like to build a Leishmania-compatible BioBrick encoding hemagglutinin (HA) from H1N1 influenza virus. We believe the unique properties of transgenic Leishmania will make it a useful model to produce human Influenza vaccine. In the future, we plan to establish this transgenic Leishmania as a platform to carry other antigen or biobricks.


Tsinghua

Genomic stability and DNA sequence fidelity are critical for normal cellular activities. If such storage center of genetic information is disrupted, detrimental consequences will take place, including but not limited to excessive cell death, abnormal proliferation, untimely cell senescence, etc. Therefore, a gene mutation surveillance system that can sensitively and efficiently detect and remove such aberrations in vivo is required.Saccharomyces cerevisiae is chosen as the model organism for designing such a gene surveillance system. As one of the most commonly used tools, it not only has a highly manipulatable genome, rapid growth speed, minimal pathogenicity, an ensemble of selectable markers, a well-defined genetic system, and most importantly, a highly versatile DNA transformation system.Essentially by designing such a system, a tool that can recognize aberrant mutation on mRNA sequences, or more generally at the transcriptomics level, is desired, because transcripts are derived from genomic sequences and hence are representatives of genomic instability and mutations. Surveillance Cas9 (suvCas9), termed for the first time by our team, is a variant of Cas9 without DNA cleavage activity and can target specific mRNA sequences by manually designed sgRNA and PAM sequences.That being said, after mutation is detected on mRNAs, how can our system respond? In a nutshell, when mutations occur, the surveillance system will detect and trigger the suicidal system. The surveillance system can be further quantitatively optimized to maximize its sensitivity and minimize potential side effects.


UrbanTundra_Edmonton

Ever since NASA successfully landed astronauts on the moon through the Apollo space program, humanity's next challenge is to venture and set foot upon the "Red Planet." Companies such as NASA and SpaceX aspire to conquer that challenge and their aspirations involve developing a successful plan to land on and colonize Mars. Our team, inspired by the book and movie "The Martian" wants to contribute in Mars colonization. Unlike its portrayal in the movie "The Martian", Martian soil contains high levels of perchlorate (ClO4) which is toxic to plants and animals. If colonization on Mars is to be made possible, detoxifying the soil of perchlorate is a necessity. Our team plans to develop an automated proof-of-concept process for the biodegradation of ClO4 to chloride and oxygen which are less harmful than perchlorate, thus remediating the soil and creating a sustainable source of oxygen for Martian colonization. The project will entail: 1. A chemistry-based method to extract and concentrate ClO4 from martian soil. 2. Genetically engineering a fast-growing lab strain of E.Coli to degrade ClO4 by incorporating three ClO4 biodegradation genes from a slow growing soil microorganism. 3. Optimizing ClO4 utilization and oxygen recovery from this genetically engineered strain using a readily available and sustainable source of colony biowaste. 4. Recycling the spent bacterial media and bacterial residue as a fertilizer for hydroponic plant growth.


Pretoria_UP

We are Pretoria_UP, the iGEM team of the University of Pretoria. We study microbiology, medical plant science, biotechnology, genetics, multimedia, electronic engineering, mechanical engineering and industrial engineering. Our team consists of 3 graduates and 8 undergraduates, as well as 1 instructor and 7 advisors. This year we are working on Synthetic RNA aptamers for thylakoid tethering in photo-electrobiochemical cells - a project called Watts-Aptamer! Project Background The world population of over 7.4 billion people, which is rapidly increasing, consumes about 3500 kWh/year per capita. The need for energy generated from renewable resources is becoming more significant in light of this demand and the threat of climate change. In recent years a lot of research into photo-bioelectrochemical cells explored different light-harvesting photosynthetic proteins. The research was aimed at discovering which proteins would serve as the best components in light-activated generation of fuels or electrical power. The proteins studied include photosynthetic reaction centers (RCs), photosystem I (PSI) and photosystem II (PSII) (Yehezkeli et al. 2014). Aptamers are RNA or DNA oligonucleotides capable of binding to specific targets with high affinity and specificity. These aptamers are usually “mined” through a process called Systematic Evolution of Ligands by EXponential enrichment (SELEX), and many have been identified against different targets including proteins, organic compounds, nucleotides and even whole cells and organisms (Germer et al. 2013). The problem: Attachment! Photo-bioelectrochemical cells hold great potential as clean, alternative energy sources. A major barrier is the attachment, efficiency and cost of the system, making scalability unfeasible. Particularly, synthetic linkers used for thylakoid attachment to electrodes are expensive and difficult to manufacture at sufficient scale. Aim of our project To design and construct an optimized photo-bioelectrochemical cell using an in planta RNA aptamer synthetic biology strategy for self-assembling attachment of plant thylakoids to graphene-coated anodes.


