Team:IBB Pune/Project

We are a team initiated by students. This is our first year at iGEM and we are excited to be a part of the whole iGEM experience. We are proud to be the first student representatives of IBB at any international level competition.

We are a group of 7 undergrads currently studying biotechnology in the third, fourth and fifth years of the Integrated Master's course at IBB, University Pune. We are a bunch of creative, hardworking and enthusiastic students. The team members know each others strengths and weaknesses very well and that makes us work as a team. We hope to succeed this year in iGEM and make a mark in the field of synthetic biology at the international level.

Brainstorming

We have had many brainstorming sessions within the team and with the instructors in which hundreds of ideas were discussed. We are listing a few interesting ideas below and we are sure that some or the other team will get rid of the theoretical/practical difficulties we faced and will do projects related to these ideas the next year if not this year.

1.Sudoku solver bacteria: This is quite a popular problem and many teams have considered doing this. We chose to solve a 4 x 4 sudoku because it is much simpler than the usual 9 x 9 one. The sudoku solving bacteria are a strain of bacteria, that will have a genetic circuit that allows differentiation into 4 types of phenotypes corresponding to the numbers 1,2,3,4. These phenotypes will include a combination of reporter proteins and signal molecules that will inhibit the differentiation to that specific phenotype. eg. "1" will inhibit the differentiation of naive cells to the 1 phenotype along rows, columns and blocks and so on. There are however many technical challenges. How do we restrict inhibition to a single box / column / row without disturbing other boxes?

2.Singing bacteria: This is the most original idea we have ever witnessed. It was a long shot actually expecting to find a paper on this and find it, we did! There is a report that bacterial cells enhance the proliferation of neighboring cells under stress conditions by emitting a physical signal (Sound signal). There was also an observation of better growth of these bacteria in the presence of these sound waves emitted synthetically. Basically our idea was that maybe we can use this sound producing property (or rather singing ability) as a reporting device for certain cell conditions. Another thought was that we can grow our bacteria by actually ordering them around! We could produce certain frequencies of sounds to make our bacteria grow whenever we want. An open induction of growth system as and when we want. We could also characterize the regulatory mechanism responsible for detection and response to an audio input and make systems that accept sound as an input and produce PoPs. [http://www.jstage.jst.go.jp/article/jgam/44/1/44_49/_article]

3.':

Overall project

1. Export tag synthesis and inducible export of desired proteins for in vivo simulation of the SNOWDRIFT game.

The export of beta galactosidase can be used to make an in vivo simulation of the snow drift game.this system will be a great way to calculate the equilibrium concentrations of cooperators and defectors by controlling the cost and benefit ratio.The most peculiar characteristic of this system is that the cost and benefit ratio here is PROGRAMMABLE and can be measured in terms of PoPs.

2. Bacterial Turing machines. We are trying to make small two-state Turing machines like unary adder and attempting to build an AND gate.

Can bacteria be used as mini computational devices?We are going to find this out by testing a system made entirely out of available bio-bricks from the registry with the introduction of two AND gates. Our primary goal is to make simple two state Turing machine like a unary adder.We will also be working on the more complicated Turing machines and also on the ways by which we could connect different two state Turing machines in combination.

3. inducible natural competence using genes from naturally competent bacteria and phages.

This project bears the primary goal of introducing two new competence inducing genes comA and comB to the registry. Bacterial competence coded by a biobrick can be used as a crucial component in cell to cell signalling systems and can even be used to facilitate RNA based signalling between two cells.