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Genesis
With the one year of experience in iGEM, this time we had the foundation laid for our second consecutive year. Unlike our first iGEM, this time we had experienced seniors to guide us. We started off with the initial and important component, team formation in a much organised way.
In the first place, a seminar was conducted for second year students to familiarise them with iGEM. Then another seminar was conducted to describe about our first iGEM project. Students were advised to read articles on synthetic biology to get a clear understanding. Then second years were called in for personal interviews for the selections. Selections were done separately for the wet lab and design teams. Finally, we had an enthusiastic and motivated team ready to rock the next iGEM.

Brainstorming

For facilitating the idea formulation process, the entire team of fourth, third and second years was divided into 5 groups, each composed of 1 fourth year, 2 third years and 2 to 3 second years. Mainly third and second years were involved in ideation and fourth years acted as a guide.
“Lost time is never found again”, Benjamin Franklin said, working under the deadlines is the optimal way we chose to prevent that. Deadlines were set for the ideation process and idea discussions. Each team used to discuss independently and brainstorm in regular sessions. By the end, each team was ready to present and defend their idea.
On the day of idea discussions, each team presented their idea to other teams and the fifth years. Each idea was subjected to rigorous inquisition and questioned for its feasibility and practicality, based on which the ideas were evaluated. After a week each idea was consolidated following the changes suggested and were made ready to present before professors.

Pitching

The extended presentations were given in front of the professors of the department. Many professors of the department were present during the presentations.The question answer session went on for 2 hours and every idea was deeply criticised. Professors stated that the ideas were very much embryonic and needed to be developed a lot. There seemed no hope, of any idea being accepted by the professors. However, after a long debate and improvisation, one of the ideas was selected for further development.
It was a crucial time for us to show our teamwork. The team was divided into 2 sub-teams. One for developing the idea and another for researching out the potential applications. Each team put their significant efforts for development of the idea by regularly meeting and brainstorming the possible changes that could be added to the idea. It was real teamwork in display then. Finally, the idea, augmented with in-depth study and analysis, was presented in front of the professors.

The hurdles in our journey

Our first iGEM was not a cakewalk for us, but it let us learn a lot in the school of hard knocks. This year, we started off with implementing the lessons learnt in our previous year. Our first focus was getting sponsorship as early as possible. So we gave corporate sponsorship a try. We formed teams and explored the possible ways to get the sponsorship. But the department refused to allow corporate sponsorship because of certain administrative difficulties. Then we had no option but to try getting sponsorship from the department itself as we did last year. But this year it was not fruitful. This was really sad and unexpected but still we were not disheartened.
Our hopes burst forth when we came to know about iBEC conducted by DBT. We applied for iBEC and started working hard to get the sponsorship money by participating and winning in iBEC. But DBT competition was late, and we had no way but to get the funds for registration from our institute.
We were counting days for the day of presentation. It was just some days before the final presentation day that DBT cancelled iBEC. Before we could try for another way to get sponsorship, DBT considered the proposal and iBEC was held. We did our best and finally the result was what we were expecting. We got the sponsorship and we were left in a state of euphoria.

Some papers which had seminal impact on progress of synthetic biology:

1. Genetic Toggle Switch in E.coli
Gardner, Cantor, and Collins designed an artificial toggle switch in E.coli using a set of 2 promoters and 2 repressors. Repressor 1 binds promoter 2 and represses it while repressor 2 does vice-versa. All the elements act in cis and are arranged on same plasmid as presented in figure. The 2 inducers used for moving from one state to another are IPTG and heat shock. The transition between states was observed using GFP expression which was activated in presence of IPTG.
Initially there is a basal GFP output. When IPTG is added, lac repressors gets inhibited and expression of heat sensitive repressors as well as GFP begins. These repressors binds strongly to its conjugative promoter and shuts down expression of lac repressors completely. After around 6 hours in their experimental setup GFP output reached the peak. To shut down GFP expression and revert back to original state a heat shock was induced which inactivates the heat sensitive repressors. This starts expression of lac repressors which soon overcome the already diluted IPTG in medium. In around 35 minutes GFP expression reaches back to normal. The experimental system was robust and hold for wide range of parameters tested.

2. Repressilator Circuit
Repressilator is considered to be a milestone in field of synthetic biology. This was first example of developing artificial genetic network with new functional properties from genetic components which occur in different natural environment.
For this they took up a set of 3 promoters and their corresponding repressors as described in figure. By disturbing the system with IPTG they were able to observe oscillations in GFP output which was controlled by a regulatory element which can be one of any given three. They described a rigorous mathematical model which holds with high validity. With this they also determined the range of parametric values where the regime of oscillations was stable and unstable. This was a remarkable piece of scientific work as it borrowed elements from electronics, physics and mathematics and applied it to artificial biology with the degree of fidelity never seen before in biology.

3. Diversity due to Combinatorial arrangement
This paper highlights diversity achieved due to combinatorial arrangement of simple, uni-functional and characterized part. With set of 5 promoters ( 2 LacI repressed, 1 TetR repressed, 2 lamda regulated - 1 activated and 1 repressed) out of which 3 are arranged in tandem on same plasmid with possibility of repeatability. The final output effect was described using GFP. They searched the library for transformants which had output as binary logical function of both the inducers - IPTG and aTc. They identified that connectivity uniquely did not determined the behaviour of networks. To understand the effects one needs to account non-linear, stochastic nature of these systems and thus unknown details of interactions between components is of crucial importance.

4. Characterization and Substitution of lux operon In this study, one of the most common autoregulatory parts from lux operon were first sequenced, cloned individually and engineered a microbial circuit which displays intercellular communication mechanisms between living bacterial cells. They first characterized the lux operon DNA sequence which codes for 2 operon in diverging fashion transcribing luxR on left and luxICDABEG in right. The proteins responsible for bioluminescence effect was well known so they cloned individually the parts responsible for concentration dependent communication effect (quorum sensing) and engineered microbial systems with intercellular communication mechanisms between living bacterial cells.

5. Synthetic production of artificial anti-malarial drug artemisinin
Synthetic production of artemisnic acid, a precursor to antimalarian drug artemisnin has been hailed as a marvelous example of potential of synthetic biology. This discovery is significant from socio-economic perspective because african countries are still plagued with malaria and due to high prices of artemisnin and plasmodium resistant strains to other drugs has created a crisis. A company named Amyris Biotechnologies has been founded to produce cheap artemisnin from microbial sources unlike current plant derivative which is very expensive.
Artemisnin production in microbial host has been explored by many groups but most efforts failed to produce either the final product or its useful precursor by large amount. Keasling's group utilized mevalonate dependent isoprenoid pathway from yeast and re-engineered it in E.coli and combining with its own DXP pathway results in acquiring benefits of bypassing regulatory elements of both systems resulting in high yield of amorphadiene. Artemisnic acid can be further converted to artemisnin using simple, inexpensive chemistry.

References:

Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000)

Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000)

Guet, C. C., Elowitz, M. B., Hsing, W. & Leibler, S. Combinatorial synthesis of genetic networks. Science 296, 1466–1470 (2002).

Weiss, R. & Knight, T. F. Jr. in DNA Computing (eds Condon, A. & Rozenberg, G.) 1–16 (Springer, 2001).

Martin, V. J., Pitera, D. J., Withers, S. T., Newman, J. D. & Keasling, J. D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nature Biotech. 21, 796–802 (2003).