Jamboree/Project Abstract/Team Abstracts

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Revision as of 17:10, 1 October 2008

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.

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.

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