Culture Shock Diary

iGEM Week 1

June 20th, 2016

09:00 - 17:00

Josh had his training today and was introduced to lab techniques that the rest of the team had worked on during the previous week. These techniques included fire drills, safety techniques as well as use of the sterile hood.

The team got split into two groups

• Group 1 (Kristina, Ollie and Josh): Made streak plates of all the colonies needed for the Interlab study. These streak plates were left to incubate over the weekend. Alongside colony cultures, liquid cultures were also made.

• Group 1 (Jake, Emilija, Ollie, Kristina, Kerry, Rupert and Lauren): Looked at research papers in order to obtain

more scientific data for the experiment. We wrote up the agenda as well as the minutes from the meeting we had. We also planned out the rest of the week and began a plan for the Wiki.

June 21st, 2016

09:00 - 11:00

• Sat down to discuss ideas for the Wiki theme as well as the layout. We came up with the idea for baseball themed cards for the team description. We were inspired by old coke adverts and "pop art" for the colouring and theme.

11:00 - 12:00

• We had a lecture on how to use COMSOL and MATLAB by Dana Ofiteru.

13:00 - 13:30

• Checked the streak plates from yesterday. The team was then split into sub-groups to research about "Beyond the bench" ideas as well as the light bulb component of the breadboard.

16:00 - 17:00

• Had a team Skype session with Edinburgh University and discussed the potential for collaboration.

June 22nd, 2016

09:00 - 11:00

• Jake and Kristina: Analysed the InterLab Results.

• Ollie and Josh: Researched papers on fuel cells and components for the light bulb.

• Emilija and Lauren: Researched components for the light bulb and tried to construct some BioBricks on Benchling.

• Kerry: Worked on the project description for the wiki. (Deadline: July 1st)

11:00 - 11:30

• Ollie and Josh: Plated the Positive Control sample from the previous day in order to have enough of that sample for the team to repeat the interlab study.

13:00 - 15:00

• Everyone but Lauren and Emilija met with Professor Ian Head, Dr.Ed Milner and Paniz Izadi from the School of Civil Engineering and Geosciences to discuss microbial fuel cells.

• Lauren and Emilija met with our supervisors to discuss the Killer BioBrick

15:00 - 17:00

• We met with supervisors (See Agenda and Minutes for the 22nd June)

June 23rd, 2016

09:00 - 11:00

• We finalized the Killer BioBrick construct.

11:00 - 12:00

• We had a lecture on modelling by Anil Wipat.

12:00 - 12:30

• Lunch break time!

12:30 - 14:00

• Continued our training in modelling BioBricks after having lunch. We were also introduced to RuleBender.

14:00 - 17:00

• Attempted to model our Killer BioBrick using RuleBender.

June 24th, 2016

09:30 - 10:30

• We had a late start due to the outcome of the EU Referendum. As a team bonding activity we all decided to go out for breakfast together before beginning work.

10:30 - 11:00

• We all went to the library and double-checked our BioBrick design that we created using Benchling. Once we had agreed on the design we met up with Jem (one of our advisors) in order to verify that everything was ready to be sent off.

11:00 - 12:00

• Before lunch we went through all of the Action Points. We categorized them into groups based on what was completed and what still needed to be done. The tasks that needed to be done were assigned amongst the team.

12:00 - 17:00

• All the previously assigned tasks were carried out.

iGEM Week 2

June 27th, 2016

09:00 - 13:00

• We visited FabLab in Sunderland. They offer 3D printing, laser printing as well as much more. We were able to tour the lab and get a better idea of what that company could offer us. We decided that the two areas which interested us were the 3D printing for our breadboard but also the formation of electrical circuits.

13:00 - 14:00

• Lunch break time!

14:00 - 15:00

• Meeting with Andrew Filby to be introduced and become accustomed to the concept of flow cytometry.

15:00 - 16:00

• Obtained components for the fuel cell. Components included methylene blue, carbon electrode, cationic exchange membrane alongside other chemicals.

14:00 - 17:00

• Went through action points and planned what needed to be completed.

June 28th, 2016

09:00 - 10:00

• Made microbial fuel cell. See below for the microbial fuel cell protocol.

10:00 - 12:00

• Liquid cultures of our samples were made and then left in the fridge overnight to be ready for incubation tomorrow.

12:00 - 13:00

• Lunch break time!

13:00 - 17:00

We went to the library where we carried out a variety of tasks

• The breadboard design was made using TinkerCad software. We designed an approximation of the sizes of different components as well as how they would fit into the breadboard.

• In the meantime the light-bulb construct was redesigned.

• The Team Wiki was looked at and altered. We tried to fix the Navigation Bar and get some information up

June 30th, 2016

09:00 - 11:00

• The InterLab study was discussed with Tom. We discussed the errors that were made (systematic and experimental). We ran through the steps of the protocol with him and explained what was done at each step. Then we discussed limitations as well as modifications for the experiment.

11:00 - 12:00

• The light-bulb design construct was run through with Jem.

12:00 - 13:00

• Lunch break time!

• The team members who were going to Paris also went into town to buy essentials and exchange Euros.

13:00 - 15:00

• More cultures were grown up for another run of the InterLab study.

• IWBDA was booked and the Paris tickets were confirmed and picked up.

15:00 - 17:00

• Started writing up the final versions of various protocols we were using (for the InterLab, for the microbial fuel cell,etc).

July 1st, 2016

12:00 - 21:00

• Half of the team travelled to Paris while the other half stayed back in Newcastle.

July 2nd, 2016

09:00 - 12:00

• Exhibition Stands in Paris.

