Team:Manchester/Notebook/data.html
Thursday, June 1st.
Friday, June 2nd.
Saturday, June 3rd.
Sunday, June 4th.
Monday, June 5th.
Tuesday, June 6th.
Wednesday, June 7th.
Thursday, June 8th.
What is human practices? We had a meeting with Dr. Robert Meckin to find out!
Friday, June 9th.
Saturday, June 10th.
Sunday, June 11th.
Monday, June 12th.
First day of induction week!!!!!
(thanks Marc and Will for helping us!)
Tuesday, June 13th.
Second day of induction week!!!!
(thanks Marc and Will for helping us!)
Wednesday, June 14th.
Third day of induction week!!!
(thanks Marc and Will for helping us!)
Thursday, June 15th.
Forth day of induction week!!
(thanks Marc and Will for helping us!)
First full team photo taken in the lab
Friday, June 16th.
Fifth and final day of induction week!
(thanks Marc and Will for helping us!)
We also upgraded our office door
Saturday, June 17th.
Weekend meet-up - MORE PLANNING!
Sunday, June 18th.
Monday, June 19th.
Planning...
Tuesday, June 20th.
Meeting with Rainer's research group (Maria and Alia) to discuss modelling the phosphate starvation operon.
Had a meeting with Dr. Andrew (Andy) Balmer to explore further about human practices. We're finally ready to officially start!!
Wednesday, June 21st.
More planning...
'To understand the literature, you must first become the literature...'
Thursday, June 22nd.
MathWorks (MatLab) free trial starts - we can start modelling our project!
Friday, June 23rd.
Skype Meeting with Markus Gershater from Synthace to learn about Design of Experiment (DoE) and how it could be applied to our experiment.
Snapgene free trial starts!
Saturday, June 24th.
Sunday, June 25th.
Monday, June 26th.
James, Adam, and Amber attended an iGEM meet-up in Edinburgh
(Thanks to the Edinburgh OG team for the great picture!)
Tuesday, June 27th.
Project presentation to organization representatives Claire Doherty (IBCarb) and Marc Corbett (BioCatNet).
Wednesday, June 28th.
EUSynBioS publish an article about our project!
You can read it here... http://www.eusynbios.org/blog/igem2017mcr/
Thursday, June 29th.
Even more planning...
Friday, June 30th.
PLANNING PLANNING PLANNING (going crazy in the office)
Saturday, July 1st.
Meet up in Jess's place to discuss project plan including DoE factors.
At the same time, a strategic iGEM Manchester meet-up in Seoul is also taking place. Owen and Maciej, two key members of the team, set off to research into Korean GMO reality at a local food market.
Sunday, July 2nd.
Meet up in Learning Commons to make project plan more presentable. Amber got into AGLC for the first time.
Important meeting with advisors and supervisors tomorrow.
Monday, July 3rd.
Meeting is canceled. More time to brush up project plan!
Tuesday, July 4th.
More time to brush up project plan! Important meeting tomorrow.
Wednesday, July 5th.
Meeting with Dr Duncan Thomas and discussed the viability of applying our project in the water industry.
Very important meeting with advisors and supervisors. Finally the whole project is set on trail and we are ready to roll!
Thursday, July 6th.
Alice is back from Canada!
DIARY entry page is created! =D
G BLock sequences are checked and double-checked before being sent to IDT for free synthesis.
Friday, July 7th.
G BLock sequences are checked and double-checked again and (finally!) sent to IDT for free synthesis. Word is that the orders will be delivered on 18th and 20th July.
Exchanged e-mails with Professor Issy Caffoor to ask about innovation in the water industry!
Saturday, July 8th.
Sunday, July 9th.
Monday, July 10th.
Interlab study: Protocol was started by Alice and Theo! Inoculating competent cells.
Tuesday, July 11th.
Interlab study: Making not-yet-so-competent cells competent.
Wednesday, July 12th.
