Difference between revisions of "Team:York/Notebook"
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<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 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>10/08:Ran an overhang-adding step-up PCR of KoPPK, pkDM12, pBC9, pBC29</li> | ||
| − | <li> | + | <li>12/08:Digested lacZ pSB1C3 with EcoR1, ran gel, and performed gel extraction and purification protocols</li> |
| − | <li> | + | <li>13/08:Digest pAdapt with Sma1</li> |
| + | <li>13/08:Ran Gibson assembly of EcPstSCAB, SmPstSCAB, KoPPK, pKDM12, EcPPX, EcPPK "colony 1 and 2", EcPhoE</li> | ||
| + | <li>13/08:Transformed BW2115 with gibson products and plated on agar.</li> | ||
| + | <li>14/08:Ran GoTaq PCR of colonies from Gibson plates and performed gel electrophoresis with PCR products.</li> | ||
</ul> | </ul> | ||
Revision as of 10:51, 8 September 2015
Notebook
The following is a weekly description of the experiments carried out each week. To see the protocols click here
Dry Lab Work Period
- 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:
- 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.
- Article published on Mind the Horizon about University of York iGEM
- 19/06:
- Lab safety induction was carried out
- 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.
Week 1 - June 23-27
- 24/07: Wet lab practice day- reviewed basic lab protocols- making LB, agar plates, competent cells, transformations, PCR
Week 2 - June 29- July 3
- 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
Week 3 - July 6-10
- 07/07: More agar plates made, next set of competent cell procedure started
- 07/07: YUfund page done and submitted
Week 4 - July 13-17
- 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
Week 5 - July 20-24
- 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
Week 6 - July 27-31
- 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
Week 7 - August 3-7
- 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
Week 8 - August 10-14
- 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
- 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.