Team:Glasgow/Weekly Report/Week 2

Week 2

Wet Lab

• Isolated DNA from the transformed plasmids, for use in PCR later in the week.
• PCR used to amplify and isolate our desired DNA from their plasmids, using the plasmids we designed in week one.
• PCR products then run on a gel to confirm they were of the correct size. Desired DNA was isolated for later use using gel extraction.
• Primers designed for GvpA , GvpC, and for the purposes of isolating FliC from the E. Coli genome. This will be used later on in the project to study the effect of the flagella in the presence of gas vesicles.
• Bacteria transformed with plasmids taken from the distribution. The parts used contained useful things such as GFP, a promoter, and vectors that will be used at a later stage. The useful DNA from these transformations was isolated and digested using EcoR1 and Pst1, to ensure the sizes were correct.
• One transformation was done using 2 different vectors containing RFP (pSB6A1 and pSB3C5), and two plasmids containing GFP, each with a different RBS. Another used instead the vector pSB1C3 and another containing the promoter J23100(CHECK) – both expressing RFP. This later transformation will be run on a gel in week 3.
• We had chosen 2 samples of our miniprepped DNA from out first transformation (one with GvpA, the other with GvpC) to be sent off for sequencing. At the end of the week, this sequenced data was analysed, and proved that out isolated DNA contained the desired sequences.
• An important step was taken this week: the ligation of our PCR-produced GvpA and GvpC - containing prefix, suffix and desired RBS – into separate pSB1C3 plasmid vectors. In order to do this, the PCR products and the vector underwent a restriction digest using EcoR1 and Pst1. The resultant DNA fragments were run on a gel and the fragments containing GvpA and GvpC and pSB1C3 were cut out and the DNA purified using gel extraction. GvpA was then ligated into pSB1C3. Seperately, GvpC was ligated into pSB1C3. The pSB1C3 was obtained by digesting the GFP-0034 BioBrick part from the distribution.
• As the above was taking place, FliC was also digested with EcoR1 and Pst1. The resultant gel showed a restriction site within FliC – a problem which must be resolved.

Dry Lab

• Exploring the modelling of bacteria movement using MATLAB – with flagella and/or gas vesicles. One of the key concepts is the Random Walk model. Most often used to describe the random movement of gas particles in air, we modified the most general model slightly to more accurately represent the bacteria movement.
• Basically, the bacteria will swim at a constant speed in a straight line, know as the “run”. After a given amount of time (mean of 1 second), it will change direction, or “tumble”, setting off at a new angle, with a distribution described by a normal distribution.
• This model was then combined with the upward movement supplied by the gas vesicles. The calculations are not finalised yet, and more accurate representations will be worked on in week 3.

Admin and Outreach

• Spoke to travel agent, getting details of flights to Boston (!) and accommodation while we're there.
• Contacted some more potential sponsors who could supply us with useful products for free or at a discount.
• Social media was updated with new photos.
• Wiki was worked upon – the engineers are still learning HTML, so it's a work in progress!
• Recombinase switch arrived – exciting stuff to come!
• Baked goods supplied by Beth – lots of fudge and even more chocolate. Exceedingly yummy.