Jamboree/Project Abstract/Team Abstracts

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Team Aberdeen_Scotland: A Synthetic Biology Approach to Pipe Repair: The Pico-Plumber

Damage to inaccessible pipe systems, such as computer cooling circuits, is difficult to rectify. An Escherichia coli synthetic biology circuit for pipe repair was designed. Pipe breach detection and the restoration of pipe integrity were implemented through exploitation of chemotaxis, and cell lysis that releases a two-component protein-based glue (lysyl oxidase and tropoelastin). Control was achieved using an AND gate with quorum sensing and the lac inducer IPTG (released from the breach) as inputs. Deterministic and stochastic models of the genetic circuit, integrated with an agent-based model of E.coli cells, were used to define the effective radii of cell migration and timing of lysis. Constructed AND gate, quorum sensing and lysis timing modules were experimentally tested. The two-component glue concept was successfully validated using in vitro alpha-omega complementation of beta-galatosidase activity. Finally, a proposal for an igem.org-based parameter database was developed to aid the rapid identifation of BioBricks parameter values.

Team Alberta: A Synthetic Biology Tool Kit for Artificial Genome Design and Construction

The creation of simplified artificial cells with specialized functions, along design principles that are compatible with the goals of synthetic biology, requires advances in two key areas. In Silico modelling tools are needed to assess the performance of artificial networks prior to assembly. Genome biofabrication must achieve rates well beyond existing methods using a modular design so that the extent to which natural systems can be made artificial can be tested. We have taken our first steps towards these goals by directing our efforts to the rational refactoring of the E. coli genome. Using flux balance analysis we have identified 117 new genes that may be essential for survival. We have developed and validated a rapid, modular biofabrication method (BioBytes) and have produced BioBytes for 150 of our 447 essential gene list. We have also built a Lego Mindstorm-based DIY biofab robot and extended the concept to a BioFab-on-a-chip prototype.

Team ArtScienceBangalore:

We consider ourselves amateurs/novices within the context of the IGEM competition. Our endeavor as “outsiders” is to bring our training in the arts and design to synthetic biology. Over this summer, we learnt the tools and techniques of synthetic biology and developed a piece of life which reflects our concerns, namely, the cultural, ethical and aesthetic implications of Synthetic Biology. Using a DIY approach and getting our hands “wet” was a critical element in the learning process. Our construct synthesizes Geosmin, an enzyme normally produced by cyanobacteria and actinobacteria. The biosynthesis of geosmin from farnesyl diphosphate is catalyzed by a single enzyme germacradienol/germacrene D synthase.E. coli, does not bear a gene that codes for this enzyme. We have expressed this gene in different strains of E. coli. Geosmin is responsible for producing the earthy smell when rain falls after a dry spell of weather.

Team Bay_Area_RSI: Breast cancer cell targeting phage

Breast cancer is the second most common type of cancer diagnosed in women. RNAi has proven to be an effective mechanism in the silencing of oncogenes. Therefore, we have attempted to build a viable system for the delivery of RNAi into breast cancer cells. First, we inserted a shRNA sequence coding for the Raf-1 protein into an AAV cassette containing two ITR's, allowing it to reproduce itself in mammalian cells. This cassette was inserted into our chosen vector, the filamentous bacteriophage FUSE-55. An antibody sequence was then added to the phage plasmid near the coat protein sequence in order to target HER2. As an additional feature, we have fused Silicatein and Silintaphin to mStrepavidin, which will bind to a protein tag in the coat, forming silicate structures on the coat of the phage, thereby reducing the immunotoxicity of the bacteriophage in vivo.


Directed delivery of specific proteins into cells would have dramatic consequences for drug delivery and expand the horizons of synthetic biology into the multicellular domain via discrete, targetted communication. Gram-negative bacteria naturally produce outer member vesicles (OMVs): spherical, bilayered proteolipids from 20-200nm in diameter. OMVs carry outer membrane, periplasmic and cytoplasmic proteins, DNA, RNA and other biological molecules. They protect their cargo from the extracellular environment and deliver it to a multitude of target cells via membrane fusion. We investigate the possibility of allowing the secretion of any protein in OMVs via fusion with novel, non-toxic partners enhanced in OMVs, using a novel Bioscaffold compatible with the current assembly standard. A new version of the award winning BSim software has been developed to study applications at the population level such as communication. The ultimate goal is to create a safe and standardised system for directed delivery of proteins into cells.