Bielefeld-CeBiTec

Our team is looking forward to start the iGEM season! Carsten Hain, Niklas Hoffmann, Judith Kampa, Marius Schöller, Mikail Sahin, Pascal Schmidt, Marten Linder, Cassandra Königs, Bianca Frommer, Fabian Roeloffs and Sebastian Perez KnocheiGEM Bielefeld-CeBiTec, Bielefeld University, Germany The impact of antibodies in modern medicine is on a permanent rise but the cost and time factor as well as the immunization of animals, which die during the harvesting process, are still problematic. Therefore we want to establish an alternative using antibody-like binding proteins that are generated in vivo in E. coli. Profiting of the short generation cycle and the exponential growth of bacteria, we want to generate binding proteins in a much shorter period of time while also being more cost efficient. Furthermore, no animals have to suffer in the process by immunization. Our goal is to develop binding proteins in E. coli in a process of directed evolution that can subsequently be utilized in diagnostic techniques and target-mediated drug delivery against pathogens. Due to the ability of our system to quickly adapt to a certain target protein under evolutionary pressure it is especially useful in concern of quickly evolving and newly arising viral pathogens. The concept of our system subdivides into the following aspects: At first, we create a randomized library of binding protein sequences in bacteria to form the starting point of our project. As scaffolds for our binding proteins, we settled on both antibody mimetics (monobodies) and natural antibody fragments (nanobodies). In the next step, we use a two plasmid system in combination with a mutant of the polymerase I which leads to a higher mutation rate in the coding regions of our binding proteins, so that there is a chance for the binding proteins to adapt to the target proteins. Finally, we isolate the strains that produce the binding proteins with the highest affinity to the target protein by using an in vivo selection mechanisms: Mediated by the binding of our protein and the target, the cell in concern is granted a selective advantage directly increasing its evolutionary fitness.


NTU-Singapore

The power of targeted genome editing for gene therapy is the primary inspiration for our team to study on the CRISPR-Cas9 system. With the accuracy of this CRISPR-Cas system, it can undoubtedly spur the development of molecular therapeutic for human diseases. However, as CRISPR-Cas system is still a newly developed genome editing tool, there are challenges faced by using CRISPR-Cas system. For instance, off-target mutagenesis, efficiency of Cas9 nucleases are still not well-compared among different bacterial species and the existed Cas9 nuclease might achieves only moderate efficiency for genome targeting. Hence, our team would like to firstly conduct a comprehensive study on characterization and evaluation of Cas9 nucleases from different species. Besides, research works on improving the efficiency of HDR for double stranded donor template will be performed as well.


Oxford

To be considered for the Oxford iGEM team, we each had to write a short statement explaining why we would make good team members. The previous years' team selected us based on this, and after the Christmas break, we arrived in January as a team of 11! From January to March, we were brainstorming potential projects - first, individuals pitched short ideas and we discussed these as a team to exclude some initial ones based on feasibility or originality, taking into account previous iGEM projects. By February, we had narrowed down to 3 projects, and split into small sub teams to conduct more extensive feasibility studies into each of these. By March, we all decided to devote our efforts to the project addressing Wilson's Disease. The problem: Wilson’s disease Wilson’s disease is a genetic disorder which causes the body to accumulate too much copper. This causes liver failure and brain damage in affected patients. Wilson’s is a rare disease because it affects about 1 in 30,000 people (250k worldwide). The drugs currently used to treat Wilson’s are copper-binders, but there are two major problems with these: 1) Toxicity: these drugs have severe side effects, and treatment course often has to stop 2) Administration: tablets need to be taken before every meal for the rest of the patient’s life Our solution: probiotic bacteria A growing field in medicine is ‘probiotic pills’ – using micro- organisms to provide health benefits. At Oxford iGEM we are exploring the potential to introduce a special bacterial population in the gut – which have been genetically modified to bind copper. This would reduce the amount of copper that can be absorbed into the blood, and therefore prevent its accumulation in the blood. Compared to current drugs, this solution offers: 1) Lifelong cure: bacteria persist in the gut and excrete the copper they bind to as they are turned over 2) Fewer side-effects: copper binding occurs in the bacteria and is isolated from the body


UCLouvain

Many brainstorming sessions took place from November through February. During those, the team and its academic supervisors discussed and explored many ideas and concept brought forward by the members. This first phase was one of divergence, which enabled us to cover a wide variety of topics and explore possibilities in many biological fields. From late February started a convergence phase during which we deepened our knowledge on the most promising ideas that emerged from the previous phase. Amongst those ideas, we selected a few that were exciting, original and feasible in the spawn of time available. Finally, in March, after short presentations form the team members, we casted a vote to choose the final project. Our project « the Gatekeeper » provides a new secretion method for recombinant proteins produced within the periplasm through the insertion of a phage porin in the outer membrane of E. coli. Following promising results describing the opening regulation mechanism of this viral protein (Spagnuolo et al., 2010) and based on well-established knowledge on secretion in E. coli, our team aims to condition the porin’s opening system to create a gateway between the intra- and extra-cellular environment. Our success would mean getting rid of the cumbersome lysis step in recombinant protein production and could give rise to continuous recombinant protein production. We will use a directed evolution approach to mutate regions known to play a key role in either the gate opening or the opening regulation (identified by Spagnuolo et al., 2010) and subject the resulting mutants to strong specific selection pressure. Through this method we will also attempt to create a regulating system for our gate’s opening/closure.


