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Jamboree/Project Abstract/Team Abstracts
From 2008.igem.org
Alberta NINT
Project Logi-col[i]: Terminator/Attenuator anti-sense Logic (T/AasL)
Two major hurdles facing the development of complex genetic logic circuits are device connectibility and device extensibility. Connectibility refers to the ability to connect the output of one device to the input of another device, while extensibility refers to the dual abilities to rationally design new devices and combine multiple devices in one organism. Our project uses terminator/attenuator (T/A) hairpin sequences (gates) to control transcription and anti-sense RNA as input/output signals to/from the devices. We call this approach Terminator/Attenuator anti-sense Logic (T/AasL – pronounced “taw‑ssel”). It solves the connectibility problems of common protein-based approaches because the anti-sense output of one device is used to disrupt formation of T/A hairpin structures of downstream devices, thus activating them. In addition, because RNA secondary structures can be rationally designed (using our m-fold derived analysis program) we can readily construct a large family of devices with minimal cross-talk for inclusion in a single cell.
Bay Area RSI
Differentiation and Targeting of Stem Cells to Infarcted Cardiac Tissue
Every year over 1.2 million people suffer myocardial infarction. The resulting heart damage requires new approaches for effective repair. Stem cell therapies provide hope. However none of the stem cell therapies currently in clinical trials addresses the need for efficient stem cell targeting to cardiac tissue or the need to replace efficiently dead tissue with new cardiomyocytes. To address these problems, we have built several genetic circuits that work sequentially to repair the heart. First, we have built an inducible differentiation circuit that closely resembles the endogenous differentiation pathway, to program cells to become cardiomyocytes. Second, we have built circuits that use the extracellular domains of chimeric proteins to target cells to damaged cardiac tissue. Upon binding, novel receptor-coupled intein-mediated signaling domains activate effector genes that then aid in integration, inhibition of cell death, and the alteration of the tissue microenvironment.
BCCS-Bristol
Bacto-Builders
Assembling particles at microscopic scales into desired patterns or structures is usually difficult or impossible. All construction projects require the manipulation of varying size components, many much larger than any individual. To make this possible, teams of individuals work together towards a common goal. To find out how to transfer this behaviour to our ``Bacto-Builders, we investigate the possibility of using large numbers of E. coli to perform a task too great for any individual cell. Specifically, this involves the physical movement of particles through direct contact with a swarm of bacteria working together in a co-ordinated manner. The ultimate goal is to engineer the bacteria to follow a set of simple rules, so that collective behaviour emerges, and particles are assembled into a desired pattern. Furthermore, patterns or structures could be evolved in real time with bacteria adapting to new dynamic requirements or autonomously forming new structures.
Beijing Normal
Intelligent PCBs detector and degrader
Polychlorinated biphenyls (PCBs) are a group of organic pollutants that are persistent when released into the environment. Our task is to design an effective as well as intelligent PCBs degrader. According to the recent research, ortho-chlorinated PCB metabolites (DHBs) are potent and physiologically significant inhibitors of DHBD, so we design a feedback activation pathway to increase the BphC transcription and expression under a 2, 3-DHBP and 4-CB inducible promoter Ppcb. As dihydrodiols and dihydroxybiphenyls are very toxic to bacterial even after short incubation time, we design a feedback repression pathway use sRNA components— sodB and rhyB. As to the sensor part, dihydroxylated PCBs are substrate of the clcA-encoded chlorocatechol dioxygenase and thus induce the clcR and related promoter, so we use this as the sensing system. T7 amplification system is added to the downstream to amplify the signal.
Bologna
Ecoli.PROM: an Erasable and Programmable Genetic Memory with E. coli
The project aims to design a bacterial reprogrammable memory with genetically engineered E.coli colonies in solid medium working as an array of binary memory cells. To engineer bacteria we designed a genetic flip-flop composed of a binary memory (toggle switch) and an UV sensitive trigger. We chose UV to have a fine spatial selectivity in programming the cells and IPTG to reset the memory. We designed a circuit with high UV sensitivity by computer-model analysis. Core elements of the genetic memory are two mutually regulated promoters, designed as independent operator sites flanking a constitutive promoter. Thus, promoter transcriptional strength and repressor binding affinity can be independently fixed. Operator libraries for LacI, TetR, Lambda and LexA repressors were cloned as BioBricks to allow the rational design of regulated promoters that is still lacking in the Registry We expect this approach to be a benefit in many Synthetic Biology applications.