Team Berkeley_Software: Eugene, Spectacles, and Kepler: Managing Synthetic Biology Device Development

Three crucial activities in synthetic biology are the creation of standardized parts, the construction and specification of devices from these parts, and the automatic assembly of these devices. Each of these activities requires software tools. Tools give users access to data as well as provide algorithmic support and abstraction to design large scale systems. We have created three software tools for these tasks. The first is a domain specific language called Eugene for the specification of biological constructs and rules for their creation. The second contribution is a visual design environment for device creation called Spectacles. Finally, we have created workflows for the Kepler design environment. This work is integrated within the Clotho design framework. We show that together they offer a powerful solution to the problems of today while also providing a path to the more exotic design activities of the future.

Team Berkeley_Wetlab: Automated assembly of cell surface display devices

The University of California Berkeley iGEM team has developed an automated approach to large-scale parts assembly that is accurate, high-throughput, reduces labor, and decreases cost. As a test bed for our system we have chosen to explore novel applications of cell surface display within Escherichia coli, the gold standard organism for bacterial engineering. Displaying peptides and proteins on a cell's surface is difficult, and many attempts may have to be made to generate a given functional protein. By automatically generating and testing a large set of diverse proteins paired with various display methods, we can search a large design space and develop guidelines for rational design of projects involving surface display.

Team BIOTEC_Dresden: Temporal and spatial control of protein synthesis by in vitro recombination inside picoliter reactors

Manufacturing functionalized proteins in vitro poses a challenge, as it requires coordinated molecular assemblies and multi-step reactions. In this project we aim to control, over time and space, the production of proteins tagged with a silver-binding peptide for in situ silver nanoparticle nucleation inside microdroplets generated by microfluidic devices. Combining a transcription-translation system with protein coding genes and a recombination logic inside microdroplets provides spatial control. Moreover, in the microfluidic chamber we can pinpoint the beginning of synthesis, and easily track and isolate the droplets. Site-specific recombination generates a molecular timer for temporal control of protein synthesis. Unlike transcriptional regulation, this method gives true all-or-none induction due to covalent modification of DNA by Flp recombinase. Determining the transfer curve of inter-FRT site distance versus average recombination time allows the onset of gene expression to be predicted. We then apply this Flp reporter system as a powerful PoPS measurement device.

Team Bologna: T-REX: Trans-Repression of Expression. A BioBrick gene-independent control of translation

The project aims to realize a device with standard biological parts for the post-transcriptional control of gene expression, regardless of the gene sequence to be silenced. We designed the T-REX device, composed of two non-coding DNA sequences: the TRANS-repressor and the CIS-repressing parts. TRANS-repressor acts as a silencer of CIS-repressing RNA target. This target includes a region complementary to the TRANS-repressor sequence antisense, ends with RBS, and is assembled upstream of the coding sequence to be silenced. Upon binding of TRANS-repressor and CIS-repressing RNAs, the access to RBS by ribosomes is hampered, silencing translation. Accordingly, the amount of TRANS-repressor controls the translation rate of the regulated gene. The TRANS-repressor sequence was determined by a computational analysis performed to minimize the interference with the genomic mRNAs and to maximize the base-pairing interaction to the CIS-repressing RNA. The T-REX device is proposed as a universal and fast switch in synthetic gene circuits.

Team British_Columbia: Development of a modular, analog E. coli biosensor

To date, efforts to design a whole-cell biosensor capable of detecting levels of one or more biological inputs and responding in an analog mode has been elusive. We have designed a system of synthetic constructs implemented in an E. coli chassis that will allow detection of continuously varying levels of a single metabolic input and report on the concentration with qualitative output depending on threshold levels of the input. Our system design utilizes RNA-level hairpin hybridization and antisense technologies linked to various reporters. Because our approach is modular and does not depend on either endogenous protein processing or exogenous RNA, we envision that such a system could find applications in many different fields, including environmental sensing, detection of diagnostic of therapeutic biomarkers, and systems biology.

