A TALE OF TWO SIGNALS
We all know about machines that convert analog signals into a digital ones. Nothing very high-tech about them, right?. But now imagine, if bacteria could do it? Wouldn’t it be amazing! iGEM IIT Delhi, our synthetic biology club, engineered this in the bacteria E. coli. They converted a sinusoidal feed into a square wave and won a Bronze Medal for their accomplishment at MIT, Boston, this year, one of the many milestones since the club’s inception a few years back. The principal investigators for the project were Prof. Zia Shaikh and Prof. Stefan Oehler. We talked to Kshitij Rai (5th year Dual Degree student of Biochemical Engineering) and Abhilash Patel (PhD student of Electrical Engineering), senior members of the team, to gain insights into the project.
The main motivation behind the project was the lack of digital responses in synthetic biology. Responses in biological circuits are “graded” i.e. there are no well defined states such as 0 or 1, instead there is a continuous response. Hence, there is limitation in their applications. The idea for this need for digital responses came up when the Nobel prizes for 2017 were announced and Prof. Hall and Prof. Young were awarded the prize for their work on circadian rhythm. Also, during the team discussion, it was felt that it would be very useful if there existed a system such that insulin could be delivered at regular intervals automatically to a diabetic patient. This periodic drug delivery system, when constructed by using a harmless bacteria, would be capable of bringing about a revolution in the scientific world.
The real time picture of fluorescing bacteria in our lab
ABOUT THE PROJECT
The project was an independently thought project. It was to be presented at the Giant Jamboree at MIT, the biggest meet of Synthetic Biologists from all around the world, by three team members, namely Kshitij Rai, Tarun Mahajan, and Tanuj Garg. The project’s conceptualization can be attributed to the rigorous brainstorming by the senior members of the club. In simple terms, their project involved a ring of five nodes, each of which was a transcriptional repressor i.e. each node suppressed the making of proteins by the next node.
These repressors are nothing but a sequence of DNA extracted from different organisms. Odd number of nodes in the ring ensured oscillations and five repressors ensured a sharp response. Hence, a sinusoidal wave was converted into a square one in a very ingenious way. The first major step was searching for some suitable repressors. Then, mathematical simulations were run to find optimal conditions for the desired behaviour. Lastly, the repressors were assembled together and subjected to the theorized conditions, giving rise to our Square Wave Generator.
A simplistic view of the function
Enzymes, various chemicals (some typical ones being TSS buffer and LB) and DNA sequences were the first and foremost requirements. The project required the use of various equipment such as a centrifuge machine, PCR machine, autoclave etc. Biotech students must be familiar with all these terms. For the rest of you, PCR machine amplifies the segments of DNA, autoclave disinfects or sterilizes the apparatus and a centrifuge machine simply does what its name suggests! When it comes to something as stochastic as synthetic biology, it is always good to carry out simulations to verify your theoretical basis before getting on with the experimentation. MATLAB, an old friend of iGEM IIT Delhi, once again came to their aid here.
Centrifuge machine, PCR machine and Autoclave machine
The necessary knowledge for the project was acquired through interaction with Prof. Shaunak Sen, Dept. of Electrical Engineering, and through research papers by Richard M. Murray and Christopher A. Voigt. Needless to say, the biotechnology lab courses helped in meticulous execution of the knowledge.
Abhilash felt that funding was A major issue. Enzymes, chemicals etc, being quite expensive, required funds in lakhs. And money of that amount is not easily forthcoming. Also, the execution of the project was itself a challenge because of many factors beyond human control, such as proper functioning of enzymes.
Kshitij further added that running such a project is a challenging task due to the many different aspects that need to be catered to, such as mathematical modeling, circuit designing, cloning to assemble DNA bits together, and several other issues, and therefore having a dedicated team is important. Finding the right set of students, with a mindset to view this project as “their own”, instead of something that they are doing for design credits, or a CV point, is extremely important and a challenge that doesn’t seem very obvious at first glance.
Abhilash and Kshitij feel that the club has crossed a major milestone in their long journey and the destination is something they are determined to reach more than ever. Speaking about the project, they feel that higher levels of perfection can be achieved and the team will surely work towards achieving that in the future. The Bronze medal might soon transform into a Gold one with just the right blend of skill, experience and luck.
A WORD OF ADVICE TO THE JUNIORS AND FELLOW BATCHMATES
Abhilash says, “Doing courses like Control Systems, Signal and Systems for Computational Biology etc. are essential for building basics and go a long way in this field. Also, biotechnology courses offering Lab experience are helpful to a great extent. Additionally, selecting a “Feasible” problem statement, which can be done within the stipulated time-frame is very important for these kinds of competitions. Also, don’t be shy to reach out to Professors or Research Scholars as they are often more than willing to help. And have patience and work with perseverance. It takes time in this field to arrive at the desired result, but as someone very rightly said, “Trees that are slow to grow bear the best fruit”.
Kshitij also resonated the same thoughts, and further added, “For students who are passionate about working in the field or want to explore it, I think it is crucial to read things well enough beforehand, and only then apply them to work. Research is not the flashy ‘We Cured Cancer in 6 months’ kind of deal. We all know it takes time, and can be long, strenuous, and an arduous process, producing very little in the end. What is important to know is that this is fine, and failures happen. However, if you lose interest in between, everything is lost, and you’re definitely not going to reach your goal that way. So when you take up such a monumental task, the important thing to note is that it will take time, and a whole lot of effort, and may still give you very little in the end. But when all is said and done, at the end, you’ll have the chance to look back at your work, and say, Hey! Did you read about that oscillator that was published in Plos ONE this week? I made that. And if that is good enough for you, you have what it takes.”
ABOUT RECRUITMENTS FOR NEXT YEAR’S PROJECT
The team always looks for people who are dedicated towards the project. Branch is never a deciding factor and there are students from all branches (Computer Science, Electrical, Maths and Computing, Chemical and Biotech). The zeal to work and passion towards the team is what is desired. Further, the club is targeting an increment in the number of PostGraduate Students applying this year. “We plan to have a separate meeting, orientation, and recruitment process optimized for post graduate students this year, as they are a crucial aspect of the project, and need to be selected additionally”. For Undergraduate students, they plan to go by the regular orientation session followed by interviews. Stay tuned for their recruitment process for next year, which will start in early January.
We would like to congratulate iGEM IIT Delhi for their achievement and salute their dedication towards undertaking such research projects year after year. BSP would like to wish them all the best for their future endeavours!