Brown
Toxipop: Conductance Measurement of Cell Lysis as a Reporter of Toxin Presence
Around the world, primarily in third world countries, contamination of drinking water is an immense problem that is difficult and expensive to detect with current technology. As such, there is a need for an economically feasible, transportable, and user-friendly detection system for water contamination that can reliably be used in the field. Our goal was to design and implement a novel biosensor with the ability to detect the presence of certain water contaminants and report that information back via a change in the conductance of a bacterial solution. An inducer specific promoter transcribes and leads to the translation of a "Lysis Gene Cassette." The subsequent lysis of the bacteria results in an increase in the solution's conductivity, indicating the presence of the inducer.
BrownTwo
A Genetic Limiter Circuit in S. cerevisiae
Numerous disease states in multicellular organisms involve anomalous expression patterns of endogenous genes. Tumor growth, associated with the overexpression of oncogenes, is one vexing example in which this occurs. While extremes of gene expression can damage living systems, normal expression is necessary for healthy function. We have designed a modular genetic circuit to limit the expression level of a gene of interest to a user-defined, tunable threshold. The limiter network reacts to the transcription of an endogenous gene within each cell, entering a regulatory state only where and when the rate of transcription lies beyond an acceptable range of activity. Along with its potential therapeutic utility, we offer our device as a foundational tool for researching gene expression in a eukaryotic model.
Calgary Ethics
An exploration of ethical, environmental, economic, legal and social (E3LS) issues of synthetic biology
Synthetic biology is a rapidly advancing field of scientific and technological inquiry. To reach its full potential its (E3LS) issues have to be investigated in a proactive and foresight manner. We are the first iGEM team focusing exclusively on investigating synthetic biology (E3LS) issues. We pursued various projects: a) development, distribution and interpretation of two online surveys, one for high school- one for non-high school students; b) development of an online course on synthetic biology (E3LS) issues; c) dialogue with the University of Calgary wetware iGEM team and the University of Guelph iGEM team about (E3LS) issues attached to their respective projects; e) involvement in the Synthetic Biology 4.0 Poster “Forward-Engineering a Regulatory Framework for Synthetic Biology: How Existing Regulatory Architecture Could Lend to the Creation of Our Own” by Laura Dress from the University of Maryland.
Calgary Wetware
Quorum-coupled Bacteriocin Release: Engineering a Champion
Microorganisms use pheromones to interact amongst themselves and with other microbial species in a process known as Quorum Sensing. In a similar sense, we have exploited the natural communication systems involving Autoinducer-1 (AI-1) from Vibrio fischeri and Autoinducer-2 (AI-2) from Vibrio harveyi, to create a model biosensor system in Escherichia coli. We have engineered the genetic circuits necessary for the production of these pheromones into two populations of E. coli (termed Bad guy #1 and Bad guy #2, as per their respective Autoinducer). In addition, our third population of E. coli (termed Champion cell) acts as a biosensor by receiving these signal inputs and subsequently initiating transcription of specific E. coli-targeted bacteriocins (i.e. colicins) in tandem with specific fluorescent proteins. The presence of AI-1 induces the Champion to produce a colicin to which Bad guy #1 is susceptible, but to which Bad guy #2 is resistant, and vice-versa for AI-2.
Caltech
Engineering multi-functional probiotic bacteria
The human gut houses a diverse collection of microorganisms, with important implications for the health and welfare of the host. We aim to engineer a member of this microbial community to provide innovative medical treatments. Our work focuses on four main areas: (1) pathogen defense, either by expression of pathogen-specific bacteriophage or by targeted bursts of reactive oxygen species; (2) prevention of birth defects by folate over-expression and delivery; (3) treatment of lactose intolerance, by cleaving lactose to allow absorption in the large intestine; and (4) regulation of these three treatment functions to produce renewable subpopulations specialized for each function. Our research demonstrates that synthetic biology techniques can be used to modify naturally occurring microbial communities for applications in biomedicine and biotechnology.
