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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
- 1: 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).
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.
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.
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.