UofC_Calgary

Each year on Earth, individuals receive 2.4 mSv of ionizing radiation (IR), which is easily tolerated by our cells. In space however, without the protection of the magnetosphere, astronauts are exposed to high levels of IR in the range of 50 to 2000 mSv which causes the accumulation of deleterious double strand breaks in DNA. Despite current research into methods of IR protection, many solutions such as radiation shield coating are expensive. Biological solutions such as the use of radioprotectors are also subjected to the sinusoidal pharmacokinetic problem resulting in the need for constant administration and the accumulation of waste. Certain naturally-occuring proteins and peptides, such as the modified Bowman-Birk Inhibitor (mBBI), have been found to confer protection against DNA damage in cells exposed to ionizing radiation. Previous studies have shown that BBI increases the survival rate of cells significantly when irradiated, by augmenting endogenous DNA repair mechanisms. To solve the problem of creating a cost effective, continuous delivery system for IR protection, we have designed a transdermal patch for the delivery of mBBI through the skin. The patch hosts recombinant Bacillus subtilis that expresses a mBBI gene tagged with a transdermal tag that allows the peptide to travel through the skin layers, and into the bloodstream for dispersal throughout the body. Using B. subtilis for the production of mBBI allows for constant delivery bypassing the sinusoidal pharmacokinetic problem. Its long term, continuous delivery will also create a cost effective solution. Ultimately our transdermal delivery system allows for the administration biotherapeutics within an efficient and practical system.


SCSU-New_Haven

Selection After researching each topic and several rounds of discussion we decided to pursue a project involving Tuberculosis. Our team wanted to add more GC rich parts to the iGEM repository and a project focusing on Tuberculosis would allow us to do so while tackling a global problem. Project Description It has been shown that different diseases cause the production of volatile organic compounds (VOCs) in the body. This seems to be true of Tuberculosis especially due to its infection site being the lungs. We want to produce a Mycobacterium smegmatis based VOC sensor activated by Tuberculosis specific compounds. Our goals Our final product should be a simple breath test device that accurately reports infection within several hours and does not require a laboratory environment to use. It should be storable in non-refrigerated conditions and have a simple indicator most likely color change.


CLSB-UK

Synechocystis sp. PCC6803 is a model cyanobacterium that is often used in biophotovoltaic cells - these produce electricity in the form of electrons evolved from the bacterium when photolysis of water takes place. This all sounds great, but the downside is that the efficiency of the process is low - electrons are produced when water is split, but only a tiny fraction of them end up leaving the cell. Some success has been had in increasing efficiency of BPV cells by adding an external mediator but this approach is not sustainable in the long term should we want to run a BPV cell for an extended period of time. Additionally Synechocystis grows extremely slowly, meaning that transformations take a long time and can make the overall process of working with this bacterium difficult from a synthetic biology perspective. This is where our vision comes in. We plan to amplify expression of the CmpA gene in Synechocystis, a gene that codes for a bicarbonate ion(HCO3-) membrane transporter protein. Increased uptake of bicarbonate ions has been linked to higher growth rates so we think that this would be a good place to start to make any additional work easier. After this, we intend to add two parts: BBa_K1172303 which produces riboflavin, and BBa_K1172501 which is a porin(channel protein across the cell membrane), with the goal of increasing the number of electrons evolved from the cell, and as such making potential BPV cells more efficient with this bacterium. We would also utilise a promoter from the registry to maximise expression of these parts, but we’re unsure which to use as of yet.. The difficulty lies in transformation of Synechocystis; it is picky as to which plasmids we can use, and any work would have to be done with replicative plasmids, as this organism is hexaploid - integrating anything into the genome proper would lie outside of our time constraints. Our project is very applicable to global issues of sustainability and energy - BPV cells are a promising solution to provide cheap, sustainable power, but not much exists yet outside of proof-of-concept and research examples. We hope to aid the development of this exciting technology by carrying out these changes to Synechocystis. Additionally making this bacterium easier to work with from a synthetic biology point of view would help out any future teams or labs hoping to work in this area, in concordance with the community spirit of the IGEM competition.