Team Brown: Engineering Staphylococcus Epidermidis to Secrete Recombinant Histamine Binding Protein in Response to Changing Histamine Concentration

The 2009 Brown iGEM Team aims to treat allergic rhinitis (hay fever) by engineering Staphylococcus epidermidis to secrete a histamine-binding protein, rEV131, in response to elevated histamine concentrations during an allergic attack. rEV131 was cloned from a species of tick, Rhipicephalus appendiculatus. We are putting the rEV131 gene into an endogenous element of human nasal flora, Staphylococcus epidermidis. rEV131 will have a secretion tag specific for S. epidermidis. To synchronize rEV131 production with elevation of histamine concentration, we are computationally designing a novel histamine receptor. This histamine-responsive receptor will induce expression of rEV131. Although S. epidermidis is a non-pathogenic species, when it reaches a certain population threshold it produces potentially hazardous biofilms. To mitigate this concern, we have engineered safety measures that prevent excessive growth by repurposing S. epidmidis’ natural population sensor to cue each cell’s "suicide" when a population has reached a dangerous size.

Team Calgary: Reprogramming a Language and a Community

iGEM Calgary contributed a second quorum sensing (QS) system to the Registry. The Vibrio harveyi AI-2 QS signalling system has been engineered in Escherichia coli . Coupled with quorum quenching, our system allows us to target biofilm maintenance. The robustness of AI-2 signalling in E. coli was characterized in the lab and compared to data from mathematical models of the system built using the Matlab Simbiology toolbox and the emerging Membrane Computing framework in Mathematica. We also undertook community outreach projects in order to enhance the synthetic biology community. Specifically, the Second Life platform was used to create an educational tool to train future synthetic biologists in an accessible, user-friendly, virtual environment. Moreover, we examined the implications of our project in light of the recently proposed proactionary and precautionary frameworks with special focus on ethical, environmental, economic, legal and social (E3LS) impact.

Team Cambridge: E. Chromi: Triggering Pigment Production in E. Coli

Previous iGEM teams have focused on genetically engineering bacterial biosensors by enabling bacteria to respond to novel inputs, especially biologically significant compounds. There is an unmistakable need to also develop devices that can 1) manipulate the input by changing the behaviour of the response of the input-sensitive promoter, and that can 2) report a response using clear, user-friendly outputs. The most popular output is the expression of a fluorescent protein, detectable using fluorescence microscopy. But, what if we could simply see the output with our own eyes?  The Cambridge 2009 iGEM team is engineering E. coli to produce different pigments in response to different concentrations of an inducer.

Team CBNU-Korea: Essarker: An Essential Remarker for a Minimal, Synthetic Genome

It is challengeable to create a synthetic genome for fulfilling the needs of energy and food. Without the assistance of computing tools, moreover, it would be much more difficult to make the synthetic genome. We here propose a key tool to help the creation of a genome as the essential step. The goal of Essarker is to help users design a minimal genome synthesized through the fundamental frame comprising the essential genes of replication. Essarker is a standalone software to manage and retrieve required sequences of genomes, and explore the essential gene order and direction and the related orthologous genes. It also identifies and visualizes the positions and orientations of genes. In addition, it shows optimal ordering of essential genes and orthologs by statistical analysis.

Team Chiba: E. coli Time Manager Since 2008

Since 2008, we have been constructing the bacteria timer that "work together". The mechanism is very simple; (1) the "Transmitter cells" generates the signal molecules, whose concentration gradually increases, (2) when it reaches a certain level, the "Receiver cells" switch on the expression of any given genes. Precise control of the time of delay of this entire process, one can pre-set the time of expression of genetic functions in a predicable manner. By using Asyl-Homoserine Lactones(AHLs) that can freely pass through the cell membrane as signal molecules, the time can be shared, in real time, by all cells within the pot. This way, receiver (timer) cells would take the action all at once in right timing, minimizing the distribution in each cell's response time. This year, we are trying to make a platform for generating an animated pictures using series of new timer cells we have constructed.

