Team:Newcastle/Notebook/Diary

Culture Shock Diary

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iGEM Week 1

June 20^th

Kristina, Ollie and Josh made streak plates of all the colonies for the interlab, which were left to incubate over the weekend and made liquid cultures for use in the lab. Jake, Emilija, Ollie, Kristina, Kerry, Rupert and Lauren read relevant literature, planned the upcoming week, wrote the agenda plan and typed up the minutes from the previous meeting, as well as starting to plan the Wiki. Josh was introduced to the training and lab techniques the rest of the group had already received, such as sterile microbe handling in the fume hoods, lab safety and fire drills.

June 21^st

The morning was spent brainstorming ideas for wiki themes and layout. It was decided to make a baseball themed cards for the team members and old Coca Cola advert was used for a colour scheme and theme. Then we had a lecture about COMSOL and MATLAB by one of our supervisors Dana Ofiteru. In the afernoon we checked the strak plates and then split into sub-groups to research Beyond the bench & Light Bulb component of the breadboard. At the end of the day we skyped with Edinburgh to discuss possible collaboration.

June 22^nd

In the morning Jake and Kristina analysed the first Interlab Results while Ollie and Josh researched papers on fuel cells and components for the light bulb. At the same time Emilija and Lauren researched components for the light bulb and tried to construct some BioBricks on Benchling. Rupert designed the Navigation bar for the wiki and Kerry worked on the project description for the Wiki which deadline is on the 1st of July.

In the afternoon all of us met with Professor Ian Head, Dr. Ed Milner and Paniz Izadi from the School of Civil Engineering and Geosciences to discuss microbial fuel cells. After that light bulb sub-team met with supervisors to discuss our light bulb biobrick and then we went to a weekly meeting with our 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.

iGEM Week 4

July 18^th

In the morning we consulted with Tom Howard on preparing for sixth form open day: discussing potential future applications of the technology - stressing interface between biology and technology such as smellivision/smelloscopes, biowarfare - detection and decontamination, detection and disarmament - not straight biosensor, system that responds to a detection. In the afternoon we were occupied with fundraising outreach, wiki markup, travel to Edinburgh & Westminster meetups arrangements, correcting protocols and investigating blue light protein.

July 19^th

Today was spent preparing for synthetic biology school taster sessions where we together with our supervisor Dr Tom Howard will present synthetic biology, iGEM and our project to sixth form students. In the afternoon we had a discussion about ethics of our project, sorted some Boston travel arrangements and wrote an agenda for Wednesday's meeting.

July 20^th

Open Day school visit - Ollie, Rupert and Kerry demoed John Adams electronics kits etc to attain feedback on design and usability and inform subsequent design rationale. Feedback for the snap-together kits was more positive than the ‘Spy’ style kit - analogs to wires much more popular than blocks that simply connect together, allow more freedom. Instructions were also much more clear when clear graphics used. Our project was explained to them and they seemed to understand, did a mini-iGEM competition and encouraged them to think about ethics and benefits/risks of their ideas.

Rulebender models for more constructs manufactured and tested, preliminary GUI designs for the raspberry pi interface drawn up, parts checked for ordering from iGEM HQ by comparison to the database. Agar plates were prepared all day for the cell survival study on Friday 22nd.

July 21^st

Contact made to secure waste water for the microbial fuel cell from the Cassie Building, responding to Open Lab to confirm our requirements and begin setup procedure for building prototypes of the board components. We also got in touch with the PEALS group (ethics committee) to begin booking a training day for our team. Pouring agar plates in advance of bug survival protocol for Friday 22nd. Delivered another sixth form open day, engagement was very strong on this day in terms of ethical debate.

iGEM Week 5

July 25^th

This morning we have spent writing bug survival protocol and preparing TBA, M9 and LB media. In the afternoon, half of the team have met with Natalio Krasnogor to pitch our project to him and the other half received FabLab induction and learned how to laser-cut components.

July 26^th

We began the day with half of our team (Josh, Kerry, Kristina and Emilija) going into the lab to carry out a trial run of out E.coli survival after heat shock experiment and hit a few snags. The space required to carry out this experiment is quite large and one sterile hood was not enough. We ran the experiment for only half an hour due to these issues. We began to make improvement for the protocol to ensure the full experiment runs much more smoothly next week.

