Welcome to Exeter iGEM's 2015 diary!

Following this diary will give you an insight into the progress of our project.

June

Starting the Interlab Study

Week One 1/6 - 7/6

Our first week was extremely busy as we all began to get to know each other as a team. We began work in the lab focusing on the Interlab study, in order to learn important lab techniques and also gain some all important iGEM credit. Beginning to understand transformation techniques, PCR and ligation was interesting to say the least, especially for the non-biologists among us.

As the week progressed the intensity of our research sessions increased. Any ideas were welcome no matter how far fetched or bizarre they seemed at the time. Naturally as we researched further the ideas were narrowed down, mostly as we discovered some were unviable for a number of reasons. We kept a focus on the time constraints of the project, the budget of the project and also facilities we have access to at the University. By the end of the week we had a handful of ideas that we split between our interdisciplinary team to research over the weekend.

Week Two 8/6 - 14/6

We started week 2 with a huge focus on the presentation we had to give on the Wednesday. Furthermore we worked out a timetable to re-do the Interlab study following some technical difficulties. We began engaging in some really good brainstorming sessions and also started to get to know each other personally. A chair was broken in a hilarious manner – still funny now.

The presentation was a success and all ideas were received well with the academics. After feedback we decided to take forward three of the ideas to give a second presentation in week three. This became the focus of the rest of the week. Going into the weekend we went on a team social that was very fun. Once again over the weekend the focus was to further research the three ideas.

Week Three 15/6 - 21/6

Presentation preparation with Joe's weird face

Week three has been the most intense week for us as a team so far. On Monday and Tuesday the presentation began to take shape. Deciding to split the group into three groups worked extremely well as each team focused on one idea and how best to present that idea. Furthermore we mixed the teams up. As some people were almost ‘attached’ to a certain idea due to the fact they had worked on it uniquely so far, we made sure everyone was working on the idea they had focussed the least on.

This was our final week of talks from certain groups and academics. Greenpeace came to talk to us and give us some important factors to consider for each idea. Wednesday arrived and we spent the morning running through the presentation before actually presenting it to a range of academics in the afternoon. Feedback was mostly positive and we were told all three ideas had great potential. We decided the deadline for choosing an idea was 5pm on Thursday. Thursday was intense. Debate, debate and more debate led us to a vote with the winning idea prevailing nine against two. It was so encouraging that we were unanimous in choosing to go for a well-deserved pint in the Devon sunshine. As I write this the day is Friday and week three is coming to a close. Today is being spent working out the GAME PLAN for how to start making some serious headway with the chosen idea. People’s strengths, preferences and interests have led to creation of various sub-teams.

P.S. We had more difficulty with the Interlab study.

Week Four 22/6 - 28/6

How is it week 4 already? This week saw the beginning of some hard-core modelling involving Brownian motion of both toehold switches and RNA using MATLAB. Many hours were spent toiling over getting the simulation just right, it seemed every time we thought we fixed it, something elsewhere would go wrong. Thankfully, by the end of the week we had a basic ‘working’ 3D model of Brownian motion, although it only worked using a few of each of the molecules (laptops don’t have much computing power surprisingly - time to look into accessing the university supercomputers!)

In the lab last week we spent our time working out what was causing MORE issues with the Interlab study. Our focus in the lab will hopefully soon turn towards our project but we refuse to be beaten by a lack of glowing E. coli.

July

Week Five 29/6 - 5/7

Lab action shot

This week’s main focus was constructing the sequence of the toehold switch, which was challenging, but good progress was made concerning the ribosome binding site, loop region, trigger, linker and GFP sequences. Our wiki is now beginning to take shape nicely with new team member profiles being constructed in addition to some photos of the lab team in action. The collaboration aspect of our project was addressed as we contributed to an iGEM newsletter about the aims and focus of our project. At the end of the week our focus shifted slightly to creating a project name and logo, which saw the establishment of Ribonostics (riboswitch+diagnostics). On Wednesday, we headed to the pub for teambuilding round two, which ended in a casual paper aeroplane competition dominated by the physicists.

