Talk:Results

a bunch of stuff about the team: photo, abstract, link to wiki, embedded blip player. Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Cellular Lead Sensor: About 40% of the world does not have access to clean water. Lead is a major contaminant worldwide. In the US alone, over 1 million children ages 1 through 5 have elevated levels of lead in their blood. Current lead detection systems are expensive and require lab analysis. Home lead testing kits are inaccurate and only detect lead at very high levels. We have created a genetic circuit in E Coli that responds to lead. The promoter and lead binding protein we use are ten times more selective for lead than for other similar heavy metals. We have also incorporated a genetic amplifier into our circuit to allow us to detect fairly low concentrations of lead. Tristable Switch - The Tri-Stable Toggle Switch represents a continuation on the theme of the Toggle Switch begun by Gardner, et al to produce stable outputs in response to transient inputs. Applications such as a memory circuit and a drug delivery system are a few suggestions, but perhaps the most promising innovation lies in the design process. Our novel approach to the Tri-Stable Switch development is founded on quantitative principles, pioneering a technique to remove the guesswork from designing and debugging biological systems.

Electric Bacteria: The goal of our project is to use directed evolution to increase the current output of the electrogenic bacteria Shewanella oneidensis (affectionately referred to as Shewie in the Gardner Lab). As the name suggests, directed evolution consists of two main steps: intentionally mutating DNA and then selecting for the expression of desired traits. In the case of S. oneidensis, certain global transcription regulators in its genome have been identified as being related to the metabolic processes of the bacteria. These global transcription regulators will be mutated via error-prone PCR and transformed into S. oneidensis in hopes of altering current output. Bacteria that express greater electrogenic capability will then be selected via flow cytometry or other viable selection methods. This process of directed evolution can be repeated with previously selected S. oneidensis in order to increase the level of electrogenesis even further.

Cellular Lead Sensor - About 40% of the world does not have access to clean water. Lead is a major contaminant worldwide. In the US alone, over 1 million children ages 1 through 5 have elevated levels of lead in their blood. Current lead detection systems are expensive and require lab analysis. Home lead testing kits are inaccurate and only detect lead at very high levels. We have created a genetic circuit in E Coli that responds to lead. The promoter and lead binding protein we use are ten times more selective for lead than for other similar heavy metals. We have also incorporated a genetic amplifier into our circuit to allow us to detect fairly low concentrations of lead.
Tristable Switch - The Tri-Stable Toggle Switch represents a continuation on the theme of the Toggle Switch begun by Gardner, et al to produce stable outputs in response to transient inputs. Applications such as a memory circuit and a drug delivery system are a few suggestions, but perhaps the most promising innovation lies in the design process. Our novel approach to the Tri-Stable Switch development is founded on quantitative principles, pioneering a technique to remove the guesswork from designing and debugging biological systems.

Selection for Infection Our project attacks the following problem: can one engineer viruses to selectively kill or modify specific subpopulations of target cells, based on their RNA or protein expression profiles? This addresses an important issue in gene therapy, where viruses engineered for fine target discrimination would selectively kill only those cells over- or under-expressing specific disease or cancer associated genes. Alternatively, these viruses could be used to discriminate between strains in a bacterial co-culture, allowing strain-specific modification or lysis. This is clearly an ambitious goal, so we brainstormed a simple model of this problem suitable for undergraduates working over a summer. The bacteriophage λ is a classic, well studied virus capable of infecting E. coli, another classic model genetic sytem. We therefore seek to engineer a λ strain targeted to lyse specific subpopulations of E. coli based on their transcriptional profiles. Together, λ and E. coli provide a tractable genetic model for this larger problem, while hopefully providing lessons applicable to more ambitious, future projects.

Engineering cellular ommunication protocols: In order to engineer interesting and useful functions in biology, a robust and extensive range of intra- and inter-cellular signalling pathways must be available. By analogy with the Internet, where adoption of the standard TCP/IP communication protocol has enabled worldwide connectivity from supercomputers to refrigerators, such a system must be accessible to cells of different heritage and structure (different “operating systems”) with the potential for processing messages received and taking action dependent on their content. In the course of our project we identified and worked on candidates for both intracellular (PoPS Amplifier project) and intercellular (Peptide signalling project) communication pathways, and additionally made progress towards adding a new Gram-positive platform for synthetic biology to the Registry.

Shaping bacterial communities: Our iGEM project is to make a Marimo-ish gathering of bacteria. Marimo is a green spherical shaped algae, which is a popular living organism in Japan. It is considered a National Treasure because of its beautiful shape and its smoothness. Our system implementation assembles an affinity tag, communication module, size control. For years microbiologists have been using agar plates to isolate cells from each other. By spreading the diluted cells on a solid surface, we can make "colonies", dome-shaped gathering of genetically identical cells. Although convenient, this is only two-dimensional. What if we can create three dimentional (spherical) colonies with controlled/ defined size? Thus we can eliminate the plating process that everybody hates. Combined with the microfluidics devices, we might be able to pick, isolate, count, or innoculate each of the floating yet independent colonies to conduct routine works in future molecular biology Two cells are used in our system: AHL senders and receivers. Senders generates the affinity tags constitutively, while receivers generates them only when they are induced by AHL. The marimo-forming involves the following steps: (1) making the sender core by sticking with the affinity tag. (2) Insert the sender core into the receiver culture. (3) The sender core produces AHL, which make the near receivers to generate the affinity tags and GFPs. (4) The affinity tagged receiver sticks with the central sender core. This will continue until the AHL cannnot reach the marimo boundary. (5) When the AHL reached the marimo boundary, the adsorping stops, which makes a finite-sized marimo bacteria.

