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Jamboree/Project Abstract/Team Abstracts
From 2008.igem.org
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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. | 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. | ||
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| + | ====[[Team:BCCS-Bristol | BCCS-Bristol]]==== | ||
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| + | ''Bacto-Builders'' | ||
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| + | 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. | ||
Revision as of 14:11, 9 October 2008
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.
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.
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.