Week Six 6/7 - 12/7

We have a first draft of our toehold switch! NUPACK has been the main agenda this week. Double and triple checking every part of our sequence means the sequence is nearly ready. Overall this week has been highly successful. At the beginning of the week, three of the outreach team headed into the Devon countryside to visit the head of a Veterinary practice. Hearing some first hand experiences of dealing with Bovine TB was extremely useful and we were also told of how our test would be implemented in the field. Taking this on board we made some considerations about the best direction to take the project from now on. Not to mention we made a very useful contact. As our project is extremely relevant in our local area we believe the ‘Beyond the Bench’ aspect of our project has huge potential. From the responses we have received so far it seems we are correct. Everyone is very engaged in what we are doing. We may be branching as far as New Zealand…Hopefully we have some exciting collaboration with fellow teams to come soon!

On Tuesday we headed out for a cheeky Nandos to celebrate Georgina’s birthday, followed by a few pints at a lovely old pub. Wednesday we decided to have an impromptu barbecue due to the nice weather. BBQ skills were questionable but everyone made it in on Thursday morning unharmed. Next week we have some important milestones we hope to reach.

Week Seven 13/7 - 19/7

Thank you Shield Scientific!

Sponsors, collaboration, researching indicators, updating our supervisors and some serious Beyond the Bench work sums up week seven. This week we have been busy contacting various companies and organisations in order to make them aware of our project and also determine if they would be willing to send us equipment. Armed with nothing but a list of email addresses and a mass of doughnuts we went email crazy. Overall we had a great response! Hopefully next week we will be the proud owners of SHIELDskin Orange Nitrile gloves to protect us in the lab WHILST looking pretty damn good. Fingers crossed we may be able to borrow a fancy microplate reader too. Wednesday we gave a presentation to our supervisor team in order to update them on the progress of all aspects of the project.

On Thursday we had a meeting with Paul James, our supervisor, to discuss the sequences of DNA we have designed for our toehold switch. Everything seemed to be in order, meaning we will be able to go ahead and order our DNA early next week. I’m sure the lab team who focussed on designing our toehold switches will be grateful to have a break from using NUPACK and UGENE for a while. However, the work never stops. Researching a wide range of indicators to incorporate into our toehold switch has taken a priority. Comparing the benefits of using a fluorescent protein compared with chromoproteins in both the lab and 'field' environment means a number of toeholds, all varying in indicator sequence, are currently being designed.

The Beyond the Bench side of our project is something we as a team believe has great potential. Understanding the extremely complex nature of eradicating TB in the UK, especially the South West, is challenging and rewarding. Collaborating with vets, farmers, politicians and academics will hopefully allow us to make a significant impact with this project.

Campus was alive this week with the sound of graduation! Seeing staff, students, parents and academics all dressed smartly created an atmosphere so infectious that we as a team decided to head into town on Tuesday and celebrate also. Honestly, the masses of free champagne had nothing to do with it. We had a great night and bumped into iGEM alumni on the dancefloor, they seemed approving of how we have taken to the challenge they laid down last year!

Week Eight 20/7 - 26/7

In preparation for the arrival of our highly awaited DNA, this week was focussed on designing protocols ready for the super exciting experiments we will be doing! Our resident lab team had to be careful not to miss any important details whilst also explaining to the non-lab members what they will be getting up to in the magical Mezzanine Lab. Collaboration within the team has been high this week as the modelling team came up with some important experimental data they need in order to make the model more accurate. We are confident this is something we can achieve.

On Tuesday we met with Phil Leighton, a highly experienced vet, to discuss our idea with him. Phil was highly receptive to the work we are doing and also had a number of important points that we as a team need to consider in order to make our test viable ‘in the field’. As a consequence of the meeting, on Thursday two members of the team travelled to a Cornish farm, accompanying Phil on a test he had to undertake on a handful of cattle. After we had made a fuss of the two Border Collies present, we saw how the testing occurs first hand, and also got the chance to talk to a farm worker in order to try and understand some of the frustrations TB causes for farmers. Our project aims, in the long term, to assist with the eradication of Bovine TB and therefore alleviate the problems it causes. The farm worker told us how TB testing is an extremely stressful event for the cattle, so much so that on this farm they have had cases of cows losing calves. Furthermore the process of herding and bringing them in is a highly time consuming activity. Hearing this first hand was extremely important for the development of our Beyond the Bench work.

