Tag: synthetic biology

Quorum Sensing and iGEM

As an electrical engineer, I’m used to being able to wire components together to get essentially interference free communication. In biological systems, this capability isn’t available. Cells communicate with each other mainly using proteins and other small molecules that diffuse through cell membranes. This means that all neighbors of a cell may sense whatever it’s transmitting, along the lines of wireless networks. Unlike wireless networks, cells don’t have IP addresses and their state is very stochastic. This makes effective cellular communication very difficult and inaccurate.

Quorum sensing seems to be the method most used by cells to communicate. In nature it’s just used to sense local concentrations of cells. This can be used by engineers to accomplish a variety of different tasks that require cells to work together.

Many iGEM projects this year deal with new ways of using quorum sensing. Many of the projects use quorum sensing to differentiate cells, while others use quorum sensing for environmental detection or generalized communication mechanisms.

Grenoble: Mercury Detection using E-coli

The Grenoble team created e-coli that switch from one state to another in the presence of mercury. If mercury is present, the cells become “sender cells” that produce a quorum sensing molecule. Cells where IPTG is dominant over mercury become “receiver cells”. These cells produce RFP if the concentration of the quorum sensing molecule is high enough. The layout of the cells causes only the receiver cells closest to the sender cells to turn red. This creates a visible indicator of the concentration of mercury in the sample.

USTC: Infection targeting anti-bacterials

The USTC-China team developed a genetic circuit that allows for differentiation of cells. Cells become either “sleeper” cells or “attacker” cells, and AHL quorum sensing causes a suitable percentage of the undifferentiated cells to become attackers. The attacker cells move towards a bacterial infection (of AIIS) through chemotaxis. When the concentration of the molecule produced by the AIIS infection becomes high enough, the attacker cells create pyosin, which causes them to die. Excess pyosin is released that kills the bacterial infection.

Monterey: Code interpretation through quorum sensing

The Monterey, Mexico team developed three different strains of e-coli. Each strain responds to a different wavelength of light by releasing a different quorum sensing molecule. The strains can communicate among each other through these quorum sensing molecules to determine which color light has been shone on them. By using bistable switches, it is possible to record the order of the light that was received.

Peking: Chemical wire toolbox

As part of their chemical wire toolbox, the Peking team developed a set of quorum sensing molecules that can be used to send signals between cells. Their goal was to create a number of orthogonal signal mechanisms to allow cells to communicate with each other without interfering with other routes of communications (basically creating the non-interfering wires I take for granted in EE).

Sevilla: Ubbit communication standard

The Sevilla team created a standard for information exchange among cells. Like the wire toolbox from Peking, the Sevilla Ubbit is a standardized communication mechanism among cells. The Ubbit is meant to be a synthetic quorum sensing molecule.

Interesting iGEM Projects

The UW just won the world championships for iGEM. iGEM is the international Genetically Engineered Machine foundation. They sponsor yearly competitions where university undergraduates can compete to build interesting genetic components (biobricks).

This seems like such a fun competition. I’m kicking myself for not getting involved in it when I was an undergrad. The UW team this year came up with some amazing genetic circuits to generate diesel in e. coli and grow proteases that break down gluten (not at the same time, these are two different projects).

It looks like there are a lot of other interesting iGEM projects from other schools, so I’ll list some of the ones that I like the most.

Bioremediation

Many modern manufacturing techniques result, either directly or indirectly (accidently), in the release of toxic chemicals into the environment. Several methods exist for dealing with this, such as dispersing the chemicals or attempting to collect and store them elsewhere. These methods are often ineffective or partially effective, and can take years to show results.

Bioremediation, which involves the use of special cells that interact with pollution, may offer a more effective solution. Several iGEM projects deal with this in some way. Some of the projects specifically attempt to create cells that would remove pollutants, while other projects make cells more robust to pollution. The latter property would make the cells more suited to bioremediation.

Panama

The Panamanian team worked on a biobrick that synthesizes rhamnolipids. These are surfactants that decrease the surface tension of water, allowing spilled oil to be recovered more easily. This may at some point be a more effective way to produce surfactants than the one currently used.

NYC_Wetware

The NYC_Wetware team focused on providing cells with radiation resistance. The hope is that radiation resistance could be used for bioremediation after nuclear accidents.

Lethbridge

The Lethbridge team worked to create a kit to clean up tailings ponds. Tailings ponds are storage ponds where oil refineries store toxic waste. The current methods of dealing with these tailings ponds can take years. The tailings pond cleanup kit produced by Lethbridge uses synthetically produced proteins to metabolize toxic organic compounds. Some heavy metals were induced to form nanoparticles, which can be removed with the generated biomass. They also looked at increasing the sedimentation rates in the ponds using cells expressing a specific antigen.

Queens Canada

The Queens Canada team worked on making multicellular eukaryotic organisms that could break down several pollutants. They modified the C. elegans nematode to sense and move towards specific pollutants. The worms also had genes inserted to detect and degrade naphthalene.

Removing Antibiotic Resistance

Two teams worked on using the CRISPR genes on bacterial DNA. These genes act as an immune system for the bacteria, giving them resistance to external plasmids and phages. Antibiotic resistance in some bacteria is due to the CRISPR mechanism.

Georgia Tech

The Georgia Tech team worked to add CRISPR fitness to non-antibiotic resistant strains of bacteria. Their hope was that this would allow the non-antibiotic resistant bacteria to outcompete the antibiotic resistant bacteria.

USC

Plasmids are can cause horizontal antibiotic resistance transfer among bacteria. By giving bacteria CRISPR resistance to certain plasmids, the USC team plans to create bacteria that cannot receive antibiotic resistance in this way.

Optical Signaling

University of Pennsylvania

The University of Pennsylvania team developed two different strains of Human Embryonic Kidney cells. One of the strains was engineered to produce light at 480nm, while the other strain was engineered to respond to incident blue light by producing blue light itself.

Vitamin Producing Yeast

Synthetic biology has the ability to improve the foods that we eat and make them more nutritious. Brewer’s yeast, one of the primary cell types used in the iGEM competition, is also used in the food production industry for breads, beers, and other foods. Since it makes such a good chassis for engineered pathways and is useful in food production, it’s a good vector to deliver manufactured molecules to humans.

Two teams focused on making yeast more nutritious.

Johns Hopkins

The Johns Hopkins team, for example, added genes to produce vitamin A and vitamin C to yeast. They then performed baking experiments to determine how easy their new yeast was to use in cooking.

Washington University in St. Louis

The Washington University in St. Louis also inserted genes for vitamin A into yeast. They also looked at the production of a similar molecule used in perfume manufacture.

Glucose Detection

Missouri Miners

The Missouri Miners team worked on biobricks to detect glucose in various concentrations. This has the potential to decrease the cost of blood sugar monitoring and increase the quality of life of many diabetics. In the long term, it could also be used to cause cells to produce insulin in the presence of glucose, which could lead to a more permanent cure of the disorder.