Goettingen

We intend to design, construct and introduce a synthetic Vitamin B12 exporter (“Synporter”) into a production organism. Thereby, we aim for facilitated and higher yields in the industrial Vitamin B12 production without requiring cell lysis. The B12 Synporter consists of a signal for a Twin Arginine Transporter (Tat) mediated export that is linked to a B12-binding domain. This construct will be expressed in S. typhimurium TA100, R. planticola and S. blattae. We will not only test these different production organisms but also different B12-binding domains.Vitamin B12 is involved in metabolic functions in all organisms, and is therefore an essential nutrient. However, it can only be synthesized by some bacteria and archaea, thus, animals have to obtain it through their diet. Thereby, only animal products like meat and dairy contain B12 in general. This B12 was synthesized by microorganisms colonizing the gastrointestinal tract of those animals and accumulated in the animals’ tissues. Vitamin B12 is one of the most essential biochemicals in the world, and its synthesis is extraordinarily complex. Since the chemical production of Vitamin B12 requires 70 synthesis steps, it is far too technically challenging and expensive. Therefore, its production is facilitated by genetically engineered microorganisms. These are able to produce Vitamin B12 in industrial amounts and achieve a high product quality. However, the produced Vitamin B12 is harvested by cell lysis, which prevents a continuous production. The efficiency of production could be increased by exporting Vitamin B12 outside the cells. To date, a natural cellular Vitamin B12 exporter is unknown.An adult needs approximately 3.0 µg Vitamin B12 per day which is essential for certain functions: it is involved in processes concerning synthesis of DNA, hormones and neurotransmitters and is involved in the formation of the nervous system and blood. Hence, a B12 deficiency can cause diverse diseases like cancer, dementia, depression, pernicious anemia and polyneuropathy.Nowadays, many people do not eat meat or animals products at all. Therefore, these people have a high risk to suffer from B12 deficiency if their diet does not provide enough B12.Vitamin B12 is also used in the industry as it is needed in the biotechnical production of various organic substances. Furthermore, it is added to diverse daily products like toothpaste, fruit gum, non-diary milk or cleaning solution for contact lenses.When we have successfully expressed our constructs in our productions organisms, we will try to maximize the Vitamin B12 yield, and possibly find ways to utilize the periplasmic space to facilitate cytotoxic B12 dependent reactions.


BostonU_HW

Fluigi is an end-to-end specify, design, and build workflow for the development of continuous flow microfluidics. With Fluigi, users can specify microfluidic devices through a high level description of liquid flow relations. Our application will automatically place and route the design schematic of the microfluidic, and our application is compatible with low cost and readily available CAD tools that will build the final microfluidic device. The Boston University 2016 iGem Hardware Team is completing this workflow by providing a front end user interface that allows simple and intuitive navigation of the application. This user interface encapsulates the whole of the workflow: users can write files that specify the function of the microfluidic. Users can then preview and edit their microfluidic design that was placed by the application. Users can use this application directly with CAD tools such as a CNC mill to fabricate their device. Finally, our application provides the ability to physically control valves and ports on the microfluidic chip through the user interface. The iGem team is also complementing this workflow by developing and releasing open source designs of our hardware, including parametric 3D print files, and firmware for microcontrollers that actuate the microfluidic valves. Finally, the iGem team is also involved in the development of the place and route software that converts a high level description of liquid flow relations into a microfluidic netlist that can that be converted into a design schematic.


Pasteur_Paris

Arboviruses are spreading at an alarming rate on a global scale. Zika, dengue and chikungunya viruses affect more than 500 million people per year. The WHO has assembled the Emergency Committee on February 1st 2016 in the fear of the Zika outbreak all over the world. To this day, the only known method to fight is to spray insecticides in large quantities on risk areas. Yet, this strategy has proven to be inefficient, mosquitoes develop resistance against the substances and these are very harmful to the environment. That is why it is crucial to develop a precise mapping strategy of the contaminated territories.Our team designed a novel system that is quick and easy to use. This device traps mosquitoes, and detects the presence of viruses thanks to a biosilica-based patch onto which we apply the mosquito lysate produced by the trap. The analysis results are then passed on to local authorities and centralized into a database, allowing a detailed real-time mapping of the location of infected mosquito populations. Therefore, our system will act as a sentinel to allow prevention and environmental surveillance. Our project includes three parts: the mosquito trap, the novel biosilica immunodetection patch and the data analysis and mapping software. The bio-nanomaterial of our patch is based on cellulose and biosilica. This material is biodegradable. The immunodetection component of the patch is customizable to detect different antigens. We present a new, easy-to-use, eco-friendly antigen detection system, that will target contaminated regions and diminish the use of harmful insecticides