Cambridge
Cambridge iBrain: Foundations for an Artificial Nervous System using Self-Organizing Electrical Patterning
We have developed a system which creates spatially organised electrical features in a genetically identical bacterial population, allowing for simulation of action potentials and other complex phenomena. This system generates electrical potentials in bacterial cells using artificially formed potassium gradients, released upon chemical stimulation. We have designed the genetic circuitry to establish a two-component Reaction-Diffusion system involving the well-characterised Lux and Agr signalling pathways, and we have modelled the intercellular interactions between these pathways to produce complex self-organising designs known as Turing patterns. To support this system we have developed the gram-positive bacteria Bacillus subtilis as a BioBrick chassis, including direct chromosomal single-copy insertion, peptide signalling, and BioBrick-compatible vectors for expression in both gram-negative and -positive bacteria. We have also tested a new assembly method for rapidly generating constructs by joining multiple PCR fragments. This work can serve as a foundation for future advances involving cellular patterning, signalling, and self-organisation.
Chiba
E.coli time manager
We control the timing of gene expression by using multiple signaling devices. To this end,we utilize molecules associated with Quorum sensing, a phenomenon that allows bacteria to communicate with each other. Our project uses two classes of bacteria: senders and receivers. Senders produce signaling molecules, and receivers are activated only after a particular concentration of this molecule is reached. Although different quorum sensing species have slightly different signaling molecules, these molecules are not completely specific to their hosts and cross-species reactivity is observed. Communication using non endogenous molecules is less sensitive, and requires a higher signal concentration to take effect. This results in slower activation of receivers.
CPU-NanJing
Adding new notes to the song of life / Customizing a biomacromolecule
In our project, we designed a novel device by which we could insert different unnatural amino acids into a certain site in target protein expressed in E coli. Of course these unnatural amino acids would bring some new characteristics of the target protein. #2: In our project, we intend to design a device which composed of a bio-timer and alternatively expressed two glycosyltransferases. The timer could be controlled by the concentration of the inducer, and the glycosyltransferase are in charge of synthesizing the polysaccharide. As a result, the molecular weight of polysaccharide could be controlled by concentration of the inducer. By exchanging glycosyltransferase, this device would provide a useful tool to obtain different polysaccharide with certain molecular weight.
Davidson-Missouri Western
E. nigma: XOR Gates, a Bacterial Hash Function, and Viz-A-Brick
The team designed, modeled, and constructed a bacterial computer that uses XOR logic to compute a cryptographic hash function. Hash functions are used to authenticate the integrity of a document by computing its digital “fingerprint,” an integer value that can be compared to the publicized value. Our bacterial computers recognize the presence or absence of two chemical signals, converting biological information into binary numbers. Given a starting “key” and a binary message of arbitrary length, various configurations of the designed system produce the hash function output. Mathematical modeling of these computers has shown that our hash functions are difficult to corrupt. We also produced a graphical interface for exploring the Registry of Standard Biological Parts called Viz-A-Brick (http://gcat.davidson.edu/VizABrick/), and other web-based tools to improve the construction of new parts with BioBrick ends (http://gcat.davidson.edu/iGEM08/tools.html).
Duke
Attacking the plastic waste problem: a two-pronged approach
Faced with the issues of plastic waste accumulation and environmental pollution, a two-pronged approach with the potential to solve these problems has been developed. Firstly, biologically produced plastics such as polyhydroxyalkanoates (PHAs) are superior to petroleum-based plastics because they are both biodegradable and biocompatible. By focusing on modulating the ratio of two PHA monomers, 3-hydroxybutyrate and 4-hydroxybutyrate, the copolymer poly(3HB-co-4HB) can be created featuring increased elasticity and utility over any particular PHA monomer. Secondly, a novel polyethylene-degradation pathway is being engineered based on the oxidation of long-chain alkanes by alkane monooxygenase LadA. The region inhibiting the binding and catalysis of polyethylene has been computationally identified and site-directed mutagenesis is being conducted at this region to yield a mutant of LadA that oxidizes polyethylene and thereby increases its biodegradability. The combination of the production of an eco-friendly bioplastic with the degradation of petroleum-based plastics is a promising method of waste reduction.
Edinburgh
A weapon of mass nutrition: The conversion of waste cellulosic biomass into starch and beta-carotene
Cellulose, in the form of biomass, is the ultimate renewable resource, and its conversion to starch would provide a hugely abundant source of material which could be used for the manufacture of biofuels or other biological products, as an animal feed supplement to release grain for human food use, or even as the basis of a food for human use. Given the present food and energy shortages, the advantages of such a process are clear. With this in mind, Edinburgh iGEM 2008 have devised systems for E. coli to degrade cellulose into glucose, to upregulate glycogen and terpenoid production, and to convert glycogen into starch. We have also designed software capable of generating a model in SBML format from a list of genes and promoters entered by the user. This is supported by a background database allowing users to build models based on published data.