Team CityColSanFrancisco:

We at CCSF have begun constructing a bacterial powered battery. The design has been generated with sustainability in mind, and aims to create an alternative to traditional fossil fuel technologies. The battery owes its capabilities to two strains of bacteria: the heterotroph Rhodoferax ferrireducens, and the photoautotroph Rhodopseudomonas palustris. Each strain will occupy its own concentration cell and after being cultured anaerobically, will either oxidize (in the case of R. palustris) ferris iron or reduce (in the case of R. ferrireducens) ferric iron. The resulting current will be collected and used to demonstrate the functionality of the battery. The reduction and oxidation reaction will be self-substaining. This process is further aided by the genetic modification of R. palustris. As a photosynthetic prokaryote, R. palustris generates glucose readily. We intend to share this glucose with R. ferrireducens by inserting a passive glucose transporter into the cells of R. palustris.

Team Cornell: Engineering the Bacillus Subtilis Metal Ion Homeostasis System to Serve as a Cadmium Responsive Biosensor

The goal of our project is to create a whole cell cadmium biosensor by attaching cadmium responsive promoters in Bacillus subtilis to fluorescent reporter proteins. Cadmium is a toxic heavy metal which has no known biological function. Ingestion of cadmium contaminated water can induce bone fractures and severe renal damage. Major sources of cadmium contamination include fertilizers, sewage sludge, manure and atmospheric deposition. Cadmium contaminated sewage is often used for irrigation purposes in many parts of the world, especially in developing nations. Crops grown in these contaminated soils are then sold in markets without any detoxification treatment. Current analytical methods such as atomic absorption spectroscopy, though highly sensitive, are significantly more expensive than bacterial biosensors and are unable to measure the amount of bioavailable cadmium.

Team DTU_Denmark: The redoxilator, and the USER fusion assembly standard

The Redoxilator: By in silico design and computer modelling followed by gene synthesis, we have constructed a molecular NAD/NADH ratio sensing system in Saccharomyces cerevisiae. The sensor works as an inducible transcription factor being active only at certain levels of the NAD/NADH ratios. By the coupling of a yeast optimized fast degradable GFP, the system can be used for in vivo monitoring of NAD/NADH redox poise. A future novel application of the system is heterologous redox coupled protein production in yeast. The USER fusion standard: Another part of our project is the proposal of a new parts-assembly standard for Biobricks based on USER(TradeMark) cloning. With this technique, not based on restriction enzymes, all parts independent of function can be assembled without leaving any ‘scars’ from the restriction enzyme digestions.

Team Duke: One-Step Construction of a Bioplastic Production Pathway in E. coli

A convenient ligation-free, sequence-independent one-step plasmid assembly and cloning method is developed [Quan J, Tian J (2009) Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways. PLoS ONE 4(7): e6441]. The strategy, called Circular Polymerase Assembly Cloning (CPEC), relies on polymerase extension to assemble and clone multiple fragments into any vector. Using this method, we are able to quickly assemble a metabolic pathway consisting of multiple enzymes and regulatory elements for the production of a biocompatible as well as biodegradable plastic polymer in E. coli.

Team Edinburgh: Defusing a dangerous world: a biological method for detection of landmines

Landmines left over from past conflicts are a major hazard in the world, killing and maiming many people every year. We have sought to engineer a bacterium able to detect TNT and its degradation products, nitrites, in the environment. Our system is based around a previously published computationally designed TNT-sensing protein derived from the periplasmic ribose binding protein, which interacts with an EnvZ-Trg transmembrane hybrid fusion protein and a nitrite-responsive repressor to trigger a pathway of TNT degradation and visualization using combined output from a bacterial luciferase and Yellow Fluorescent Protein. We envisage that the detection system could be applied by spraying the organism on soil where the presence of landmines is suspected, and detecting luminescence using low-light sensing. Once located, the mines could be safely removed. This system could be extended to detect other analytes in the environment.