McMasterU

GI tract cancers are an enormous public health issue, and together are responsible for more deaths than any other form of cancer. One of the major difficulties with diagnosing and treating these cancers, especially when localized to the intestine, is access to the tumour - patients often do not exhibit obvious symptoms until the later stages, when treatment options are limited.We looked into a few different ways of tackling this issue, from improving existing diagnostic methods to developing new avenues for treatment. One of the consistent themes that came up in our brainstorming process was the potential for us to use the host's cell-mediated immune response to fight cancer. Cancer immunotherapy is a rapidly growing field, and clinical trials for certain forms of leukemia are already underway.Thus, this year, McMaster iGEM sought to augment the power of the host immune system to fight against GI tract cancers, using a specially engineered strain of commensal lactobacillus bacteria. When completed, our bacteria will be able to sense the presence of tumours in the gut, bind to specific receptors on tumour cells, and begin secreting pro-inflammatory cytokines in this tumour microenvironment. This will recruit T cells to the site of the tumour and elicit an anti-cancer response, effectively stopping the cancerous growth using the body's own toolkits. This summer, we aim to develop a proof-of-concept of our idea, and create a bacterial strain that can secrete IL-2 under tightly controlled, tumour-specific conditions


Virginia

Our team split into three small groups in March and each proposed a refined project idea. Our other ideas included lysin synthesis to treat acne and the development of a bamboo chassis to combat air pollution. After much heated debate and further research into project feasibility, we chose to focus our research on biocontainment. We wanted to use a large-scale approach to improve the field of synthetic biology. By developing a reliable biocontrol standard, we aim to promote practical, safe implementation of biological devices. Project Description The field of synthetic biology currently struggles with the issue of containment both in laboratory settings and real-world environments. This shortcoming prevents the widespread implementation of useful engineered devices and calls for a cellular-based containment system that can operate in an open environment and provide security comparable to physical containment. Although several biological methods currently exist for containment, these methods allow some degree of genetic escape through horizontal gene transfer, spontaneous mutagenesis, or utilization of environmentally available compounds (1). The Virginia iGEM team proposes to use the CRISPR/Cas9 system to redesign leucyl-tRNA synthetase to confer metabolic dependence on modified leucine in Escherichia coli. Our goal is to create the foundation for a reliable, standardized, and universally applicable biocontainment system.1. Mandell, Daniel J., Marc J. Lajoie, Michael T. Mee, Ryo Takeuchi, Gleb Kuznetsov, Julie E. Norville, Christopher J. Gregg, Barry L. Stoddard, and George M. Church. "Corrigendum: Biocontainment of Genetically Modified Organisms by Synthetic Protein Design." Nature 527.7577 (2015): 264. Web.


Bordeaux

A 2008 report by the INPES, a French public institute, has shown that 45% of the 25-45 year-old population considers that they do not sleep enough. This lack of sleep causes a fair bit of negative impacts : decrease of focus, weakened immune system, cardiovascular disease risk increase ... Even if these statistics are high, today's medical knowledge is not sufficient enough when it comes to healing people who suffer from sleep disorders. A classic example would be sleeping pills for chronic insomnia. However, they only treat the symptoms, not the source. This drew our attention, enough to provoke unanimity for this project within our team.This year, iGEM Bordeaux aims to study DSIP, a sleep-inducing peptide which seems to be promising for the given dilemma. In order to understand in which mechanisms this peptide is involved, it will be produced by the bacteria E. coli and then given to the nematode C. elegans. It would be interesting to directly produce this peptide in C. elegans too.Another aspect is to control the nematode's sleep pattern. On the one hand, we want to make a photo-inductible system that can be used on sleep genes' promoters. On the other hand, we aim to create a new tool to modify the sleep genes using epigenetics the sleep genes : EpiCrispr. Based on the CRISPR-CAS9 concept, we want to design it according to two strategies : both will use a fusion technique between a methylase and CAS9, but the second approach is inspired on Sun-Tag technique.Our final goal is to compare the two approaches - the photo-inductible system and the EpiCrispr system - and see which one would be easy to handle for the C.elegans's sleep control.


HUST-China

Auto-regulation parts are very commonly used regulation elements in gene networks which form kinds of biological process such as bio-oscillation, cell cycle, etc[1]. In nature, prokaryotic cells mostly employ negative feedback regulation to ensure their physiological homeostasis[2]. While in  eukaryotic cells, they commonly regulate their homeostasis with both negative and positive feedback[3]. The positive feedback systems, which underlie bi-stable or binary response in cells, are very important and powerful parts for synthetic biological research and development. In bi-stable system, transition between two stable states could occur when the system’s input parameters change. For example, the feedback system of cI/cro in bacteria phage γ triggers a binary switch that decides the fate of cells. Considering the functionality and significance of positive feedback to universal synthetic biology applications in bi-stable or even multi-stable systems, this year, HUST-China team tries to build a set of positive feedback fundamental tool kits for synthetic biology engineers. The systems we design will not only be adaptable to any input and output, but also can change its threshold to meet the requirement from different project purpose. As the positive feedback regulation system can transform an input pulse into stable states or outputs, it can also be applied as signal filter in circuits. Additionally, to make it a competent basic tool kits, we tries to provide both prokaryotic and eukaryotic versions, for synthetic biology engineers to compare and select for further application.