EPF-Lausanne
Genetic network generating spatial patterns through cell-cell communication and controlled information processing
Biological systems are unique in their ability to combine information and energy to generate complex entities. Genetically encoded networks drive many of these patterning processes. Furthermore, developmental studies have highlighted the importance of gradient formation and cell-cell communication for the generation of cellular patterns in the early stages of life. It has been shown that simple networks can form both static and dynamic patterns. Nonetheless, a system whose pattern formation is dependent on combinations of multiple signals has yet to be demonstrated. Here we address this question by designing a network, involving two different quorum-sensing based signaling mechanisms. Upon introduction in E.coli, the system can sense the relative amounts of two input molecules. Using a pre-define set of rules which was selected on its ability to generate spatial patterns, the cell can then express its final state by emitting red or green fluorescence and transmit its state to its neighbors.
ESBS-Strasbourg
Cell Cycle Dependent Toggle Switch in Eucaryotic Cells: Approach to a Binary Cell Division Counter
Our team aims to establish a regulatory network over several cell generations in budding yeast. This model organism as chassis offers ideal conditions as it has been the primary source for studies on the cell cycle. More specifically, we want to construct a toggle switch that is triggered by cell cycle dependent factors. The construction consists of two subassemblies of identical composition, each with a positive feedback loop for the own expression pattern and a repression of the competing module. Switching is achieved by directed degradation of transcription factors at a specific time frame within the cell cycle. This should result in a binary expression pattern like for example GFP expression in every other cell cycle (0-1-0-1). The system shall be extendable by adding further "bits" of similar construction (e.g. for the second bit the pattern 0-0-1-1). The device would thus be an approach to a binary cell division counter.
ETH Zurich
Make yourself simpler, stupid! Or how engineering a self-minimizing cell leads to the Minimal Genome
This year's ETH Zurich project tackles a fundamental problem of synthetic biology: the minimal genome. Exploring the minimal set of genes that is able to support life is a question of significant biological interest. Additionally, one of the main complications when implementing genetic circuits is possible cross-talk with endogenous pathways. Thus, an organism carrying a minimal genome would provide a simple chassis for biological engineering. Our approach is based on an iterative cycle of genome reduction and strain selection. We propose a novel method to randomly delete chromosomal fragments by controlled expression of restriction enzymes and ligases in vivo. Furthermore we develop a chemostat-based selective condition for cells having a smaller genome by constraining nucleotide availability. Computationally, we analyze the genome for optimal cutting sites, and perform flux balance analysis on a genome scale model to predict growth of reduced genome strains. Finally, we simulate the restriction enzyme control circuit and the selection mechanism.
[Team:Freiburg | Freiburg]]
Modular Synthetic Transmembrane Receptor Systems Interfaced with Nano Breadboards
Signaling through membranes is a characteristic of life. Transmembrane proteins control proliferation, differentiation, and cellular response and are key for the formation of multicellular organisms. Controlling such proteins enables modifying cellular behavior and ultimately programming cells at will. The complex rules for transmembrane signaling often require engagement of several proteins in a fine-tuned spatial and temporal manner. To tap possibilities of transmembrane programming, the Freiburg 2008 iGEM team provides an extensible system comprising an external framework with spatial resolution, a concept for modifying natural receptors, and a modular set of fusion-Biobricks for the construction of synthetic receptors. Spatial resolution in nanometer scale is provided by DNA-Origami modified with distinct patterns and combinations of ligands. Receptors are decoupled from their natural ligands by fusion with artificial binding domains. The Biobrick collection contains signal sequences, binding domains, transmembrane domains, and effector domains featuring split enzymes and split fluorescent proteins for immediate readout.
Groningen
Conway's Game of Life in Real Life
Conway's Game of Life is a simple cellular automaton famous for generating complex "life-like" patterns. The goal of this project is to explore the possibility of implementing cellular automata, particularly the Game of Life, as a regular spatial arrangement of bacteria. Communicating the number of neighbors is implemented using the well-known HSL quorum sensing system. A novel component is the circuit implementing the automaton's ruleset, to determine the state to switch to upon detecting "too few" , "enough" or "too many" neighbors. This "interval switch" was designed and implemented by altering the binding site affinity of the signal molecule complexes to correspond to the levels of HSL coming from the neighbors. Finally, the "ON" state of the cells is indicated by GFP production and production of new HSL signals, and the "OFF" state by their absence. The system was implemented partially in vivo and we have developed in silico models.