Week Nine 27/7 - 2/8

Revolution! Week nine has been an extremely important week for us as an iGEM team. On Tuesday we said goodbye to our beloved Emilia who leaves us to go and work for Shell in Houston for the next year - not bad going to be honest! We all went out for a team meal and then on to the cinema to see Inside Out. We all want to wish her the best of luck on the adventure ahead of her. She was very excited when we gave her a cuddly E. coli teddy to take with her. However, Emilia leaving gave us a wake up call. Although we have made excellent progress up to now, in the last week or so we have been slipping behind - not ideal now we are also a member down. Therefore on Tuesday we had a team meeting to introduce some new rules to make sure we are all working for each other, working for the good of the team and also are aware of the work everyone else is doing. Introducing a team brief at the beginning of each day, a summary at the end of each week and a new deadline system means we will back up to speed in no time. Due to the technical difficulties we had with the Interlab study we decided to order DNA constructs to approach the task in a different way. This week our constructs have been arriving meaning this lab work will begin early next week. After some difficulties with our Toehold DNA it had to be reordered, meaning this DNA is still highly awaited for!

We Skyped Manchester-Graz this week and discovered the extremely exciting project they are working on. Hopefully we will be able to find areas of our projects that overlap and will therefore allow us to collaborate. Hearing how they are approaching the Beyond the Bench aspect of their project was particularly useful as both our projects involve dealing with disease.

August

Week Ten 3/8 - 9/8

It seems we have reached the stage in our project where the lab work is going to be a main priority as we get busier and busier with experiments to carry out. As the deadline for submitting Interlab data is approaching quickly, we spent week 10 working on constructing our G-blocks, transforming them and plating out E. coli god knows how many times. At the beginning of the week we were mostly optimistic that we should see some form of glowing, however we ended the week on a low as a lack of bright green E. coli has left us in a state of disarray. We sent our samples off for sequencing to try and make some sense of what has happened. Some good news is that our Toehold DNA arrived meaning we will be able to begin the testing of the science behind our project next week, HOORAY!

Away from the practical lab work we have been extremely busy in all other departments. Our model is progressing nicely, hopefully it won’t be long until it is finished. I think the modellers are tearing their hair out with the list of ‘demands’ the lab team have been making. On Thursday we had a big team meeting in order to decide exactly what we want our Wiki to look like and settle on a theme that will be uniform among pages. Further to this we also worked out what each section of the main menu and submenus will contain, something that is highly useful as deciding on all the pages that will be on the wiki means people can now begin to build these pages. It won’t be long until the wiki freeze is here - we are glad we as a team sorted that this week.

Twitter was very entertaining this week and we as a team managed to organise a Skype par-tay with a range of other teams. Hopefully this will work, it will be great to hear about the other projects and also see what areas we may be able to collaborate on. For Outreach we have chosen to make an informative video on the highly subjective topic of Bovine TB, we are currently making an initial plan for this.

Week Eleven 10/8 - 16/08

Woahhhhhh. This has been an intense week. Our Toehold DNA arrived at the beginning of the week and we began the process of getting it to the stage where we can actually test it, however after transformation problems we haven’t been successful in getting past the first stage. As time is flying by, we used this week to decide on what parts we want to further characterise as a team to make sure we are meeting the medal criteria. Lab work is still going to be very busy as we work hard to try and get our Toehold switch to work.

On Wednesday the model team Skyped with Oxford’s 2015 iGEM modelling team to try and work out possible collaborations. As our model is currently a simulation, we are keen to try and integrate a mathematical model into the work we are doing. Fingers crossed this will go ahead! Then on Wednesday afternoon we had another Skype. Initially this had been planned to be with 6 other teams but we only managed Warwick, Manchester and Sydney as the internet was having a nightmare. We all spoke for well over an hour about all the different aspects of our projects and we started to get quite excited about Boston - it really won’t be long until we get on that flight!

We’ve been short on numbers this week and on Thursday we said goodbye to Amy, one half of our physicists, as she goes off on her year abroad at Iowa University. We all wish her the best of luck and are already looking forward to seeing her again in Boston. That’s now two people we have had to say goodbye to during the summer :(. As Outreach has been one of the main driving forces behind our project, it is a shame that during the last two weeks there hasn’t been much progress. However we should have the Outreach team back to full strength next week meaning we can begin to make some serious progress - including getting our video filmed.