Team EPF-Lausanne: E. Colight

Recent discoveries of photoreceptors in many organisms have given us insights into the interest of using light-responsive genetic tools in synthetic biology. The final goal of our project is to induce a change in gene expression, more specifically to turn a gene on or off, in a living organism, in response to a light stimulus. For this we use light-sensitive DNA binding proteins (or light-sensitive proteins that activate DNA binding proteins) to convert a light input into a chosen output, for example fluorescence, through a reporter gene such as RFP. Demonstrating that the light-induced gene switch tool works in vivo would show that easier and faster tools can potentially be made available in several fields of biology, as such tools can induce more localized, more precise (time resolution and reversibility) and drastically faster genetic changes than currently used ones, thus allowing research to evolve even better.

Team Freiburg_bioware: Universal endonuclease – cutting edge technology

Gene technology is driven by the use of restriction endonucleases. Yet, constraints of limited sequence length and variation recognized by available restriction enzymes pose a major roadblock for synthetic biology. We developed the basis for universal restriction enzymes, primarily for routine cloning but also with potential for in-vivo applications. We use a nucleotide cleavage domain fused to a binding domain, which recognizes a programmable adapter that mediates DNA binding and thus cleavage. As adapter we use readily available modified oligonucleotides, as binding domain anticalins, and as cleavage domain FokI moieties engineered for heterodimerization and activity. For application, this universal enzyme has merely to be mixed with the sequence-specific oligonucleotide and the target DNA. Binding and release are addressed by thermocycling. We provide concepts for in-vivo applications by external adapter delivery and activity regulation by photo switching. Additionally, an argonaute protein is engineered towards a DNA endonuclease.

Team Freiburg_software: SynBioWave – A Collaborative Synthetic Biology Software Suite

Synthetic Biology, which aims at constructing whole new genomes, is pushed forward by many users and relies on the assembly of genetic elements to devices and later systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We are building a software environment enabling multiple distributed users to analyze and construct genetic parts and ultimately genomes with real-time communication. Our current version demonstrates the principle use as well as the power of the underlying Google Wave protocol for collaborative synthetic biology efforts. Many wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico. The initial developments of 'SynBioWave' lay the ground for basic layout, calling and data exchange of wave-robots in a clear and open process, so that future robots can be added and shared easily

Team Gaston_Day_School: Development of a Red Fluorescent Nitrate Detector

Increasing levels of fertilizer required for mechanized farming can result in elevated nitrate levels in soil and groundwater. Due to contaminated food and water, humans are at risk for Methemoglobinemia caused by enterohepatic metabolism of nitrates into ammonia. This process also oxidizes the iron in hemoglobin, rendering it unable to carry oxygen. Infants in particular are susceptible to Methemoglobinemia, also known as “Blue Baby Syndrome”, when formula is reconstituted using contaminated water. In order to prevent Methemoglobinemia, it is essential to detect high concentrations of nitrates. Fnr-NarG is an aerobic mutation of the nitrogen-sensitive promoter NarG that was provided by Dr. Lindow at UC Berkeley. By combining Red Fluorescent Protein with an aerobic mutant strain of NarG, the creation of Red Fluorescent Nitrate Detector (RFND) is possible. RFND is economically efficient because of its ability to self-replicate.

Team Groningen: Heavy metal scavengers with a vertical gas drive

Heavy metal pollution of water and sediment endangers human health and the environment. To battle this problem, a purification strategy was developed in which arsenic, zinc or copper are removed from metal-polluted water and sediment. In this approach Escherichia coli bacteria accumulate metal ions from solutions, after which they produce gas vesicles and start floating. This biological device encompasses two integrated systems: one for metal accumulation, the other for metal-induced buoyancy. The uptake and storage system consists of a metal transporter and metallothioneins (metal binding proteins). The buoyancy system is made up of a metal-induced promoter upstream of a gas vesicle gene cluster. This device can be changed to scavenge for any compound by altering the accumulation and the induction modules. The combination of both systems enables the efficient decontamination of polluted water and sediment in a biological manner.

