From 2013.igem.org

Revision as of 17:13, 1 August 2013

Quorum Sensing Notebook

Goal:

Subgoals:

We planned out that we will transform E. coli with the civI/civR system found in Chromobacterium violaceum. We will design MoClo devices that include these systems. In the meantime, we are beginning to design primers that will make the civI/civR system into a MoClo system by adding the the fusion site in addition to the BBS and SpeI sites. Then, we will develop a PCR strategy.

Our advisor, Traci, emailed different labs and PIs that work with Chromobacterium violaceum. Dr. Jim Thoden from the Holden Lab at the University of Wisconsin sent us genomic DNA.

We designed forward and reverse primers for CviR/CviI systems and ordered those primers. We are currently waiting on acquiring the primers to begin PCR.

Today, we did Phusion PCR using the genomic DNA of Chomobacterium violaceum as the template for the CviI and CviR systems. We ran the PCR product on a gel and the CviI did not appear on the gel. The CviR system appeared and we gel extracted the parts.

The gel concentrations are as follows:

We redid the PCR for CviI. We ran the PCR product on a gel and we did the gel extraction. we quantified the concentration on the NanoDrop.

We ran a Level 0 MoClo reaction with the higher concentration of CviI and CviR.

We did a transformation using Bioline Gold E. coli and plated the samples on IPTG + Xgal.

We pulled the plates and picked three colonies and plated them on a stab plate and set up liquid cultures for incubation.

We set up CviI_CD and CviR_CD for sequencing in triplicate.

We analyzed the sequences for CviI and CviR and all of the samples we sent in matched the expected sequence.

We made glycerols and archived the highest concentration of each CviI and CviR.

Traci ordered the promoter pVioA_AB from IDT. It should come in from 4-10 business days. We are to treat it as PCR product and do L0 MoClo reaction. We can build the following four Level 1 devices and combine them together for a L2 device.

INSERT SBOL OF L1S

We are still waiting for the pVioA promoter. In the meantime, we are making I13453_GB (pBAD)and sending four samples out for sequencing

One of the I13453_GB samples were a match so we can make glycerol stocks and miniprep plasmid and archive the parts in our registry.

We ran reactions for:

E-J23100_EB-BCD2_BC-CviR_CD-B0015_DF-F

F-I13453_FB-BCD2_BC-CviI_CD-B0015_DG-G

G-I13453_GB-BCD2_BC-XFP_CD-B0015_DH-H

Today we transformed yesterday’s reactions using Bioline competent cells and plated the transformations on IPTG and Xgal for blue white screening.

We picked white colonies for overnight cultures.