Team:Calgary/26 May 2009

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 JEREMY Plasmid Isolation of luxOD47A in pCR2.1 TOPO and psB1AC3 vectors The purpose was to isolate plasmid containing luxOD47A, as a means of starting the construction of the mutant circuits. TOPO T/A and psB1AC3 vectors containing luxOD47A were isolated using the Sigma GenElute Plasmid Mini-prep kit. 100μL of ddH2O were used to elute, and the purity and concentration of each plasmid were measured using the NanoDrop Spectrophotometer.



 KATIE Challenges Faced with PCR
 * Working on the virtual PCR machine and completed a general PCR first
 * Making it work for PCR with three different types of DNA and placed it initially in three separate scripts and only one would run if it had all of its items. I really want to find a better way to do this so I will continue to work on this.

Problem: Items are not being found and it is causing an error on the debug channel and it was not happening before so I will have to find what I have changed in the past day to see what went wrong. It seems to be something that goes wrong within the for loop I have since it seems to be locating everything when there are items missing. I will most likely see to this problem tomorrow.



 KEVIN Plasmid Isolation of Pqrr4 for Reporter circuit The Pqrr4 was isolated from TOPO T/A and biobrick AC (pSB1AC3) using Sigma’s Genelute Plasmid Mini-prep kit (sigma) according to the specifications of the manufacturer. Nanodrop utility along with the Spectrophotometer was used to measure the concentration and purity of the isolated plasmid. The wavelength was set at 260nm. HTML Code, just as an example for now Wiki Code Table 1. Purity and concentration of Pqrr4 measured with Nanodrop utility and Spectrophotometer
 * The two TOPO vectors were from the same colony, thus labelled "Green tube" instead of C1. The two BBK plasmids were also from same colony, so same label applies.



 PATRICK What's in a (DNA Part) Name? Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.

Continued developing the script for sending names from one part to the next, so that each could learn where the other was. The problem was that each DNA part in a polymer needs to know the key of the next part, in order to direct the RNA Polymerase to the next part when it visits the current one. Yet object keys weren't stable between sessions, so we needed some additional internal name for each part to go by. Each part would know its internal name, and the name of the next part in the sequence. Then it can use that name to obtain the key of the next part via a message and reply.

I first began to use comma separated values (CSV) to encode my messages, which worked so well I never needed to change it. This is thanks to some good built in tools for CSV handling in the linden scripting language.



 PRIMA Back from Dragon's Den We returned home on the evening of May 26th, weary from the experience and yet somehow craving more of it. Having satisfied both of our original ambitions, we were pleased with the result and thankful that we were more than just another meal for a few Dragons in the vicinity. Armed with a new sense of promotional direction, more contacts who can help support our initiatives, and the same stunning good looks that we had before we left, we are excited to implement some of these ideas to help capitalize on our marketing potential.

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</a> VICKI Plasmid isolation with mini-prep

Purpose: To isolate the plasmid DNA from the rest of the bacteria for colonies containing LuxPQ on TOPO II Blunt and LuxPQ BBk on psB1AC3.

Reference: The user manual and the Sigma Aldrich site

Kit: MP70 GeneElute Plasmid mini-prep kit. Note that it had been previously used, which may be a problem for contamination.

Materials and methods: Procedure was carried out in accordance with our Plasmid Isolation protocol. When complete, we stored our isolated plasmids in the freezer for concentration measurement and content analysis over the next 2 days.

Results: We were left with tubes containing the described plasmids. Quantifiable details on their concentrations and actual contents are outlined on the May 27 and May 28 entries.

DNA concentration measurements with the Nanodrop spectrophotometer

Purpose: To measure the DNA concentration of LuxPQ plasmids that were isolated in the May 26 miniprep

Materials and Methods: The DNA measurement area was cleaned with isopropanol and KimWipes to clear off any trace residue from previous uses. The sample wavelength was set to 260 nm. A blank measurement was made with 1 uL of ddHOH. 1 uL of the sample in question was added to the Nanodrop measurement area. The measurement was made; the sample area was wiped down; and a new sample was measured.

Results: