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: Can sound be used as a stimulus for protein production? 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.self prep bacteria: Self prep bacteria are strains of bacteria that can inducibly express proteolytic and lipolytic enzymes followed by lysis cassette.this will provide us with a lysate without protein and lipid contamination and will yield pure DNA.This plasmid can be used to prepare cloning strains for which plasmid mini-prep will be much easier and fast.

4.multi product strains: there are many projects in iGEM 2008 about time switches that regulate protein expression.This can be used to produce two products, one primary and one secondary metabolite to economize the fermentation process.

Overall project

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

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.

This project bears the primary goal of introducing new competence inducing genes (com) to the registry. Competence genes enhance the automated uptake of surrounding genes and further expression.These genes are derived from naturally competent bacteria such as Acinetobacter and Streptococcus species.The biobricks produced can be used to form competent bacteria which do not have to be induced to take up foreign DNA by chemical means and hence can become permanently competent. Competent bacteria can simply be grown. In addition, 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.