Team:CCA San Diego/Experiments

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Experiments

A description of the research, experiments, and protocols we used in our iGEM project.

All characterization and measurement data for our parts is on the corresponding Registry part pages.

Project Development

Horizon 2.0, a continuation of last year's Horizon project, focused on the degradation of toxic compounds of oil spills known as PAHs (Polycyclic Aromatic Hydrocarbons), while striving to produce clean biohydrogen energy as a result. Horizon 2.0 officially kicked off in February 2019. First, our team conducted an extensive literature review to deepen our understandings of PAHs, biohydrogen energy, and plasmid assembly techniques such as Golden Gate and Gibson (see Project Design). We also investigated ways of testing several aspects of our project, such as the MATLAB modeling of our pathways as well as using H2 Blue and a scanning fluorometer for various measurements (see Measurement).

Our next order of business was to design our constructs and degradation pathways. With the aid of websites such as Uniprot, we were able to successfully construct these, and also test them theoretically using MATLAB's Symbiology tool (see Modeling). We were extremely fortunate to be able to receive lab space and invaluable guidance from the J. Craig Venter Institute (JCVI), a renowned bioinformatics research center here in San Diego. The main parts of our lab were conducted in July-October, ranging from the tweaking of the aforementioned constructs to the Gibson assembly of plasmids and subsequent bacterial transformations and observations.

One key aspect of our project's development was the idea of using a bioreactor. Inspired by scientists and public concerns about the potentially harmful impacts of E. Coli in the oceanic ecosystems, we successfully 3D modeled and designed a bioreactor. The integration of the bioreactor helped provide a safe and controlled environment for PAH degradation, thus eliminating concerns from our target communities about side-effects. The bioreactor also gave us the ability to simulate both aerobic and anaerobic respiration with our E. Coli, allowing the the simultaneous processes of PAH degradation and biohydrogen production. This switch between respiration types was also coded by our team using C++ and Arduino (see Software). Our team has also applied for a patent on the aforementioned bioreactor (see Entrepreneurship).

Overall, due to the large-scale negative impacts of oil spills such as the Deepwater Horizon Oil Spill and a local one near our community, our iGEM team was inspired to create Horizon 2.0 - a project aiming to degrade toxic compounds in PAHs while producing biohydrogen as a by-product.