Purdue

Purdue iGEM 2016: Clean Water for All This year our team is taking a holistic approach to improving clean water access in the world. To do so, we are engineering two strains of E. coli: one to uptake phosphorus so as to prevent toxic algal growth in lakes and streams and another to express functional, organic nanowires to generate energy from organic waste and improve microbial desalination cell efficiency. By expressing these genes in E. coli we hope to provide a platform for further study and application in agriculture, the environment, and alternative energy. Why Clean Water? While brainstorming for our 2016 project, we decided that we wanted to pursue a project that was specific enough to be applicable to the needs of our community, yet broad enough in scope so as to benefit the global community as a whole. The two biggest two issues we found that met these criteria were the domestic and agricultural misuse of phosphorus and our current energy-intensive and economically expensive water treatment practices.To give more detail, phosphorus is a nonrenewable resource essential in agriculture, yet projections estimate that global phosphorus could be all but depleted in 30-40 years. Still, excess phosphorus in lakes causes algae growth that harms the ecosystem. It is our belief that wastewater treatment is a key place to prevent phosphorus from entering lakes while also allowing the phosphorus to be harvested for further use. As to the other side of our project, microbial fuel and microbial desalination cells (MFCs/MDCs) are systems capable of intaking waste or salinated water and then using bacteria to produce an electric current for energy use or the removal of dissolved salts. Currently we know little about which bacteria can grow and function inside of MDCs/MFCs, but by introducing nanowires like those present in Shewanella bacteria into E. coli we hope to engineer the tools of discovery for other scientists, engineers to make the next great improvement. What We Hope to Accomplish Our ultimate dream is to develop a self-contained unit (microbial fuel or desalination cell) capable of removing various nutrients and impurities (i.e. phosphorus/nitrogen) from grimy, opaque water, polluted by industry, agriculture, and daily living, which can then produce clean, sparkling, drinkable water. This unit would be applicable in both the developing and the developed world and would require little more knowledge than what is required to maintain a small swimming pool.


Aix-Marseille

Platinum is one of the rarest and most valuable metals in the world. Thanks to its physical and chemical properties platinum has become a key component for the functioning of our society. The reason that platinum is so valuable is that it occurs in very low concentrations and associated to other atoms. Because of this, there are only a few mines in the world that are profitable to exploit. And since recycling methods are not very developed, it is only a question of time until mining is no longer a solution. Unfortunately, predictions state that all known economically workable platinum deposits will be exhausted in 2064. The end of platinum could lead to a great socioeconomic crisis.As an initiating step towards solving this issue we decided to design a novel method of recycling platinum from a recently discovered source - soil next to highways.Many studies during the past few years have shown that there are great quantities of platinum deposited in the soil next to big highways, often in higher concentration than in mines. The reason for this accumulation is the constant automobile traffic. Indeed, platinum is present in the catalytic converters of cars and trucks and it is released in very small amounts at each use of the engine. Therefore the platinum accumulates around the traffic routes, on asphalt, in soil, even in plants. To safely exploit this resource, we imagined a concentrating system that could be integrated into existing water processing and phytoremediation systems.Our goal is to concentrate platinum as much as possible. We decided to do it in two distinct steps. The first step relies on the affinity of siderophores to bind solubilized Platinum atoms and thus favor the further solubilisation of more platinum compounds. We accomplish this by inserting a plasmid containing the four enzymes (Des A, Des B, Des C, Des D) necessary to synthesise our siderophore - Desferrioxamine B, into E. coli. As a second level of concentrating the platinum even more, we plan to use the principle of biosorption. A modified fliC protein complex will be cloned into E. coli and enable the flagella of the bacterium to bind platinum atoms. This specificity will be possible thanks to a peptide that will be inserted into the sequence of the fliC. The benefit of using the biosorption is to obtain nanoparticles of platinum, a highly valuable form of the metal.