Other members of the team (Ollie, Jake and Rupert) went to work on profiling the voltage-current response of various media, TAE, TBE, LB and 1M NaCl solution. This required the team to build a testing rig and adapt containers to allow the experiments to take place. After profiling the voltage-current response of the media we investigated the temperature change caused by the Joule heating effect on the material.

We discovered that we needed a larger voltage than previously anticipated to produce a localised heating effect. This was because the resistivity of our media were found to be higher than originally anticipated. To counter this we started to investigate ways of increasing the current throughput, e.g. by increasing the conductivity. We also learnt how to make microfluidic devices as these will be easier to induce a heating effect in.

The team worked in the computer cluster carrying out a range of tasks such as writing up improvements for the E.coli survival protocol, writing our bios for the experiment website and working on our presentation for the Scottish meetup on Thursday 29th at Edinburgh university. Our presentation is set to be an altered version of that given at the sixth form day on Wednesday and Thursday of last week. The presentation will contain information about our project and where we can see our research and ideas in the coming years. We are also posing some important ethical issues that we have and will be encountering throughout our project.

July 27^th

The morning we have spent preparing presentation for the Edinburgh meet up on Thursday 28th of July and preparing for launching our experiment.com fundraiser page. In the afternoon we prepared agenda for the meeting with our supervisors and attended the meeting afterwards (see 27th July meeting agenda and minutes).

July 28^th

Today we attended iGEM 2016 teams Scottish meet up in Edinburgh where we have spent the day exploring the city, listening to other teams iGEM presentation and sharing ideas with like-minded people (see more Collabotions:Edinburgh).

July 29^th

In the morning two members of the team visited OpenLab to discuss breadboard design. Other computer scientists were working on the designs for the Rasberry Pi. The rest of the group were repeating bomb calorimeter experiments. In the afternoon we typed the minutes and started working on action items and updating the wiki.

August 1^st

In the morning Kerry, Jake, Rupert and Kristina were working on the Simulation Project, while Lauren was writing agenda and Ollie was in the FabLab working on the breadboard design. Emilija and Josh have spent the morning conducting Battery BioBrick research and registering for Flow Cytometry facility.

In the afternoon, Ollie, Kerry and Rupert were designing new breadboard components and Emilija and Josh were continuing their research on Battery Biobrick and started protocol design for Battery component. Alternative constructs protocol design was done by Jake and Lauren was doing RBS strength prediction.

August 2^nd

In the morning, Ollie and Jake performed conductivity experiments, Lauren looked over cloning protocols and continued with Kristina's experimental work. Rupert was going through code for simulator and clean it up. Josh investigated battery modifications and Emilija wrote the Scottish iGEM meet up feedback.

In the afternoon Ollie and Rupert designed cell holder component for the breadboard while Jake and Lauren went to see our supervisors Jem and Tom about BioBrick assemly. Kerry promotedexperiment on social media platforms and worked on the breadboard requirement spec and Emilija have written pros and cons for Foundational Advance track and updates missing diary entries.

August 3^rd

In the morning Lauren, Jake and Kristina discussed alternative constructs, ethics of our project and simulator with our supervisor Tom. Ollie continued investigating platinum wire and foil sources. Kerry worked on the requirements specification for the breadboard. Rupert spent the morning working on the designs for the breadboard kit, specifically exploring free alternatives to solidworks design software. Emilija updated medal requirements page for the wiki and started registration for iGEM Giant Jamboree. Josh looked in the registry for parts that can be used for new battery construct.

In the afternoon Lauren, Jake and Kristina built 4 new constructs on Benchling platform and developed Human Practices simulator ideas. Ollie completed technical drawings for new breadboard component designs and filled out design rationale document. Kerry arranged a local newspaper "The Chronicle" to write a story about us and our project. Rupert worked on wiki and formatted sponsors page.

Emilija filled the forms to register for Flow Cytometry facility and arranged a meeting with Dr. Goksel Misirli. Josh prepared battery report/ Then we all attended afternoon meeting with our supervisors.