Interlab study: Competent cells are extraordinarily competent!
11.00 am GMT: Skype call with Peshawar iGEM 2017! Visit their website: https://2017.igem.org/Team:Peshawar
Thursday, July 13th.
Thanks to IDT our PPK gBlocks arrived today! 5 days earlier than expected! We get started trying to clone them into both the iGEM submission vector (pSB1C3) and our expression vector (pNIC28).
Friday, July 14th.
Ligate pSB1C3/pNIC28 and PPK constructs, transform - only the pNIC28 ones worked, so try the pSB1C3 PCR product (from Will) instead of the linearised backbone in the kit.
Thanks to IDT our EutMN gBlocks arrived today!
Saturday, July 15th.
Sunday, July 16th.
Monday, July 17th.
Restriction digest of PPK in pNIC proved that transformation worked! Sequencing is in order.
Skype call with an iGEM alumni - Ben Reeves from CustoMem.
Tuesday, July 18th.
More PPK stuff.
Meeting with supervisors for update on everything we have been doing.
Wednesday, July 19th.
Interview with Jonathan Abra - Innovation UK
EutS and EutMN Gblocks arrive from IDT, and the eut lab work starts!
Thursday, July 20th.
Cloning EutS + EutMN into pSB1C3 - restriction digest, ligate, transform
Skype call with Virginia iGEM about potential collaborations
Friday, July 21st.
We have colonies! Put plates in fridge over weekend, ready to inoculate on Monday and miniprep on Tuesday.
Saturday, July 22nd.
Sunday, July 23rd.
Monday, July 24th.
Phone call with John Liddell from the Centre for Process Innovation
Tuesday, July 25th.
Conference Call with Department of Environment, Food and Rural Affairs (DEFRA)
Checking pSB1C3-EutS + pSB1C3-EutMN transformation - miniprep, restriction digest and run agarose gel to confirm size
Wednesday, July 26th.
Results from yesterday = all negative; but skeptical as we have lots of colonies.. try colony PCR of the plates.
Thursday, July 27th.
pSB1C3-Eut S + MN colony PCR (using primers VR + VF2) results = several successful EutS colonies, none for EutMN. Redo digest, ligation and transformation of EutMN. Miniprep EutS and restriction digest to confirm.
Meeting up with Warwick iGEM team during International Biology Olympiad in Coventry. Visit them at https://2017.igem.org/Team:Warwick
Friday, July 28th.
EutLK Gblock arrives from IDT: we can get going with cloning - restriction digest, ligation, transformation
Humanity Hallows publish an article about our project!
http://www.humanityhallows.co.uk/igem-manchester-2017-the-path-to-recycling-fertilisers/Gone all the way to Seoul just to see you, Korean iGEMers! Very ardent talks on very spicy project details at a very rewarding evening meetup with a very passionate Korea University iGEMers.
Saturday, July 29th.
Phone Call with Dr. Linda Kahl - BioBricks Foundation
Sunday, July 30th.
Monday, July 31st.
We have colonies on the EutMN plate - inoculate!
pSB1C3-EutS: miniprep those showing positive by colony PCR - restriction digest and run gel to confirm size. Results = several produce expected results - can now send for sequencing.
Tuesday, August 1st.
pSB1C3-EutMN miniprep, restriction digest and agarose gel = expected result.. now can send for sequencing!
pSB1C3-EutLK colony PCR. Result = all negatives. So try to optimize the digestion and ligation of EutLK into pSB1C3.
PPK Design of Experiments: to optimise expression, the following factors and their interactions were considered: OD600 (at time of induction); post-induction temperature; post-induction harvest time; IPTG concentration.
Call with Dr. Benjamin Tam from Isle Utilities!!
Wednesday, August 2nd.
EutLK cloning into pSB1C3: try with pSB1C3 PCR product (from Takano lab)and pSB1C3 supplied by iGEM in kit.