TAS_Taipei

Cataracts is the leading cause of blindness in the world. Oxidation of the lens crystallin protein, which leads to its misfolding and aggregation, is the main cause of cataracts. Among the 20 million people affected annually, over 50% are caused by old age. Currently, eye surgery is the only effective method for treatment. This method, however, is expensive and invasive. Therefore, our goal is to prevent and treat age related cataracts non-invasively by producing an eyedrop that includes glutathione reductase (GSR) for prevention and Cholesterol 25-Hydroxylase (CH25H) for treatment. GSR catalyzes the conversion from Glutathione disulfide (GSSG) to glutathione (GSH) in order to prevent crystallin oxidation. CH25H converts cholesterol into 25-hydroxycholesterol, which is a molecule that can reverse aggregation and restore solubility of the crystallin protein. To deliver proteins into the lens more efficiently, we engineered an eyedrop containing biodegradable Chitosan nanoparticles that encapsulate the proteins.Currently, we are working on building our Biobrick constructs. In order to prevent direct contact between human body and bacteria, we assembled polyhistidine tag behind each gene we want to express to purify proteins. Furthermore, we used a strong promoter and strong ribosome to maximize protein expression. To test if GSR prevents and CH25H treats cataracts, we simulate healthy lenses and cataract lenses. We extracted the lens protein of a type of freshwater fish and dissolved the protein in Tris/DTT/EDTA buffer, which mimics the environment of the fish lens. We added GSH to test for the effectiveness of the antioxidant. For treatment, we added 25-hydroxycholesterol after adding hydrogen peroxide into the lens protein solution for 24 hours. We measured the opacity of the solution by measuring the absorbance using a spectrophotometer, which reflects the severity of cataracts condition.While we strive to develop an accurate experimental model to test our methods of prevention and treatment of cataracts, we have also taken various measures to further our research, educate the public, and fundraise for cataract patients. Through interviews with ophthalmologists and veterinarians, we gained insight into the specific requirements of an efficient solution for cataracts. In order to spread awareness of cataracts and synthetic biology as an emerging field of study, we presented our project to other students and taught introductory biology classes about the basics of synthetic biology. Finally, we conducted surveys and interviews to learn more about the opinions of the people in Taipei about the issue of cataracts and cataract surgery.


LMU-TUM_Munich

In the present decade, the possibilities enabled by 3D printing and scanning have led to an industrial revolution in prototyping and the production industry as well as in households. Predictably, this new way of simple, tailored fabrication will have an enormous impact when applied to the fields of personalized medicine and synthetic biology. Bio-printing has the potential to meet the huge global demand for replacement organs and therefore to greatly increase the life quality of elderly people. Successfully developing bio-printing requires a strongly interdisciplinary team for a harmonized development, including: i) bio-printers with special print heads, ii) BioInk composed of proteins providing mechanical stability, and iii) cells that need to be understood, engineered and adapted by means of Synthetic Biology. We will transform an affordable household 3D printer into a bio-printer for Synthetic Biology applications. This includes engineering a printhead for bioprinting and adapting the 3D printer software, through which bioprinters will be made accessible for a broad scientific community. Additionally, our team has developed a new BioInk that is based on the ability of proteins to specifically interact with their clients: The challenge is to develop a BioInk that remains fluid in the printhead and will rapidly assemble when printed to provide mechanical stability. Our new approach utilizes the affinity between biotin and the biotin-binding proteins streptavidin and avidin -- the strongest non-covalent interaction in biology. In employing this tight molecular interaction, our team has designed an innovative dual-component “protein glue” (BioInk) that opens unprecedented opportunities for the field of bio-printing. Regarding the third main field, we will use genetically engineered cells for bio-printing. We have engineered tunable cellular membrane proteins that allow the cells to interact with the surrounding matrix formed by our new BioInk. Subsequently, we will engineer functions into our printed cells that allow the printed tissue to be employed to treat different diseases. For a controlled release of these chosen therapeutic proteins, we have also used existing knowledge on optigenetics to render production of these therapeutic proteins inducible by illuminating the therapeutic implant with a tissue-penetrating lamp.


Toronto

The University of Toronto will be developing a portable synthetic biological sensor for gold, and a deep neural network for discovering novel genes involved in gold biomineralization. Biological methods can be used to detect metal ions, complexes and nanoparticles. Biosensing refers to a collection of techniques which utilize existing biological pathways and complexes to detect specific metals in various samples, such as those from soil and drinking water. Biosensing has been found to occur in relation to iron, zinc, copper, silver, gold and cadmium. Here, we propose an environmentally-friendly approach to biosensing through design and implementation of novel synthetic biology solutions for the mining industry. By creating cell-free paper-based biosensors, we intend to develop a quick, easy and affordable method for detection of gold in soil samples. Our team plans on tackling through use of a transcriptional activator, GolS, and its variants, which induce their associated reporter genes in the presence of gold ions. These reporter genes will be selected to act as visual indicators. Our computational team will augment this project by engineering a smartphone application for colorimetric analysis. This will be done using the smartphone’s camera input of the visual indicators to estimate the amount of gold present in a sample. The computational team will also be developing a pipeline to identify gene clusters related to a given function of interest. This data mining module will allow its user to search for homologous gene clusters as potential gold resistant or accumulation genes like alternatives to the del cluster.