Week Twelve 17/8 - 21/8

Our trigger RNA arrived this week just in time for us to discover that it is the wrong sequence! We eventually figured out that this was because the software we used automatically deletes uracil bases so we ended up with a much shorter sequence than expected. We ordered the RNA again, but it will take approximately three weeks to get to us! This holdback has resulted in a change of plans for the lab team who have been focusing their efforts on the characterisation of chromoproteins as well as continuing the Interlab study. Wednesday was a particularly exciting day because we got the chance to use our shiny new FLUOstar plate reader, courtesy of BMG labtech.

Exeposé, our university newspaper, asked us if we’d be happy to be the focus of the science & tech section and join them for an interview - of course, we said yes. The interview went pretty well and gave us the opportunity to reflect on the past two months and to realise how much we’ve learnt in such a short time.

Our wiki is still building improvements including a carousel of images for our home page. Beyond the Bench team have been busy preparing for our meeting with George Eustice MP, Minister of State at DEFRA.

Week Thirteen 24/8 - 28/8

Monday morning began with a long drive to the Penryn campus in Cornwall. We had our meeting with George Eustice, which was informative and enlightening. If our project goes well, he will let the appropriate people know. This week in the lab we successfully expressed 3 different chromoproteins cell free; the repeats were consistent with initial testing. It was nice to see something go right in the lab. We also finished up experiments and data analysis of the Interlab study constructs to submit the data to iGEM before the deadline later in the week.

The modelling team decided to restrict our system simulation to a cylindrical shape to more accurately reflect the lab work. We also began designing the banner and poster for the UK meetup next week. We had a frantic late night session at Todd’s house to finish off the presentation and poster, in order to send off the poster for printing the next morning at 9am!

Jasmine also skyped NAIT Edmonton and talked about Policy and Practices within the New Application track.

September

Week Fourteen 31/8 - 5/9

In the morning of bank holiday Monday, we had a skeleton crew of three working on the presentation, fine tuning it, ensuring it was the best it could be, and deleting unnecessary slides. We spent the first half of the week preparing for the UK meetup at Westminster University in London later on this week. On Thursday morning we got the cheap and cheerful Megabus up to London, and settled in the Travelodge, practicing the presentation to be performed the next morning.

On Friday, four of our bravest team members presented our project to a plethora of other UK teams. We also supported our supervisor Paul James, who had his own presentation to give on the work of the Exeter Microbial Biofuels Group. We spent the two days of the meetup mingling with other teams and learning about their projects. A huge thank you to Westminster, who were so, so welcoming and wonderful as hosts, and thanks feeding us pizza before the mad dash to the train station to go home!

Week Fifteen 07/9 - 11/9

We are nearing the end and all areas of the project are being pushed to finish. Lab work has been carried out into the evenings and weekends, and this has resulted in some good news - our construct Green J23100 works! In the presence of trigger RNA the switch is on, and in the absence of trigger it switches off. This is major news for the team and provided a much-needed morale boost. Work has began on turning the constructs into BioBricks, keeping the lab team busy!

Our outreach team has also been working hard, arranging visits to local sixth form colleges and engaging with the public to get footage for our outreach video. We Skyped Amy in Iowa, to keep her up to date on the project and discuss modelling solutions. The week in general has seen a lot of discussion with our advisors about all aspects of the project. Todd created a prototype test tube in Open SCAD, and we consulted the physics department on the finer details of this prototype.

Lastly, we spent some time arranging our swag to give out in Boston - to see what we have you’ll have to visit us at the Giant Jamboree!

Week Sixteen 14/9 - 19/9

The final week was a tiring, stressed out trial, but we managed it. We spent late nights writing up and proofreading wiki content, entire days in the lab frantically trying to squeeze as many results out of our toeholds as possible, and many many hours filming and editing our video footage. Bielefeld kindly provided information on their home-made cell-free kit for our costings section, making our test significantly cheaper.

As well as all this, university began with Freshers week, meaning campus was rammed and workspace was limited. It also meant some mornings were met with hungover team members! Still, the outreach team managed to visit two sixth form colleges to speak about synthetic biology and our project. On Friday we presented our project to the physics department.