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Welcome to the NRP UEA iGEM 2012 Wiki Lab Book

Please choose the relevant link to access our diary of that week!

Week Zero | Week One | Week Two | Week Three | Week Four | Week Five | Week Six | Week Seven | Week Eight | Week Nine | Week Ten | Week Eleven | Lab Protocols | Experiments


Week 3

Over the weekend the group met up to discuss the two potential projects we could go forward with using our synthesised gene and the Biobrick it will ultimately produced. We developed two main themes; one was a multi-sensor system sensing oxygen-containing physiologically-relevant molecules and reporting on the levels of each molecule; the other was a comparator circuit sensing levels of molecular species and using novel gene expression to express reporters for specific molecules within the environment to quantitatively measure them. We decided on the latter as we felt it would have the highest scientific impact, a diagram of the gene system for one of the sensors is given below.


The concept behind the project involves the mRNA control region of one sensor binding to the mRNA control region of a second sensor and thus for one sensor to 'switch off' the other to a certain degree, and for the overhang to be used to measure levels of a substrate molecule. For example in our nitric oxide-sensing project a sensor for nitric oxide and nitrites (sensor 1) may be used in conjunction with a sensor for only nitrites (sensor 2); the control region of mRNA produced from sensor 2 would switch off sensor 1 per the levels of nitrite in the environment, and therefore all expression of sensor 1 would be directly related to nitric oxide levels in the atmosphere.

Day 1


Amy (our artist) came to visit us today in order to discuss our video. She, Joy and Rachel began to storyboard the film and work out how to incorporate the decision made over the weekend into the video. They came up with some fantastic ideas and the whole team sat down to discuss them before Amy left to organise making props. Joy also got in touch with the UEA Drama School in order to see whether we could hire a studio in order to film our video.


From the transformation of the two promoters carried out on Friday, we inoculated some colonies into culture. This will be used later for characterisation of the promoter. From the two plates, we noticed that one plate had bigger colonies and one had very small colonies. The larger colonies were from the agar plate inoculated with transformed E.coli with promoter 1.

To characterise the promoters and other Bio-Bricks we may be interested in, an input of NO will be needed. Our solution to this is to use a nitrate salt like potassium nitrate. A stock solution (1M) was made up today by Lukas. This was taken to be autoclaved.

Day 2


We were going to inoculate the E.coli with the transformed Pyear promoters that

Day 3


After our hunt for the fluorometers and speaking to Dr. Yeoman the previous day we decided that we needed to find whether we could use fluorescent proteins today in order to go on to design the DNA for the control region and reporter/enzyme. After a social media call-out for fluorometers in our faculty we were pointed in the direction of Dr. Tom Clarke who very kindly offered us the use of his fluorometer, as well as training on it and potentially even the use of a fluorescence microscope. He also gave us advice on the project and suggested that pigments and the use of a spectrophotometer would perhaps give the better quantitative results and informed us that fluorescence may be particularly labour-intensive and time consuming. We decided to spend the rest of the day researching other ways of reporting on the substrate levels in the environment.

We began by investigating various pigments and looked at projects such as E. chromi to find biobricks of the pigments we would require. One problem we fell into was the absorbance of the pigments overlapping, which would ultimately cause our results to be inaccurate if they were produced in an environment. We then decided to look at proteins with unique absorbancies as our reporters, as well as enzymes that would produce colourful products. Our main problems involved using proteins that were not already incorporated into biobricks, using proteins whose absorbance and emission spectra did not overlap, and using proteins that would not interfere with the ribosome binding site and

Day 4


. Going down all avenues to search for which reporter would be the best for our project, including fluorescence, absorbing proteins, pigments and enzymes with coloured produce.

. Decided to test fluorescent biobricks we already had to determine how easy they would be to use.

. Began to look at how to construct the mRNA for our synthetic gene.

Day 5