Guelph
Reprogramming microbes to cater to or silence their hosts: beta carotene production and RNAi delivery
In humans microbes help digest our food and produce vitamins to supplement our diet, while plants such as corn harbour microbes within their tissues, which can extend the metabolic capacity of their host. In order to exploit these patterns of microbial habitation, we attempted to modify the broad host range plasmid pDSK-GFPuv to contain either a synthetic operon of metabolic genes belonging to the soil microbe /Erwinia uredovora/, or Biobrick compatible RNAi constructs targetting expression of either GFP or corn TB1 genes. These plasmids were to be electroporated into either probiotic /Escherichia coli/ /Nissle //1917 /or endophytic/ Klebsiella pneumonii /342. Assays will then show whether a genetically modified enteric microbe could be made to produce vitamin A in a modelled human intestine, or whether a common corn endophyte could stably express and deliver RNAi signals against expression of GFP and corn TB1 genes while living inside a growing corn plant.
Harvard
BACTRICITY*: Bacterial Biosensors with Electrical Output
The metabolically versatile bacterium Shewanella oneidensis adapts to anaerobic environments by transporting electrons to its exterior, reducing a variety of environmental substrates. When grown anaerobically and provided with lactate as a carbon source, S. oneidensis transfers electrons to an electrode of a microbial fuel cell. We sought to engineer S. oneidensis to report variations in environmental conditions through changes in current production. A previous study has shown that S. oneidensis mutants deficient in the mtrB gene produce less current than the wildtype strain, and that current production in these mutants can be restored by the addition of exogenous mtrB. We attempted to control current production in mtrB knockouts by introducing mtrB on lactose, tetracycline, and heat inducible systems. These novel biosensors integrate directly with electrical circuits, paving the way for the development of automated, biological measurement and reporter systems. *Bacteria As Current Transmitters Report Induced Changes Important To You
Hawaii
A BioBrick toolkit for cyanobacteria
We aim to extend the current BioBrick registry to a greater range of organisms, including cyanobacteria. Cyanobacteria are studied for their ability to produce useful compounds, including biofuels and biopolymers. These "little green factories" require only salts, light, water, and carbon dioxide for photoautotrophic growth. A cyanobacterial "toolkit" would enhance our ability to utilize this system. We designed: 1) mobilizable broad-host range BioBrick vectors derived from RSF1010, 2) a cassette for protein secretion from Synechocystis sp. PCC 6803, and 3) a nitrate-inducible cyanobacterial promoter BioBrick. Our toolkit was designed for conjugative gene transfer from Escherichia coli to Synechocystis to achieve the controlled production and recovery or bioproducts, demonstrable by induced secretion of green fluorescent protein. Though our parts were targeted for work in cyanobacteria, they may be compatible with other Gram-negative systems including Agrobacterium, which is capable of plant transformation.
Heidelberg
Ecolicence to kill: Engineering E.coli for targeting pathogenic microorganisms
Microbial communities known as biofilms are particularly resistant to conventional therapies. Biofilm formation depends on signalling molecules called autoinducers. Our aim is to exploit this communication mechanism by engineering synthetic bacteria that are able to target harmful autoinducer-secreting species and to kill them. We engineer “killer” E. coli cells having two complementary modules: The “sensing module” comprises the modification of E. coli’s chemotaxis system to make killer cells move towards a prey-secreted autoinducer stimulus. The “killing module” ensures that once in the vicinity of the prey, at high levels of the stimulus, a bacteriocidal mechanism is activated. In our model system, autoinducer-secreting “prey” cells are represented by a second E. coli strain. We further developed computer models that show the dynamics of both modules and probe the efficiency of the system in defined spatial environments. Future directions include adjusting the system to target real pathogens or even cancer cells.
HKUSTers
Does God play dice with the cell?