Light mediated behavior modulation in the fruit fly: The aim of this project is to engineer a behavior in the common fruit fly. It is well known that the fruit fly is capable of learning through reinforcement, and many experiments in classical and operant conditioning have been done to demonstrate the fly's capacity for learning and memory. By applying reward and punishment in the presence of certain neutral stimuli, the fly can make associations and learn to avoid or seek out these previously neutral stimuli. The current hypothesis in the literature is that, like humans, punishment and reward in insects are mediated by different neurotransmitters. It is believed that in insects, dopamine mediates punishment and octopamine (an invertebrate analog of norepinephrine) mediates reward. In our project we seek to further develop an existing method that allows for direct activation of these putative reward or punishment circuits by application of blue light to the intact animal. We hope to use this method to engineer defined, and even complex, behaviors in the fruit fly by using the blue light flashes to directly ‘reward’ or ‘punish’ behaving animals in real time.

A Microbial Biosensor Device Assembled with Ion Channels for Iron Detection under UV Irradiation and Different Levels of Oxygen: The Colombian-Israeli team is made up of students from different cities in Colombia and Israeli high school students. The students who are currently attending different universities pursue careers within the sciences and engineering. Each and every one of us has a different personal motivation that drives us in our daily work for this year's IGEM project. As a group, we also shar a motivation that brings us together withing our team: to put into useful practice our passion for biology, math and computer science but most of all, to be creative. We want to find new solutions and new ways of solving problems and overcoming obstacles found in science through synthetic biology. For this year's IGEM project, our team's objectives are to enhance the detection levels of the sensing device with the implementation of ion channels and to use these results as reference to develop other types of sensing devices to be used in different conditions. Biosensors are useful molecules and/or cellular tools that allow detection of the presence of different metals including iron (II/III) and other compounds, even at detection levels beyond the limits of conventional methods (Colombian IGEM. IET Synthetic Biology Journal. 2007). Last year, the Colombian IGEM team developed a microbial biosensor device for iron detection under UV irradiation using synthetic biology. This year, in association with the Israeli team, we will develop a more sensitive biosensor device, in order to detect different levels of iron, including those below that of 0.5 ppm. The device will also be tested at different levels of oxygen and UV irradiation. Plasmid isolation, preparation of competent cells and cell transformation are being currently carried out in the laboratory at the Universidad Agraria in Bogota, Colombia. New parts designed by the Colombian group as well as parts from the MIT BioBrick will be assembled, in order to construct the genetic machine. This year, sequences from both upstream and downstream will be used for our project. One of the main new features of our device will be exposed to different environmental conditions such as oxygen levels, temperatures and varied light intensities. As we carry out all of our experiments within our laboratory, we are also developing a mathematical and computational model.

Hamiltonian Path Problem: As a part of iGEM2006, a combined team from Davidson College and Missouri Western State University reconstituted a hin/hix DNA recombination mechanism which exists in nature in Salmonella as standard biobricks for use in E. coli. The purpose of the 2006 combined team was to provide a proof of concept for a bacterial computer in using this mechanism to solve a variation of The Pancake Problem from Computer Science. This task utilized both biology and mathematics students and faculty from the two institutions. For 2007, we successfully continued our collaboration and our efforts to manipulate E. coli into mathematics problem solvers as we refine our efforts with the hin/hix mechanism to explore another mathematics problem, the Hamiltonian Path Problem. This problem was the subject of a groundbreaking paper by Adleman in 1994 where a unique Hamiltonian path was found in vitro for a particular directed graph on seven nodes. We were able to use bacterial computers to solve the Hamiltonian path problem in vivo.

Bio-Powered Electricity and Light: This year's Duke iGEM team is interested in tackling problems associated with engineering bacterial systems to be easily controllable by clean, macroscopic inputs in order to create useful, macroscopic products. We became obsessed with trying to find solutions to these problems. We wanted to make bacteria we could control like a computer, with electric fields and light and heat. Not stopping there, we wanted to make bacteria that could generate their own electric fields, and their own heat, and after they'd been programmed, interacted, and formed networks, we wanted bacteria that could yield precise and complex materials. Of course, we broke this up into several smaller projects
* Electric field-activated transcription factor
* Bacterial communication with light
* Synthesis and property-control of bioplastics
* Bacterial solar fuel cell

Training E.coli: "All E.coli 's are equal, but some E.coli 's are more equal than others..." (freely adapted from "Animal Farm" by George Orwell) ... this is what George Orwell would have written, were he a synthetic biologist. In the E.coli colonies on petri dishes, all bacteria are equal; except for some special ones. Our project is about designing such special E.coli that are "more equal" than the rest: they have the ability to be trained in order to memorize and recognize their environment in the future. Their story will be presented through this wiki ...