Results from yesterdays DoE experiments are analysed and the best conditions for optimal PPK induction are identified.
Thursday, August 3rd.
EutLK + pSB1C3 ligations: try different ratios of insert to vector in attempt to optimize.
Friday, August 4th.
pSB1C3-EutLK transformation.
Interview with Dr. David Tompkins and PhD student Katie Ward - Aqua Enviro
Woah! Another group photo and not a moment too soon! #iGEM2017 #TotallyLegit #9Nerds
Saturday, August 5th.
Sunday, August 6th.
Monday, August 7th.
pSB1C3-EutS and pSB1C3-EutMN sequencing primers have arrived, so now send the to eurofins for sequencing.
Tuesday, August 8th
Meeting with United Utilities. https://www.unitedutilities.com/
Wednesday, August 9th
Unfortunately all pSB1C3-EutS and pSB1C3-EutMN samples send for sequencing had deleterious mutations. We have some other samples which showed positive results on the restriction digest, so send those and try.
Continuing try to clone pSB1C3-EutLK: colony PCR.
Thursday, August 10th
We now have a correct, fully sequenced pSB1C3-EutS and pSB1C3-EutMN ready to assemble together, submit, and characterise as a new biobrick.
Friday, August 11th
Saturday, August 12th
Sunday, August 13th
Monday, August 14th
pSB1C3-EutSMN biobrick assembly: restriction digest of pSB1C3-EutS + pSB1C-EutMN and gel extraction of pSB1C3-EutS 'cut' and EutMN 'cut' fragments. Ligation at 3:1 ratio.
pSB1C3-EutLK Colony PCR showed all negative results.
Overexpression (conditions determined by previous DoE experiments conducted) and purification of the PPK constructs using a nickel affinity column. Once isolated, each will be used in an ADPglo (Promega) assay to assess kinetics regarding polyphosphate production.
Tuesday, August 15th
Transformation of pSB1C3-EutSMN.
Wednesday, August 16th
pSB1C3-EutSMN results: a few colonies (negative plate clear). Inoculate overnights.
Thursday, August 17th
pSB1C3-EutSMN miniprep, restriction digest and agarose gel to confirm insert: 3 positives = send for sequencing.
We made a poster! iGEM UK meet up, here we come! #iGEM2017 #iGEMUKmeetup #MirrorDimension #CanYouReadBackwards.
Friday, August 18th.
Try to assemble pSB1C3-EutLK using Gibson assembly. Also PCR EutLK gblock up, as it is running very low.
pSB1C3-eutSMN sequenced and correct - our first composite part ready to send, characterise and hopefully (when we have EutLK) assemble with pSB1C3-EutLK.
UK meet-up! How lucky were we to meet Dr Stefanie Frank, the co-author of the academic paper on which we base our project!
Saturday, August 19th
Sunday, August 20th
Monday, August 21st
pSB1C3-EutS/MN/SMN overnight cultures ready for induction (characterisation) experiments to follow.
Tuesday, August 22nd
pSB1C3-EutS/MN/SMN induction with 250uM IPTG, 0.1uM Tetracyline, or both, respectively.
Wednesday, August 23rd
pSB1C3_eutLK - colony PCR (all negative)
pSB1C3_eutS/MN/SMN induction experiments begin
After weeks of trying to set up a visit, today is finally the day!! Site visit to Davyhulme Treatment Works!!
Thursday, August 24th
Induced eutS/MN/SMN cultures are harvested and protein lysates run on SDS PAGE to assess protein production.
EutLK gblock PCR to synthesise more, ran on a gel and extracted.
New cultures for EutS/MN/SMN induction experiments set up to be harvested (after 4hrs and 20hrs), and assessed via western blotting.
Friday, August 25th
Saturday, August 26th
Sunday, August 27th
Monday, August 28th
Bank holiday = we can't get into the lab!
