Team:Cambridge/Diary/Week 3

Monday

We aimed to start doing something towards our project today. To this end, Tom and Oli began making up a batch of competent bacillus (strain 168) for freezing and future use. The protocol for this can be found here.

Paul and Andreas went over to the photonics department to begin the process of making our circuit for the analysis of the bacterial luciferase signal. They also began formalizing the design of the actual instrumentation so it could be made over the next few days.

Jolyon managed to find an endogenous fluoride riboswitch that had been reported in bacillus subtilis. As a novel biobrick, this would have obvious applications in the analysis of water purity. Such a device could also be pitched at persons a la General Ripper, concerned about fluride contaminating their "precious bodily fluids", though such a marketing strategy could produce somewhat sporadic orders.

Some of us also started using the faintly egomaniacal geneious program for the analysis of DNA.

All in all, a fairly productive first day!

Tuesday

Oli and Tom continued with the rather elongated protocol for creating competent bacillus.

Jolyon contacted the team in Yale who had discovered the bacillus based riboswitch for the detection of fluoride. Hopefullly we should be able to integrate it into some sort of reasonably fast acting novel bacterial biosensor which we can then hook up to our standardized bioluminescence. In order to bring about this standardization, Andreas introduced the biologists to some of the principles of control theory, so we had some of the conceptual tools to change the shapes of the input/output curves. One important possibility is using these control theory principles to reduce the noise of the response.

Andreas and Paul also started on the software for our device today. Our current plan is to use an Arduino board to detect our inputs, write this to a python file and then read this via C to make a user interface. Very snazzy.

In addition to this, Emmy got the completed home page online! Considerable! A graphic designer as well as a biologist in our midst...

Wednesday

The first results of our light sensor made by Andreas and the user interface made by Paul came out today. See the lab book for the results.

We also built up a schedule for when each of our individual modules should be finished by. Our final schedule can be seen on the calender (Can we get our Google calender on this wiki?. Hopefully we shouldn't look too unprepared when UEA visit tomorrow. By the way, UEA are visiting tomorrow.

Continued wrangling for the already constructed plasmids also took place, with Tom trying to get his hands on an optimized lux operon for use in bacillus. Whether or not it is actually codon optimized is, at this time, unknown. If the worst comes to the worst however, we can just get DNA 2.0 to synthesize the whole thing and optimize it for bacillus. We may have finally found a use for our synthesis budget.

Lastly, we finally manage to make up and freeze our stocks of bacillus. At eight fifteen, Tom and Oli finally exited the building after a ten hour protocol. At least we won't have to do it again for a while.

Just how competent our attempts at competency were will be tested tomorrow.

Thursday

The UEA team visited today. See pictures of their visit in the gallery (Need link to gallery when we start the page). Hopefully we should be able to collaborate as soon as they manage to create their biosensor for nitrate.

Andreas and Oli tried transforming the bacillus stock we made up yesterday. The plasmid used was Tag RFP-T which gives choramphenicol resistance and should turn the colonies pink. We will have to wait overnight to see if the week has been wasted.

We've also started designing the primers we need for the various steps in the procedures. Jolyon made some potentially effective ones for extracting the fluoride riboswitch region from the bacillus genome. Using Gibson assembly, it should then be possible to insert this upstream of our reporter, i.e the mOrange/luciferase fusion. See our project page for how we imagine this should turn out in the end.

Friday

Our transformants actually seem to have worked! See the lab book for a lovely image of our pink colonies.

Stuart took an inventory of the large quantity of freezer stocks left over from last year. Lots of molecular biology stuff - enzymes, buffers, DNA ladders, loading dyes etc. etc. Plus many helpfully unlabeled tubes from years before 2011. We probably won't be risking those.

Emmy and Paul worked with the old lux operons from 2010, inserting the plasmids into the bacillus made up two days ago, as well as into some e.coli. Hopefully we should have some bioluminescence to test by the end of the weekend - useful for the Arduino kit which is becoming ever more developed as the hours go by.

Cake days Link to the cake spreadsheet? were instituted today, with the inaugural sample being Emmy's banana bread. They may also act as excellent bargaining chips for enlisting the aid of reticent PhD students.

Andreas has managed to find some optical filters, which he later tested in the spectrophotometer. The data was plotted in MATLAB by Oli. Andreas has also discovered that he hates the odour of e.coli. How fortunate that we are working mostly with bacillus instead, which has the delightful aroma of unwashed feet.

Saturday

Emmy came in today to check on the e.coli and bacillus plates she and Paul made up yesterday. They don't seem to have grown...