Team:IIT Madras/Scribbles

From 2011.igem.org

Revision as of 20:58, 5 October 2011

1. Biomolecular Sensor

We propose to make a bio-molecule sensor which can detect the presence of a particular bio-molecule (say a protein).

We have discussed two possible pathways systems:

• Surface receptor/ Ab can identify the biomolecule by binding to it and sending corresponding signal to the core gene complex which will show the respective result probably by an FP.
• Ab on the flagella will detect the bio-molecule and this will result in dysfunctional flagella. So in presence of chemotaxis the coloured cells will be scattered in the media separated from the other cells with functional flagella.

2. A new Screening technique

If we can express the Bacterial Rhodopsin pathway in E. coli, this can be used as a new screening technique for cloning. We can hence screen it using two inputs Light and maybe Lactose.

3. Perceptron Learning

Bacteria can be used as a processor. It should be viewed as a weight matrix. Thus we are making the bacteria/weight matrix “learn” certain inputs and analyze the same after learning.

This can be a good foundational advance and also we can find its importance in medicine wherein the “learned matrix” can be introduced into the body and the output can be analyzed. In this example bacterial matrix is detecting other bacteria, which is essentially having bacteria as input and bacteria as a processor.

4. New Technique for Protein expression

Instead of expressing protein by a Double stranded DNA vector. It would be if we express the protein on the capsid of the virus which is easily isolated from the bacteria and hence protein isolation is improved and easier.

5. Allergen Sensor

Theory: Many people are allergic to many things. The common test to identify the respective allergens is to inject very small quantities of allergens into the body and look for allergic responses. Idea: What if we can express some common allergens as surface proteins on the bacteria? This can be used to elicit some antigen-antibody response or we can have this showing some colour code for different allergens interactions.

6. Using RuBisCO as a CO2 sensor

Theory: RuBisCO is an enzyme with carbozylase and oxidase action. It acts on the substrate ribulose bi phosphate. An important enzyme in "fixing" CO2. Now, in the process of evolution the effectiveness of this enzyme didnt increase. Its a very slow enzyme and the carboxylase action of this enzyme is preferred when the local co2 conc is high. We studied the c3 and c4 pathways for better understanding.
Many scientists view this as a solution to global warming if this enzyme has better kinetics, then plants can grow soon and fixation of co2 can be a faster process.
A concept called directed evolution was done wherein this enzyme was introduced into E.Coli. Random mutations were performed to get a better enzyme. The best achieved was kinetically 5 times better compared to the wild type.
Rubisco can be easily introduced in E.Coli without any problems of folding due to chaperonions called groES and groEL present in E.Coli.And a part of the C3 cycle should be introduced too for the availability of substrate. And we should find a promotor which is regulated by one of these intermediates.

7. Rust Eating Bacteria

Theory: Introduce enzymes required to convert Fe2O3 to Fe into bacteria. Could be used for rust treatment. Comments: The whole concept was looked at very skeptically since the team had problems with the use of eating away Fe2O3 and how the Fe would be deposited. The source of energy for the same also was vague. Protein called Ferritin was talked about which could potentially help us prevent rust.

8. Organic Touch Sensor

Inspiration: Thigmonastic movements of mimosa pudica

Theory: Turgorins are molecules released in mimosa pudica which opens up the k+ gates and cl- gates. k+ ions move out of the cell along with water molecules and cl- ions enter the cell - there is a loss in turgor pressure which is why the elaves close - similar mechanism is seen in venus fly trap - as the fly sits on the leaf, the turgorins reduce the turgor pressure at leaf blade- which causes the leaves to close upon the insect and then the digestive juices are secreted.

Outcome: A plate of cells- touch sensitive- when a finger is used to trace a letter on the plate, those cells are activated- either we can have the turgorins being replaced with a fluorescence protein or we can have it being expressed with fluorescence protein- half life of the protein must be low - then the sensitized cells create the image - a software can be used to analyse the letter and can be displayed or even say pronounced.

Difficulties: We were not able to find the exact pathway of these thigmonastic movements work.

9. UV Sensor

Theory: UV is very important for DNA Repair and Vit D Synthesis. So these proteins/promotors involved in this can be used.

Outcome: Changes in UV is recorded by these promotors. It can be linked to a fluorescence protein.

Difficulties: Vitamin D synthesis is mostly in mammalian cells and DNA Repair is in eukaryotic cells.

May be this will involve usage of yeast.

10. Flesh Eating Bacteria

Theory: Necrotizing fasciitis is a disease in which human flesh is eaten up by the bacteria. The idea was to modify the bacteria causing this or to transform the mechanism utilized in this bacteria to make E.Coli selectively cause fasciitis which is used to eat up tumor tissues.

Outcomes: The pathway involved is very complex and cannot be transcribed into E.coli. Also the bacteria is too dangerous to risk using it as a treatment method.

11. Deinococcus Radioduran

Theory: Implementing the RecFOR genome reconstitution of Dienococcus Radiodurans pathways in eukaryotes to speed up or improve the genomic DNA repair.

Outcomes: Loads of possible versions of the same were thought of. The pathway was explored in a little detail.

Conclusions: The pathway involves high degree of specialisation in terms of the DNA repair pathways, and the organisation of genes. It also involves the formation of a 4 Cell colony which survives as a single cell with a single transcriptionally active genome. Many other difficulties were instrumental in suppressing the idea to a large extent.