Team Harvard: Interspecies Optical Communication Between Bacteria and Yeast

Optical communication is central to interactions between many multicellular organisms. However, it is virtually unknown between unicellular organisms, much less between unicellular organisms of different kingdoms of life. Our team has constructed a system that allows for interspecies, bacteria-to-yeast optical communication. To permit bacteria to send an optical signal, we expressed in E. coli a red firefly luciferase under IPTG induction. In yeast, we used a yeast-two-hybrid-system based on the interaction between the red-light-sensitive Arabidopsis thaliana phytochrome PhyB and its interacting factor PIF3. Interaction between PhyB and PIF3 is induced by the red light from the bacteria, resulting in transcription of the lacZ gene. This is an excellent demonstration of the principles and potential of synthetic biology: this system not only allows for interspecies optical communication, but enables us to optically bridge a physically separated canonical lac operon using light as a trans-acting factor.

Team Heidelberg: Spybricks - a starter kit for synthetic biology in mammalian cells

Mammalian synthetic biology has a huge potential, but it is in need of new standards and a systematic construction of comprehensive part libraries. Promoters are the fundamental elements of every synthetic biological system. We have developed and successfully applied two novel, in silico guided methods for the rational construction of synthetic promoters which respond only to predefined transcription factors. Thus, we have been able to create a library of promoters of different strength and inducibility. To characterize the promoters, we have developed standardized protocols for comparable measurements of promoter strength by either transient or stable transfection. These synthetic promoters can be used as “spybricks” which enable the construction of assays for simultaneously monitoring several pathways in a cell. However, the potential of synthetic promoters goes far beyond this application: e.g. in virotherapy, these promoters could be used for selective gene expression in target cells.


Team TU Delft: Bacterial Relay Race

In our project, we aim at creating a cell-to-cell communication system that allows the propagation of a set of instructions coded on a plasmid, and not just binary information as in quorum sensing. To achieve this goal, we have designed a communication system based on three different modules: a conjugation system, a time-delay genetic circuit, and a self-destructive plasmid.
Cell-to-cell communication systems are important because, in most synthetic biology applications, the desired tasks are generally accomplished by a population of cells, rather than by a single cell. The proposed communication system could be used for creating a distributed sensors network, or it could help to better understand and possibly reduce antibiotic resistance in bacteria.
Furthermore, we have conducted a survey to study the perception on synthetic biology and related ethical issues, among iGEM participants, students and supervisors. We have focused on the top-down and bottom-up approaches as applied to biology.

Team Groningen: Heavy metal scavengers with a vertical gas drive

Heavy metal pollution of water and sediment endangers human health and the environment. To battle this problem, a purification strategy was developed in which arsenic, zinc or copper are removed from metal-polluted water and sediment. In this approach Escherichia coli bacteria accumulate metal ions from solutions, after which they produce gas vesicles and start floating. This biological device encompasses two integrated systems: one for metal accumulation, the other for metal-induced buoyancy. The uptake and storage system consists of a metal transporter and metallothioneins (metal binding proteins). The buoyancy system is made up of a metal-induced promoter upstream of a gas vesicle gene cluster. This device can be changed to scavenge for any compound by altering the accumulation and the induction modules. The combination of both systems enables the efficient decontamination of polluted water and sediment in a biological manner.

Team PKU_Beijing: Conditioned Reflex Mimicking in E.coli

We are engineering our E. coli cells to process the correlation information of two enviornmental signal, similar to the process of conditioning in higher orgamisms. We have constructed and tested a series of AND gates which can sense the two signals: the conditioned and unconditioned stimuli. With the presence of both signals, the AND gate outputs a repressor protein and then changes the state of the bistable switch, which acts as a memory module. In this way, our E. coli cells can convert the information about the concurrence of the two signals into its memory. After the memory module is switched and given the "conditioned stimulus", the E. coli cells will pass the information to the reporter module and thus exhibit the "conditioned response."