12:00 - 14:00

• Lunch Break

14:00 - 15:30

• Roundtable 1 - Synthetic Biology: Challenges and Risks
  • François Képès - Research Director at CNRS, founding director of the Epigenomics Project an iSSB
• Héloïse Muller - PhD at Institute Pasteur
• Andrew Tolonen - Leader of Tolonen group at the Genoscope-CEA
• Christophe Genisset - Security Officer at SGDSN (French Secretariat for Defence and National Security)
• Alexei Grinbaum - Researcher at LARSIM, the Philosophy of Science Group at CEA-Saclay

15:30 - 16:00

• Coffee Break

16:00 - 17:30

• Roundtable 2 - Synthetic Biology: A New Economic World
  • Philippe Jais - Chief Executive and Scientific Officer at Eukarys
• Cyrille Pauthenier -President of Abolis Biotechnologies
• Samuel Juillot - CSO at Glowee (In absentia - sent a PhD student in his place)
• Michael Krel - CEO at Enobraq

17:30 - 18:00

• Talk from Randy Rettberg about iGEM and its importance in the world

July 3rd, 2016

09:00 - 18:00

• Site-seeing around Paris

18:00 - 02:10

• Travel back to Newcastle

iGEM Week 3

July 4th, 2016

09:00 - 17:00

• COMSOL Training Day. The Multiphysics libraries were looked at and the sample projects were completed. Then using the sample as a guideline, we started trying to make a model for our experiment.

July 5th, 2016

09:00 - 13:00

• The InterLab study was run again. See below for the protocol.

13:00 - 14:00

• Lunch break time!

14:00 - 16:00

• COMSOL modelling continued. Errors came up with regards to Temperature Coupling so we were working on trying to solve the error.

• In the meantime, the rest of the team was working on the Action Points and trying to complete what hadn't been done yet.

16:00 - 17:00

• Attended a seminar entitled: "Synthetic Biology: Perspectives from artificial life" which was conducted by Professor Martin Hanczyc. His area of expertise revolved around microbial fuel cells and therefore his seminar was of great use.

• He seemed interested in our iGEM project which led to us Skyping him at a further date described later on.

July 6th, 2016

09:00 - 09:30

• Checked the plate reader in order to obtain the results from the InterLab.

09:30 - 12:00

• Results from the InterLab were processed and put into an Excel document. In the meantime, other members of the team were completing more of the Action Points which had not been done yet.

12:00 - 13:00

• Lunch break time!

13:00 - 14:00

• Skyped Chennai. We were able to exchange ideas and propose collaboration seen as they needed us to carry out some surveys in order for them to see how their project idea would be perceived in the UK and whether or not it would be accepted.

14:00 - 15:00

• Planned and prepared for the afternoon meeting with our supervisors.

• We went over the agenda and made sure that we were fully ready for any questions which were going to be asked.

15:00 - 17:00

• Had meeting with our supervisors.

July 7th, 2016

09:00 - 12:00

• Started preparation for plasmids to be sent to DNA 2.0

12:00 - 13:00

• Lunch break time!

13:00 - 14:30

• Continued preparing cultures for freezing and for the plasmids to be sent to DNA 2.0.

14:30 - 15:30

• Ollie and Lauren filmed for the School of Biology

15:30 - 17:00

• Went over and completed Action Points.

July 8th, 2016

09:00 - 12:00

• Mini-prepped plasmids to be sent to DNA 2.0

12:00 - 13:00

• Lunch break time!

13:00 - 14:00

• Using spectrophotometry, we measured the absorbance values of the plasmids as well as their concentration and packaged up the sample chosen to be sent to DNA 2.0.

14:00 - 16:00

• Went over and worked on Action Points

16:00 - 17:00

• Meeting with Patrick Degenaar to discuss our experiment and potential limitations which it may have.

July 11^th

Today we designed the cloning strategy for the light bulb construct which is expected to arrive at the end of next week. We also arranged for our light bulb construct to be sent off to DNA 2.0 for synthesis. Once this had been done we worked on developing our bug survival protocol ready for conducting the experiment in the following week. Later, we prepared for this week's meetings by producing detailed plans for each of the sub-teams in the form of gantt charts. To finish off the day we Skyped with experiment.com representative Chistina Tran to discuss crowdfunding for our iGEM project and iGEM challenge.

July 12^th

Today we prepared to compete in the experiment.com iGEM challege, writing up descriptions of our work with the aim of attracting crowdfunding. In tandem with this we polished up our wiki pages, in particular we wrote up biographies for the people who have supported us.

We also registered, and arranged travel for, the Westminster iGEM meetup in August. Finally, we met with our supervisors to discuss cloning strategy for when we get our construct back from DNA 2.0.

July 13^th

We spent the morning looking for funding opportunities and sent out emails to organisations seeking funding. And prepared for our weekly meeting with our supervisors. We also prepared our constructs containing bicistronic RBS and rpoH gene to be sent to IDT to be synthesised.

July 14^th

Today was a day of meetings. First up we skyped with the Edinburgh team to discuss possible collaborations and side projects as well as our experiences on the iGEM project thus far. Following this we skyped with Dr Martin Hanczyc from the University of Trento who had recently given a seminar at the university on improving the output of microbial fuel cells to see if he could provide any advice on improving our fuel cell.

After a brief lunch break during which we finalized our Boston travel details and sent them off to be booked we met with Prof. Gatehouse. There we discussed ethical issues related with GMOs and our project.

July 15^th

Today was spent running bomb calorimetry experiments in order to determine the specific heat capacity of various media in order to inform our COMSOL modelling.