Davidson/Missouri Western iGEM2008

Davidson College - Missouri Western State University

iGEM 2008

iGEM 2006 Useful Information

The University of Calgary 2006 iGEM team is working on the following project. A petri plate is inhabited by two strains of genetically engineered E. coli bacteria. The first strain---the Senders---have been engineered to emit two chemical signals into the plate environment: Aspartate and Acyl Homoserine Lactone (AHSL). The senders themselves are activated by light. The second strain---the Receivers---have been designed to respond to each of these signals in a different way. The Receivers express Green Fluorescent Protein in the vicinity of AHSL. The Receivers also move towards areas of greater Aspartate concentration. The same bacteria also decrease Aspartate levels where they are present, as this is a nutrient and constitutes the reason for why they are attracted to it in the first place. Our goal is to make the Senders and Receivers create interesting behaviour dynamics visualized by fluorescent patterns.

http://parts.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM2006&group=iGEM2006_Calgary

Berkeley: networks of cells communicating via conjugation; demonstrated the transmission of a coded message

http://parts2.mit.edu/wiki/index.php/University_of_California_Berkeley_2006

“We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessable by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.”

Mexico: cellular automata

http://parts2.mit.edu/wiki/index.php/IPN_UNAM_2006

“We wish contribute to the iGEM project development various protein based bio-components. We will work along three main lines: complex and reversible dynamical systems and formal languages, that support particles and multiple reactions, related to the molecular transformations.”

“We study two-dimensional cellular automaton, where every cell takes states 0 and 1 and updates its state depending on sum of states of its 8 closest neighbors as follows. Cell in state 0 takes state 1 if there are exactly two neighbors in state 1, otherwise the cell remains in state 0. Cell in state 1 remains in state 1 if there are exactly seven neighbors in state 1, otherwise the cell switches to state 0. CA governed by such cell-state transition rule exhibits reaction-diffusion like pattern dynamics, so we call this Diffusion Rule.”

“Using the diffusion rule we can generate a dynamical pattern over a system, like turn on/off ligth with alive o dead cells that shows a luminescence, examples include fluorescence, bioluminescence and phosphorescence.” “Starting with any configuration, the cells alive are represented in yellow (the activator) and dead in black (the inhibitor), see figure 4. The system is created defining an inicial state over the base configuration (see figure 3). The luminescence is obtained by the evolution of this initial pattern.”

Brown:Bacterial Freeze Tag http://parts.mit.edu/wiki/index.php/Brown:Bacterial_Freeze_Tag#Overview 2006 igem

This project involves programming bacteria to be able to play a game of freeze tag. Bacteria will be engineered to swim around a microfluidics device until they reach a certain proximity to the 'IT' cell and then they will lose their ability to move. This loss of motility will be combined with a change in color from Green to Blue. When another bacterium, which is moving (not the 'IT' cell), reaches a certain proximity to the 'frozen' bacteria it will again regain its ability to move and turn from Blue to Yellow.

TetR promoted with LuxI downstream. LuxI is an enzyme that produces AHL and will produce the red fluorescent protein (RFP). The AHL produced is exported from the cell where it then forms a complex with the LuxR protein that is produced by the AHL sensor within the Receiver cell.

The AHL sensor is TetR promoted and forms the LuxR protein which then forms a complex with AHL. This LuxR and AHL complex then activates the pLuxR promoter. Downstream of the pLuxR promoter is the LacI protein. LacI inhibits the pLac promoter on the "Freeze Machine".

A promoter that is regulated by LacI will promote the production of LasI, MotB, and cI. This will subsequently inhibit the production of CFP and LasR. In the presence of LacI, however, MotB, LasI, and cI will not be produced. CFP will therefore be produced along with LasR and LacI. This results in the "freezing" of the cell.

McGill University Split YFP http://parts.mit.edu/wiki/index.php/McGill_University_2006

The idea behind the project is fluorescence complementation, which involves the joining of two leucine zipper proteins, Fos and Jun, each fused to a half terminus of YFP. Originally, the Fos and Jun proteins were fused to a beta gene coding for a membrane protein. The project involved performing a PCR reaction to produce two inserts, the N-terminus and the C-terminus of YFP, and then ligating these inserts into 2 vectors, containing Jun-beta and the Fos-beta respectively. The two fusion proteins (Fos-beta-YFPC and Jun-beta-YFPN) were expressed in the cell membrane of two populations of E. coli. We then allowed these two cell types to combine, resulting—ideally—in the complementary binding of the Jun and Fos proteins when the cells are in close contact. Consequently, the two half YFP fragments bind to form full YFP, and the cells will fluoresce.

Penn State http://openwetware.org/wiki/IGEM:PennState/2006

The bacterial relay race takes advantage of an ability to control cellular motility using inducible promoters such as those involved in nutrient catabolism or quorum sensing. “Receiver” bacteria move in response to small-molecule signals either added to the system or originating from motile, “sender” strains. The most significant challenges relating to this project stem from difficulties of tightly controlling the target motility gene motB. Low levels of motB expression result in system failure (constitutive motility), and resolving this issue is essential to developing reliable modular systems that are the hallmark of synthetic biology

Tokyo http://parts.mit.edu/wiki/index.php/Tokyo_Alliance:_Conclusion

Our project is to make this Noughts-and-Crosses in vivo. -1. Inputs -1. Chemicals -1. To indicate each square -1. To be spreaded into all squares. -1. Outputs -1. Reporter of SYANAC: GFP Reporter of Human: RFP

We can say we will expand the number of regulator genes we can use to build logic gates and through this project we made simple constructing method.