Stochastic fluctuation in a cellular context and the lambda-phage bifurcation have been extensively studied. However, from a bottom-up synthetic aspect, we aim to exploit the cellular "noise" to build an E. coli version of a computational device, the "Random Number Generator". One random binary digit can be generated by capturing an initial Polymerase binding event with a pair of mutually exclusive promoters. Reciprocal inhibition using two repressors shall achieve unilateral expression of the "switch", with fluorescence reporters indicating the probability of each alternative occurrence. Balancing the two sets of affinity and kinetic parameters and maintaining a single copy of this synthetic device integrated into the bacterial chromosome shall improve performance. If successful, coupled with other reporters we envision multiple extensions of this "Randomizer", including a Memorizer that utilizes a hierarchy of XOR-calculations to "store" a multi-digit random number, and intriguing pattern generation involving chemical gradients and random "population behavior".
iHKU
Formation of new patterns by programming cell motility
The ability of living organisms to form patterns is an untapped resource for synthetic biology. The HKU iGEM2008 team aims to generate unique patterns by rewiring the genetic circuitry controlling cell motility. Specifically, E. coli cells are programmed to autonomously regulate their movement by sensing local cell density. Interesting patterns are formed by two types of newly engineered cells. The high cell-density motility-off cells spread outwards and spontaneously form a distinctive ring of low cell density surrounded by rings of high cell density whilst the high cell-density motility-on cells form a Fuji-mountain-like structure. Moreover, we build a theoretical model that satisfactorily fits our current experimental data, and also predicts some parameters which may significantly affect the ring formation. The study of this self-organized spatial distribution of cells helps us to understand principles underlying the formation of natural biological patterns, and synthetic non-natural patterns have various potential applied uses.
IIT_Madras
StressKit: A BioBrick library of Lac-repressed σ24, σ28, σ32 and σ38 promoters for Escherichia coli
Regulated gene expression is an essential part of the synthetic biologist's toolkit. Bacteria have evolved 'generalized stress responses' which generate genome-wide changes as responses to globally-integrated information. Specific types of stress upregulate specific 'alternative σ factors', which activate transcription by binding to nucleotide signatures at the -10 and -35 boxes of their cognate promoters. We set out to design, construct, and validate a library of σ dependent promoters for E.coli, with the following specifications: the promoters must conform to the BioBrick standard; they must be modular so they can be used multiply in devices; and they must be LacI repressed but σ dependent, off by default but behaving like native σ dependent promoters in the presence of IPTG. We're currently characterizing the library of promoters (σ24, σ28, σ32 and σ38) against the unmodified Lutz-Bujard promoter, using spectrophotometry and fluorescence microscopy.
Illinois
Cell-based and in vitro antigenic sensors for medical diagnostics
The unifying motivation behind our research this year is the creation of novel diagnostic tools for medicine: we are conducting three parallel research projects to create cell-based and in vitro biosensors. We are engineering a bimolecular fluorescence system in which two halves of a fluorescent protein, each fused to an antigenic epitope, will bind to the two sites on an antibody in human serum to cause a detectable fluorescent signal when antibodies against this specific antigen are present. These proteins can be produced in bulk through a bacterial expression system. We are also pursuing similar diagnostic objectives using a eukaryotic system; we are designing strains of yeast able to respond specifically to immunogenic epitopes or antibodies, and activate a fluorometric or enzymatic response accordingly. We are fusing antibodies against immunological targets to cell surface receptors of transcriptional signaling pathways, which would become activated only in the presence of these pathogens.
Imperial College
Designer Genes – Biofabricator subtilis
The Imperial College iGEM Team has constructed a genetically engineered Biofabricator, using the Gram-positive bacterium Bacillus subtilis, with application from BioCouture to tissue engineering. Our Biofabricator subtilis is designed to produce self-assembling biomaterials using light as a trigger, and it achieves this in three stages: (i) based on the principles of holography and an endogenous light-sensing mechanism, our engineered bacteria is captured at desired locations; (ii) next, bacterial locomotion is suspended by using a recently-discovered clutch mechanism that disengages the flagellum from the motor protein; (iii) finally, once bacteria are stationary, biomaterial production is triggered leading to self-assembly and the formation of bio-scaffolds at specific locations.
