WELCOME TO PENN STATE iGEM 2014!

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Our Lab Information

• Escherichia coli, DH10B
• Pseudomonas putida, KT2440
• Pseudomonas fluorescens, B2

Sam demonstrating BSL-1 laboratory PPE

The Risks of Our Projects Now

What are the risks to the safety and health of lab members?

What are the risks to the safety and health of the general public (if any biological materials escaped from your lab)?

What are the risks to the environment (from waste disposal, or from materials escaping from your lab)?

What are the risks to security through malicious mis-use by individuals, groups, or countries

What measures are you taking to reduce these risks? (For example: safe lab practices, choices of which organisms to use.)

The Risks of Our Project in the Future

What new risks might arise from your project's growth? (Consider the categories of risk listed in parts a-d of the previous question: lab workers, the general public, the environment, and malicious mis-uses.) Also, what risks might arise if the knowledge you generate or the methods you develop became widely available?

CODON OPTIMIZATION PROJECT:

A great success in the field of codon optimization would allow for the optimization of genes at the codon level that were previously considered difficult to repress, tune, or even express at all. The ability to break these barriers would allow researchers, industry specialists, and possibly unauthorized individuals the ability to tune the expression of genes expressed by altering them at the codon level. It is foreseeable that companies generating biological products such as medicines that are coded by weakly expressed genes could find a way to generate stronger genes that code for the exact same products. Because any gene could be optimized in this manner, it is also theoretically possible that the production of toxins or other dangerous biologically produced molecules could be increased - as with any synthetic biology technique. This scenario is not likely, and does not carry significant risk for several reasons. FIrst, alternative methods of increasing output of metabolic pathways are already extant, and the use of codon optimization as a tool for doing so would not be the easiest, quickest, or most cost effective method. Second, to codon optimize a gene, large scale DNA synthesis equipment and know how is required, and any group sending a dangerous genetic element for codon optimization would have to go through the additional layer of security of a commercial entity, and would thus be even less likely to use our method.

An interesting application of our project, if it were to truly allow for much more efficient optimization of existing genetic systems, is that scale up of biomolecule production could be done much more quickly than is now possible. This is significant because it is foreseeable that in the future a rare chemical or medicine derived from biological sources could require rapid scale up, and the ability to quickly optimize coding sequences could be extremely valuable.

BIODETOXIFICATION PATHWAY PROJECT:

Our strains of Escherichia coli and Pseudomonas putida are engineered to be unable to survive outside of the laboratory and we use antibiotics to prevent other bacteria from growing. However, if our materials should ever become contaminated with wild-type bacteria, they could potentially transfer antibiotic resistance markers between hosts. We are inserting the neomycin resistance marker into the genome of P. putida and intend to remove it via homologous recombination in a second round of cloning. If that sample becomes contaminated, it is theoretically possible that other bacteria could acquire this antibiotic resistance. The late stage goal of this project is to engineer E. coli with a pathway to degrade the furfural toxin, which would allow it to survive in the presence of furfural and also metabolize it for energy. At a larger scale we could unknowingly be selecting for a more robust bacteria if any wild-type E. coli was ever able to acquire the pathway or antibiotic resistance markers.

Does your project currently include any design features to reduce risks? Or, if you did all the future work to make your project grow into a popular product, would you plan to design any new features to minimize risks? (For example: auxotrophic chassis, physical containment, etc.) Such features are not required for an iGEM project, but many teams choose to explore them.

CODON OPTIMIZATION:

Since transgenic organisms almost always grow slower than their wild type counterparts, our hosts, shackled with a metabolically demanding reporter gene such as GFP would stand little chance at reproduction in the wild. In addition, by knowing the sequence of DNA in the plasmid harboring the fluorescent gene, measures could be taken to disable the transcriptive or translational machinery in these organisms. We are committed to making this data available to anyone who would require it.

BIODETOXIFICATION:

The biodetoxification project currently uses an auxotrophic strain of E. coli, in which it cannot grow without leucine. In the future we would intend for others to use similarly auxotrophic strains for biofuel production. If a strain of E. coli was engineered that it could live on furfural, this facility would have to be kept separate from other facilities producing furfural and other furan derivatives. E. coli could survive and grow in the presence of furfural and could contaminate stocks for other applications.

Our Equipment

Thermocycler for Digestions and PCR's

Incubator Shakers

Centrifuge

Table Top Centrifuge

Tecan

Nanodrop

Electroporator