Tuesday, August 29th
“A great man is one who leaves others at a loss after he is gone." - Paul Valery
Farewell Maciej, have a great time in Japan and see you in Boston!!
Wednesday, August 30th
EutS/MN/SMN cultures inoculated overnight
Thursday, August 31st
eutS/MN/SMN overnight cultures induced and incubated for 4 and 20hrs.
Friday, September 1st.
eutS/MN/SMN cultures harvest and protein lysates ran on gels and western blotted.
They say Adam is still waiting ‘till this day!
Saturday, September 2nd
Sunday, September 3rd
As part of our outreach activities, we have organised a Microcompartment Day in the office! This will surely become an annual celebration!
Monday, September 4th
gibson assembly of pSB1C3-eutLK
Tuesday, September 5th
pSB1C3-eutLK - colony PCR
Wednesday, September 6th
pSB1C3-eutLK - restriction digest and ran on gel = insertion confirmed.
Thursday, September 7th
pSB1C3-eutLK sent for sequencing
Friday, September 8th
Saturday, September 9th
Sunday, September 10th
iGEM Manchester Ambassador, Maciej, deployed to Yokohama (Japan) to investigate the progress of our friends from Botchan_Lab_Tokyo Team!
Monday, September 11th
pSB1C3-eutS/MN/SMN/LK induction experiments: using fresh transformants and only inducing for 4hrs (suspect that proteins are toxic, as we are struggling to see their production, the cultures grow very slowly, and cloning them in the first place was difficult).
Tuesday, September 12th
Wednesday, September 13th
Thursday, September 14th.
Since western blot for Eut protein analysis are not showing any results, we are going to try to assess eutM production after 4 and 20hrs using the plate reader (eutM is tagged with GFP).
Friday, September 15th
Saturday, September 16th.
Sunday, September 17th
Monday, September 18th
Preliminary results from the eutM-GFP plate reader experiments looks good - let's implement 'design of experiments' to optimise eutM production.
Tuesday, September 19th
Univerity officially starts for us!! And we still have so much to do..
Continued assessment of eutM-GFP production using DoE - testing incubation temperature, Tetracycline concentration, IPTG concentration, medium grown in, and post-induction harvest time.
Wednesday, September 20th
Thursday, September 21st
Friday, September 22nd
Saturday, September 23rd
Sunday, September 24th
Monday, September 25th
Tuesday, September 26th
Wednesday, September 27th
Thursday, September 28th
Friday, September 29th
Saturday, September 30th
Sunday, October 1st.
Monday, October 2nd.
Tuesday, October 3rd.
Wednesday, October 4th.
Thursday, October 5th.
Friday, October 6th.
Saturday, October 7th.
Sunday, October 8th.
Monday, October 9th.
Tuesday, October 10th.
Wednesday, October 11th.
Thursday, October 12th.
Friday, October 13th.
Saturday, October 14th.
Sunday, October 15th.
Monday, October 16th.
Tuesday, October 17th.
Wednesday, October 18th.
Thursday, October 19th.
Friday, October 20th.
Saturday, October 21st.
Sunday, October 22nd.
Monday, October 23rd.
Tuesday, October 24th.
Wednesday, October 25th.
So it’s not apples today! Strategic skype call with our fruit expert, Maciej, deployed to Japan to investigate the influence of GMM plants on the consumer behaviour in the fruit industry! Result of investigation: apples are expensive in Japan
Thursday, October 26th.
Friday, October 27th.
Wondering what this might be? That’s our Phosphostore device for biological wastewater treatment plants! Check out our Entrepreneurship page for more details as it is now officially completed!!!
Saturday, October 28th.
Sunday, October 29th.
We have finally completed our iGEM collaboration. All 137 iGEM participants from 10 teams, 10 countries and 5 continents created a comprehensive document on GMM legislations around the world. Thank you for your efforts!
Monday, October 30th.
Tuesday, October 31st.
Wiki freeze coming in hot! *panic
