Ideation Timeline

Parkinson's Disease

Parkinson’s Disease is a truly debilitating neurodegenerative disorder, caused by misfolding of a protein known as alpha synuclein in the dopaminergic neurons of the brain. However, an early diagnosis followed by prompt treatment can significantly alleviate the impact of the disease and improve quality of life. After looking for early biomarkers of the disease, we found a study that identified misfolded alpha synuclein in the gut tissue of patients 20 years before the onset of symptoms.

Based on this, we did a thorough literature review about various diagnostic tools that can be deployed in the gut, ranging from stool samples to even quantum dots! Additionally, we studied the biochemistry of alphasynuclein in detail, looking for a reaction pathway that could be harnessed as a diagnostic tool. Crucially, we were trying to develop a non-invasive technique, since all the previous studies used highly invasive biopsy samples to identify misfolded proteins.

We decided against this idea, since the research connecting myenteric alphasynuclein misfolds to eventual onset of Parkinson’s is in the nascent stage. Additionally, integrating synthetic biology into our solution would most likely require a genetically modified bacterium to interact with the myenteric plexus. This is a biosafety and biosecurity hazard and not a very realistic approach. Additionally finding a model system to work with would have been challenging, since we are dealing with a very specific mammalian cell type in which the biomarker is localized.

Heavy Metal Extraction From Water

We realized that the release of factory effluents, containing many harmful components and heavy metals, was a growing issue. To identify water bodies contaminated with such substances, we proposed the use of bioluminescent proteins from Vibrio fischeri. This bacterium uses a lux-operon to produce an enzyme known as luciferase to elicit bioluminescence. However studies observed that the bioluminescence was inhibited and had changed characteristics when the bacteria was cultured in media laced with various heavy metals.

This changed response could be used to rapidly identify polluted water based on the change in luminescence of V. fischeri compared to a standard.

Biofilm Disintegration

Biofilms are ubiquitous. They are present everywhere – in construction sites, under the soil and even inside the body. In the latter case, they can be very difficult to treat, since most drugs have no effect due to the structure of biofilms. An external matrix of exopolysaccharides (EPS), among other cellular secretions, surrounds the core of the biofilm. This gives the persistor cells bound to the surface exceptional resistance to all kinds of redressal mechanisms, even antibiotics.

For humans, biofilms can cause significant problems if they form in surgical equipment, implants of other parts of the body. They can only be removed manually since and drugs have a very small effect. When the biofilm matures, the bacteria migrates to other locations, forming a new biofilm.

We proposed to use a “bacterial drill” to destroy biofilms and the bacteria forming them. A modified carrier organism would be equipped with enzymes that can lyse the EPS secreted by the persistor cells. Due to these this enzymes, a hole would be drilled through which the carrier organism gains access to the persistor cells. On contact with these cells, the carrier would express genes for a cocktail of antibiotics, which would destroy the biofilm at the source by killing the persistor cells.

However, finding a chassis microbe that could carry the metabolic burden of carrying so many genes proved to be an issue. We would also have to link the carrier to move towards the center of the biofilm through some sensing mechanism, which we could not identify. Most of all, an eventual issue would be the release of such a GMO in the body, due to the inherent risks.

Breakthrough

We recognized our problem identification approach to be haphazard. Our advisors very kindly reminded us of our motivation to pursue an iGEM project—the desire to bring about tangible good while doing cool science. Therefore, we made the conscious decision to set our eyes homeward even as our ambitions rocketed skywards.

Eutrophication, as we slowly learned, was an all-pervasive problem. Bengaluru was drowning in a cesspool of its own filth.

We then turned to the possible causes of the problem. Across water bodies, research groups and researchers, one culprit was common: nitrate leaching. Tracing the roots of the problem led us to the roots of plants; more specifically, the fertilizers used to help these plants grow. Read more about this issue and how we chose to tackle it in our project overview.

Mapping the road ahead

To build a comprehensive project, we required a framework outlining everything we needed to keep track of. We reached out to Aayushi, Aditya, and Anirudh—all prominent contributors to their own iGEM teams in the years past. Having consolidated their advice, we built a skeleton of a plan. Step one was the identification of milestones.

The path ahead was treacherous and littered with question marks. It did not help that the entire team was first-year undergraduates, a unique situation we described to the VIT-Vellore team on their podcast. Since we had an idea of the problem we wished to tackle, we built a roadmap to keep us on track.

While the plan has been altered multiple times as our iGEM cycle progressed, we have tried to stick to the broad goals of the initial framework. To see how it has evolved alongside us, head on over to our experimentation page.