Bulgaria

With the dawn of synthetic biology and the ever increasing utilization of microfluidics in experimental practice a new understanding of single-cell biology has emerged. We now realize a lot more of the inner mechanisms that regulate individual cells. Our team aims to make the detection of carbon, phosphate and nitrogen starvation in cultured cells easier and faster. In order to accomplish this we will insert different fluorescent protein genes in a bacterial plasmid. Those will be expressed together with Escherichia coli’s starvation genes and this way we will observe light in different parts of the spectrum according to the needs of the cell culture. After stimulating the transformed cells the fluorescence will be detected through signal monitoring system. The data will be used to visualize the level of expression i.e. the phase of starvation. We want to make a cell culture that is cheap, easy to cultivate and that shows us exactly what it lacks in its environment. If we are successful this approach could be used in many different fields including pharmacy, bio-engineering, improving the efficiency of bioreactors in general and many more. We have our strains and successfully made our first electroporation.


IIT_Kharagpur

Spider Silk Humans and silk have been intertwined together for a long time now. We have seen it around nearly everywhere, be it in your clothes or be it from Spiderman’s web shooters! This silk has immense potential hidden in its threads. We are all familiar with silkworm silk. It’s a well­studied and developed industry. What we are concentrating on however is spider silk. Spider silk has many applications. Its unique properties of strength, elasticity and well as being lightweight allow it to be an excellent biomaterial. It can beused to forge artificial tendons and ligaments, or even bridge cables. It’s the stuff that can be used to make air bags, cords for parachute or even body armour. Along with this, spider silk has low immunogenicity, thus making it an ideal candidate for biomedical applications such as drug delivery systems and scaffolds for tissue engineering. Cultivating silkworms may not be such a headache but these spiders put up a lot of fight. So we need some way in which this can be done on an industrial scale. Bacterial Silk As we are all aware, the microbes that grow on everything around us can grow at amazing rate. Not only that, but they can be made to synthesize proteins of our interest with a little genetic tweaking. This brings us to our project. We aim at synthesizing recombinant spider silk protein (MaSp2) in E. coli along with a system to effectively deliver it outside the cell. There have been advances in synthesizing spider silk in bacteria. Some of them by previous iGEM teams themselves. But the successful ideas have involved lysis of the bacterial cells to get to the protein. We would like to combine one of these successful efforts with a secretion system. This will allow us to produce the silk protein, and then reuse the cells for more of the same. Our idea Our idea hinges upon the use of a site specific retroviral protease. We aim at synthesizing recombinant spider silk protein (MaSp2) in E. coli and anchoring it to the outer cell membrane, followed by the cleavage of the same using a HIV1 aspartyl protease. The silk protein will be fused to a fragment of OmpA protein that will display it on outer surface of the E. coli. A HIV protease cleavage site will be introduced between the OmpA fragment and the silk protein assembly. A second construct containing the cleavage site and the HIV protease will be fused to the OmpA fragment. Induction of the second protein construct will initiate cleavage by the protease in cis that will release the protease and allow it to cleave in trans and release the spider silk protein.


Aalto-Helsinki

The Aalto-Helsinki 2016 team started working in the beginning of March. Our brainstorming sessions resulted in more than 50 ideas, of which some were good, some were bad and some were really, really bad. We narrowed the ideas down to the top 5 and then did research to figure out what would be the most promising idea. Ultimately we decided to work with cyanobacteria and the problem they pose every summer in Finland. Cyanobacteria, or blue-green algae, are a problem in Finnish waters especially in the late summer, when they develop big blooms. They produce toxins that can be harmful to people and animals. We decided to concentrate on the most common cyanotoxin found in fresh waters called microcystin-LR (MC), which is a hepatotoxin. We studied MC'™s toxicity mechanisms extensively to figure out the best way to tackle it. The toxicity mechanism in mammalian cells is based on the MC'™s inhibitory effects on protein phosphatase (PP) 1 and 2a. When the PPs are inhibited their target proteins remain phosphorylated which eventually leads to hyperphosphorylation. This results in production of reactive oxygen species that ultimately manifest as oxidative stress. We also found out that the same basic mechanism also happens in yeast cells. So we decided to take advantage of Saccharomyces cerevisiae's oxidative stress response to detect MC. We also want to degrade the toxin. There are a few bacteria that naturally degrade cyanotoxins. We decided to use an enzyme called microcystinase (MlrA), found in some Sphingomonas strains. The degradation leads to a nontoxic product, which is the linear form of the otherwise toxic cyclic heptapeptide. We will study the enzyme kinetics of microcystinase and also the toxicity mechanisms in yeast cells, in order to gain a deeper understanding about the system.We have also worked together with Finland'™s environment center (SYKE). As one of our public outreach projects, we will collaborate with them and work on their Levavahti (Algae Watch) -app. We will try to model a dynamic population model so we could predict how the cyanobacteria blooms will grow and develop, and have this as one of the features in the app.