Cling E-coli: This year Harvard's team consisted of eight undergraduate students, with backgrounds in molecular and cellular biology, biochemistry, engineering, and computer science. With the help of six faculty advisers and four teaching fellows, plus one education advisor, we devised and executed a single project with three subsections. Cling-E. Coli 1. Bacterial Targeting 2. Quorum Sensing 3. Fec Signal Transduction Our efforts were focused on engineering bacterial surface proteins to express peptides that will target bacteria to specific substrates. We then sought a biological read-out for whether the engineered bacteria interact with the substrate. For this purpose, we employed two distinct detection methods: quorum sensing and the Fec iron response system. By the end of the summer, we successfully demonstrated that bacteria expressing well-characterized tags on their surface could bind to specific substrates. Separately, we characterized the quorum system with multiple types of promoters and reporters, and we are on our way toward a combined targeting-quorum system in the near future. In addition, we are working on inserting random peptide libraries into the bacterial surface proteins; we will then screen for the ability to bind to a variety of substrates. Eventually, our project may have applicability in medical imaging and localized drug synthesis and release. Theoretically, if our project is successful, bacteria (or other microorganisms) could be targeted specifically to a certain tumor cell. At a certain density, quorum sensing may allow for the bacteria to emit a signal that could be detected by medical imaging devices. If the reporter gene encoded for drugs or vitamins, synthesis can also be evoked through enriched targeting. Furthermore, binding through a modified Fec system may allow for binding alone to transduce a signal and elicit a response in the cells.

Infector Detector: Our project tackles the ongoing problem of catheter-associated urinary tract infections. To do this, we looked at how infections develop - as biofilms - and designed a system which would be able to detect their presence. We have created a system which is capable of detecting one of the types of signalling molecules found in biofilms, AHL, and visibly report its presence by producing a fluorescent protein.

Solar Bacteria: The goal of the project is to produce bacteriochlorophyll by establishing a strong metabolic pathway in E.Coli. A generic metabolic pathway for chlorophyll synthesis in plants is given here (Generic Chlorophyll Biosynthesis). The biosynthesis of bacteriochlorophyll is similar; the part that our project focused on is shown here(Bacteriochlorophyll Biosynthesis). In order to channel the flux of carbon through the bacteriochlorophyll biosynthetic pathway, the flux through the first branch point between the native E.Coli pathway and the chlorophyll pathway must be optimized. The enzyme magnesium-chelatase is responsible for converting protoporphyrin IX to Mg-protoporphyrin IX. Because this reaction must occur to a large degree, we want to use an enzyme that has the most enhanced activity. Since all photosynthetic bacteria utilize very similar bacteriochlorophyll synthesis pathways, they all have their own versions of Mg-chelatase to perform the Mg-insertion reaction. A large part of the project is to subclone the genes for Mg-chelatse, for three photosynthetic bacteria—Rhodobacter sphaeroides (purple bacteria), Synechocystis sp. (cyanobacteria), and Heliobacillus mobilis (heliobacteria). After subcloning, the enzymes are overexpressed and their activities are measured. Besides the establishment of a strong initial input of flux through the bacteriochlorophyll photosynthesis pathway, we have also explored the latter parts of the pathway. These latter steps are crucial for catalyzing reactions that would lead to the final product—bacteriochlorophyll.

Modular two-gene oscillator Our project is a continuation of one of the projects we presented last year: a two-gene oscillator with an 'On' and 'Off' switch using LacI and LuxI. This simple relaxation oscillator could be used as a modular component for the synchronization of other complex oscillating systems such as the repressilator. Quorum-sensing coupling between cells is achieved with a diffusible autoinducer AI (AHL) made from LuxI which promotes the synthesis of LacI from pLux. As Lac accumulates, it represses pLac which controls the synthesis of LuxI.

3D light controlled "coliforming": The formation of complex scaffolds of extracellular matrix is one of the problems facing the emerging discipline of tissue engineering. One way to produce such scaffolds would be to have them secreeted by cells joined together in a three dimensional structure. We concieved the idea of using two light sources of different wavelength, impinging on a suspension of cells from differnt directions to induce the cells at their intersection to join to each other and thus create a three dimensional structure. Since we plan to implement the system in Ecoli we called it coliforming. Implementation of this concept requires two new biobricks of more general application and these are the focus of this year's submission to the Igem competition.
1. A new light receptor like the Red light receptor, but sensitive to a different wavelength. This is being developed based on work in the Spudich lab with Sensory RhodopsinII and by Alan Grossman with ComP (kinase), ComA(target) and PsfA(promotor) two component signalling system. Implementation is by dirrect sythesis of the required fusion genes, using the Geneart offer.
2. A protein generator for gas vesicles to make the suspension of cells neutrally bouyant. This is based on the work in the Cannon lab. Implemenation is by removal of restriction sites using site dirrected mutagenesis of Maura Cannon's plasmid and PCR primer based engineering of biobrick prefix and suffix.