Johns Hopkins
The Yeast Sex Detector: Visual Mating Type Determination System for S. cerevisiae
A haploid S. cerevisiae yeast cell is either mating type ‘a’ (MATa) or mating type ‘α’ (MATα). In the elucidation of biochemical and genetic processes in yeast, it is often necessary to initiate sporulation of diploid yeast cells. The meiotic products of sporulation are four haploid cells; two MATa and two MAT α. To continue analysis, differentiating between the haploid cells is often crucial, and the necessary assay can take 2 to 3 days. Our detector, consisting of fluorescent proteins that are preferentially expressed depending on the mating type, will cut this time to seconds. Simply shining a UV lamp over the cells will reveal the mating type, allowing for the cells to be easily separated. This device could assist most yeast geneticists on a daily basis, as well as aid in the study of HO strains of yeast that switch mating-type at every mitotic division.
KULeuven
Dr. Coli, the bacterial drug delivery system
Imagine a bacterium that produces a drug when and where it is needed in the human body. It would have several advantages over classical drugs and could have many medical applications. In this framework we proudly present our team's project: Dr. Coli, the bacterial drug delivery system. Dr. Coli senses the disease signal and produces the appropriate amount of drugs to meet the individual patient's needs. And when the patient is cured, Dr. Coli self-destructs. To do this, a molecular timer registers the time since the last disease signal sensed. But when the disease flares up again, this timer is reset and drug production is resumed. Within the time frame of the iGEM competition, we developed a proof of concept of Dr. Coli. The most important assets are massive reuse of standard biobricks, different control mechanisms and extensive modeling.
Kyoto
Cells as physical power suppliers: Raise the Titanic!
In many biotechnological contexts, bacterial cells are considered as "chemical facilities." A number of studies have genetically engineered cells to produce various desired compounds. They further aim at accurate and precise regulation of material production. Cells are also power suppliers in terms of their motility. This aspect, however, has been much less featured. Here comes our project, which started with the gigantic goals of lifting up the Titanic from the deep-sea with bacterial power. Toward our general goal – to engineer cells to carry larger order of objects – we have been designing and constructing cells so that these micro-order entities can move a centimeter or larger objects. We have equipped E. coli with the functions of attachment to an object surface, cell density dependent buoyancy production, and regulatable flagella and examined by quantitating the parameters to what extent our goal is achieved. Our study presents the possibility of bacterial physical power.
LCG-UNAM-Mexico
Singing bacteria: Controlling Escherichia coli's nickel efflux pump
Our project is to make bacteria sing. This will be achieved through the control of E. coli's nickel efflux pump, RcnA. The main idea is that a change in the concentration of extracellular nickel will translate into a change in the medium's conductivity, which we will measure. This will be read by a computer and, depending on the value, emit a sound. This way, bacteria are "singing"! The RcnA gene is placed under the control of phage lambda's CI repressor, which is itself produced in the presence of AHL and LuxR. LuxR is produced constitutively in the cell, so the addition of AHL will be the input signal and limiting step. The final objective is to express the extent of RcnA's repression (and so the extracellular nickel concentration) as a function of AHL present in the cell.
Lethbridge CCS
Ligase-Independent Cloning as a Standard for BioBrick Preparation
While there is an established BioBrick format, there is not yet a standard method for turning a gene of interest into a BioBrick. Ideally, such a standard method would be easily adopted, even by amateurs, and would lend itself to automation. A significant drawback of several existing techniques is their dependence on ligase treatment, which is often problematic. We propose a ligase-independent cloning (LIC) method, based on the technique of Aslanidis & de Jong (1990), as a possible standard for novel BioBrick preparation. Instead of short overhangs and ligase treatment, LIC uses long overhangs to circularize plasmid vectors for transformation without the use of ligase. The LIC method reduces the number of enzyme steps required for cloning, thus lending itself to easy adoption, automation, and real biological 'engineering.'
Melbourne
Building a temporal controller in E. coli using red-light sensor and riboswitches
This year Melbourne iGEM competition team seeks to build a temporal controller in E. coli. The idea is to build a system, which is modular and should have all components in the form of biobricks, which expresses gene(s) at a specific time in a sequential manner. In this study, we show the design, modeling and some experimental results towards a proof of principle of the system. The design uses the leverage of existing biobricks of red light bacterial photography system, positive feedback loops and riboswitches. We propose that the architecture presented should scale well with increasing number of genes to be temporally regulated. It is anticipated that such system will be useful in metabolic engineering because enzymes can be turn on and off in a sequential manner.
