Revision as of 11:02, 8 September 2015

Notebook

The following is a weekly description of the experiments carried out each week. To see the protocols click here

28/01: Brief introductory meeting about the iGEM competition
17/03: The official iGEM team to represent the University of York was formed!
Daily dry lab research begins, primer and construct designs made and ordered.
05/05: Article published in Nouse (University newspaper) about the 2015 iGEM team.
03/06: We were invited to Science and Technology Alumni Network discussion event (outreach)
04/06: Article published on the University's central news about this years iGEM team.
12/06: A meeting was held with Yorkshire Water to discuss water remediation processes in the Yorkshire region
13/06: We were invited to a University of York Biology Alumni event
15/06:
1. Some of us went to a round-table discussion about the impact of Santander at York as some of the team members won the International Connections Award by Santander.
2. Article published on Mind the Horizon about University of York iGEM
19/06:
1. Lab safety induction was carried out
2. We passed out pamphlets at the York Festival of Ideas to raise awareness about the iGEM competition and synthetic biology.
26&27/06: We participated in giving talks to prospective students about iGEM.

24/07: Wet lab practice day- reviewed basic lab protocols- making LB, agar plates, competent cells, transformations, PCR

01/07:Competent cells made
02/07:Plates were streaked with two isolates of each deletion wanted from the Keio collection [PPX, PPK, PstA, PstB, PstC, PstS and PhoE] These have been collected and put in the incubating (37°C) room.
03/07:Competent cells were tested with iGEM transformation efficiency kit

14/07: Vistited Badger Hill Primary School and held a bacteria workshop for the students
15/07: first day of demonstrations of cell transformations and aseptic technique to sixth formers
16/07: second day of demonstrations to sixth formers:analysing transformations and building bioreactors
17/07: analysing bioreactors with sixth formers
17/07: first attempt at phosphate assay

20/07:Phosphate assay was started for KEIO collection
20/07:Colony PCR on SmPstSCAB, EcPstSCAB and EcPhoE
20/07:Next set of competent cells made
22/07:X-Gal/IPTG Plates made
22/07:Digested pSB1C3 with EcoRI and DpnI, then used Gibson Assembly to insert our adapter genes in.
23/07:Visit to AgeUK LunchClub to explain about the GM
23/07: Glycerol stocks of Sinorhizobium meliloti
24/07:Ran gel electrophoresis of PCR from 22/07

28/07:First day of outreaching event to Saint Helen's CHurch, York, to carry out strawberry extraction practical and briefly explain about the steps involved for GM
29/07:Second (and the last day) of outreaching event to Saint Helen's Church, York, to carry out strawberry extraction practical and briefly explain about the steps involved for GM
30/07:After several repeats the phosphate assay team managed to get significant data

03/08:Plasmid (pBC 29 Keasling collection )loss experiment initiated
05/08:Q5 PCR of SmPst, EcPst, EcPhoE
06/08:Inoculated overnight cultures of ApPst, ApPPK (SK-12, BA-91, UW-1)
06/08:Ran GoTaq Colony PCR of same colonies of ApPst, ApPPK (SK-12, BA-91, UW-1)
06/08:Ran gel electrophoresis of colony PCR
06/08:Inoculated overnight cultures of BW25113, pkDM12, KoPPK
07/08:Purified plasmids from overnight cultures of ApPst, ApPPK (SK-12, BA-91, UW-1)- "mini-prep"
07/08:Used Nanodrop machine to measure concentration of miniprep products
07/08:Performed an analytical digest of purified plasmids with EcoR1 and Pst1

10/08:Transform competent cells with plasmid (?)
10/08:Ran GoTaq colony PCR of ApPst, screened for correct product, ran gel
10/08:Performed a gibson assembly of EcPhoE Q5 PCR product (from 05/08)
10/08:Ran a gel of SmPst and EcPst Q5 products (from 05/08), then digested with Dpn1, nanodropped, PCR purified and performed a gibson assembly10/08:Ran an overhang-adding step-up PCR of KoPPK, pkDM12, pBC9, pBC29
11/08:Ran a Pseudomonas aeruginosa colony PCR to amplify PaOprO and PaOprP
12/08:Digested lacZ pSB1C3 with EcoR1, ran gel, and performed gel extraction and purification protocols
13/08:Digest pAdapt with Sma1
13/08:Ran Gibson assembly of EcPstSCAB, SmPstSCAB, KoPPK, pKDM12, EcPPX, EcPPK "colony 1 and 2", EcPhoE
13/08:Transformed BW2115 with gibson products and plated on agar.
14/08:Ran GoTaq PCR of colonies from Gibson plates and performed gel electrophoresis with PCR products.

17/08:Make liquid cultures of colonies that were verified with the gel on the 14th(EcPPX, EcPPK, pKDM12)
17/08:Attempt colony PCR of different colonies for gibsons that did not work (EcPst, KoPPK, SmPst, EcPhoE)
17/08:PCR amplified the digest of lacZ pSB1C3 (from 12/08) to make sure that no product is in the plasmid
17/08:
17/08:

@@ Line 116: / Line 116: @@
 <li>10/08:Ran a gel of SmPst and EcPst Q5 products (from 05/08), then digested with Dpn1, nanodropped, PCR purified and performed a gibson assembly</li.
 <li>10/08:Ran an overhang-adding step-up PCR of KoPPK, pkDM12, pBC9, pBC29</li>
+<li>11/08:Ran a <em>Pseudomonas aeruginosa</em> colony PCR to amplify PaOprO and PaOprP</li>
 <li>12/08:Digested lacZ pSB1C3 with EcoR1, ran gel, and performed gel extraction and purification protocols</li>
 <li>13/08:Digest pAdapt with Sma1</li>
@@ Line 125: / Line 126: @@
 <h3>Week 9 - August 17-21  </h3>
 <ul>
+<li>17/08:Make liquid cultures of colonies that were verified with the gel on the 14th(EcPPX, EcPPK, pKDM12) </li>
+<li>17/08:Attempt colony PCR of different colonies for gibsons that did not work (EcPst, KoPPK, SmPst, EcPhoE)</li>
+<li>17/08:PCR amplified the digest of lacZ pSB1C3 (from 12/08) to make sure that no product is in the plasmid</li>
+<li>17/08:
+<li>17/08:
 </ul>