METU Turkey
Light Controlled Metal Carrying E. coli
Heavy metal contamination of drinking water is a major problem in many developing countries. It requires expensive techniques to get rid of these contaminants. In this project we aimed to develop metal cleaning techniques which (1) should be cost effective (2) and should not let further contamination in course of cleaning. By using available systems from the nature we tried to develop a bacterial machine which can bind/release heavy metals and whose movement can be controlled by providing specific light wavelengths. To accomplish our aims we introduced metal binding proteins and bacteriorhodopsin to control pH which are located on the extracellular surface of membrane and phototactic capability to control movement by light.
Mexico UNAM-IPN
Design of an experimental device to detect events of horizontal gene transfer in Escherichia coli
Horizontal gene transfer is an evolutionary mechanism that contributes to the acquisition of new genetic material among organisms; as such it helps bacteria to acquire antibiotic resistance and other genetic devices. The main goal is to design a devise that would detect events of horizontal gene transfer among bacteria. Genetically modified E. coli were monitored until a detectable sign appears in the media, indicating an event of horizontal transfer. In order to detect such events, we will use plasmids as the genetic material that could be transferred in a bacterial culture.
Michigan
Circadian Clocking... in E. Coli
The human body's "clock" regulates the daily cycles of many physiological and metabolic processes, such as the sleep?wake cycle and feeding rhythms. It is controlled by the interplay of numerous molecular factors that orchestrate complex feedback loops and processes that are fundamentally mediated by gene expression and the events that follow it. We are working on constructing a synthetic clock, affectionately deemed "The Sequestilator," that is analogous to the mammalian clock. Our clock consists of two parts: an activator with constitutive expression and a promoter that drives the production of a repressor that binds and "sequesters" the activator away from the promoter. While intuitively it seems that this system may reach a steady state rather than oscillate, simulations have shown that under certain rapid equilibrium and tight binding conditions, this circuit does exhibit oscillations. We are currently involved in building and testing of this device.
Minnesota
Minnesota, Hats Off To Thee: Bacterial suicide, comparator and computer-aided synthetic biology
The University of Minnesota is sending their first team to the iGEM competition this year. Our group is composed of two subgroups: Team Comparator and Team Timebomb, each of which is working on an individual project. Team Timebomb is working to engineer a bacterial clock, based on which bacterial cells will 'commit suicide' after a predetermined number of divisions has been reached. Team Comparator is engineering a bacterial comparator, which is one element of a feedback controller. Team Comparator is also developing two computational tools: the SynBioSS Designer and the SynBioSS Wiki. SynBioSS stands for the Synthetic Biology Suite, which is freely available at synbioss.sourceforge.net . It is a suite of algorithms for automatically generating, storing and retrieving networks of reactions, which can model and simulate BioBricks gene networks. Computer-aided synthetic biology at its best!
Tsinghua
Modeling and reconstruction of the Escherichia coli chemotaxis system/Construction of a Polyhydroxyalkanoates(PHA) production induced-lysis cell
1：Inspired by the chemotaxis system of bacteria, we isolated and reconstructed a set of genetic modules in order to reconstitute an independent and interchangeable chemotactic device used as pollutant detector. Novel cybernetics terms and methods are introduced in while in silico modeling together with related softwares are also established to simulate the effects.
2：In this project we are going to establish a novel bacteria strain which will sense the production of PHA, a degradable material used in environmentally friendly plastics. The key of this construction is to find a link between the amount of PHA particles and gene expression. A wildtype circuit and an artificial device are combined together to achieve this purpose. Lysis genes from phage are introduced to break the cell and release the particles.
University of Lethbridge
The "Bacuum" Cleaner - an intelligent self-propelling keener cleaner
Tailing ponds used to store discarded waste from oil refineries pose a major environmental dilemma. Our goal is to create modified E. coli capable of seeking out and degrading toxic aromatic pollutants created during the oil refinery and mining processes. Our "Bacuum" cleaner will respond to a destructive compound through interaction with a programmable riboswitch. The riboswitches will switch at varying concentrations of target ligand, thus altering the induced signal. At low concentrations, we intend to have our riboswitch express the motility protein cheZ in E. coli, directing the bacterium towards higher concentrations of our target molecule. Once it reaches a threshold concentration, a catabolic pathway capable of degrading our target pollutant will be activated. To create these riboswitches we plan to use SELEX to reprogram the theophylline riboswitch. We chose 2-chlorobenzoate, a compound related to polychlorinated biphenyls (PCBs), as our target molecule.
