Attributions and Acknowledgements:

The 2015 Exeter iGEM team has been supported, advised, and generally guided in the right direction by scientists of various disciplines, and industry professionals. We would like to thank every person who contributed to the project, no matter how significant or small the contribution.

Supervisors

Our supervisors were always there to guide us, encourage us, and provide constructive feedback to the team. They organised the foundation of our iGEM experience and supported us with an informed perspective on our ambitious concepts. A huge thanks to:

Dr Thomas Howard - Shell Open Innovation Independent Research Fellow, advised us with our project ideas and putting us in contact with relevant academics, as well as general modelling assistance. Tom was always around, helping us out with all aspects of the project - in fact, there’s not much he didn’t do for us!
Dr Paul James - Research Fellow, aided us in the lab and with operating various specialist equipment, and was a huge help in organising the iGEM itinerary. Paul advised us on everything and anything lab-related and guided the team with all aspects of the project.
Dr Elizabeth James - Associate Lecturer and Associate Research Fellow, was alway there to help us out with organising the outreach side of the project, target setting, finances, and general admin.
Dr John Love - Professor of Synthetic Biology, and our iGEM coordinator, guided the team and officiated much of the project. Without him, we wouldn’t be an iGEM team!
Dr Christine Sambles - Research Fellow, guided our ideas from the start and, in particular, gave us insightful advice on bioinformatics and using the NUPACK program.

Advisors

We were also helped through the project by our advisors, who gave us technical guidance and help in the laboratory at every step of the project. Many thanks to:

Ryan Edginton, Postgraduate Research and Exeter iGEM alumni, advised the team on time management, wiki construction, and general iGEM insight. He also put the team in contact with some academics within the university.
Dr Anja Nenninger - Postdoctoral Researcher, was enthusiastic and supportive throughout the project, and had some invaluable advice on laboratory techniques. We’d like to thank her for letting us use her buffers, ladders and, on more than one occasion, her bunsen burner!
Ross Kent - Molecular Biologist, was knowledgeable and understanding whilst we developed our skills and techniques in the Mezzanine laboratory, and had insightful advice on the technical parts of the project.
Dr Charlotte Cook - Postdoctoral Researcher, forwarded us relevant papers to read, provided us with specialist knowledge and assistance on cell free systems and dealing with RNA. We’d like to thank her for exchanging equipment with us - notably cell free kits & competent cells - so that we could get all our lab work done on time!

The Mezzanine Lab

We would like to thank the rest of the Mezzanine laboratory researchers for not only sharing their lab space, equipment, and materials with our team, but guiding and advising us on the technical aspects of the project. Many thanks to:

Dagmara Kolak - Mezzanine Laboratory Manager, trained us in basic laboratory skills and etiquette during the laboratory induction, and was always there to help us with general lab advice when we were at a loss!
Dr Chloe Singleton - Associate Research Fellow, offered us specialist advice on dealing with unstable RNA, and general laboratory guidance. She also helped coordinate the arrival and setup of our microplate reader.
Jamie Gilman - Postgraduate Researcher, offered us specialist laboratory advice, assisted and allowed us to use the robotic pipetter.
Richard Tennant - Postgraduate Researcher, assisted us with running FACS and Imagestream for our Interlab extra credit.
And to the rest of the Mezzaniners - thank you for putting up with us!

Human Practices Contacts

We contacted various other experts in the area of bovine T.B., and were privileged enough to be able to meet many of them in person as Devon is an area severely affected by the disease and so many bovine T.B. experts work here. Many thanks to:

Michael Ross of Saved and Safe, a company dealing with animal health, offered his guidance and contacts to the team. Michael is an expert in bovine TB management and was enthusiastic in pushing the outreach side of the project to go out and meet farmers and vets.
Phil Leighton is a local vet working for XL Farmcare. We hosted him at the university - his practical knowledge of TB testing in the field was eye-opening for the team and informed the design of our prototype TB test. He also offered us the opportunity to visit a farm and observe TB testing, which we gladly took up.
Richard Sibley is another local vet we have met with on several occasions. He has over 30 years of experience and runs myhealthyherd.co.uk, a tool designed for farmers and vets to help reduce disease among livestock. He provided an insight into the effects of bovine TB on both farmers and vets, and guided the design of our prototype TB test with practical knowledge.
George Eustice - MP for Camborne, Redruth, and Hayle, and appointed Minister of State at DEFRA, met with us in August to discuss the impact and awareness of bovine TB in the UK. We enjoyed meeting him and discussing the Ribonostics project.

General Acknowledgements

And finally, we received help from many sources inside and out of the university and would like to acknowledge all that guided, advised, and generally dealt with us. Many thanks to:

Jonathan Fieldsend is a computer scientist based at the university, he helped on our project by offering advice and guidance on our model. His input was gained through numerous meetings and had vastly shaped how our model looks and works. In the first meeting we had with him we changed the coordinate generation, plotting facility and completely restructured our code into functions. This was all included to speed up and make our code more efficient. In following meetings he offered more specific advice to improve it even further. We now have a model capable of providing a visual simulation and numerical output.
Marian Littlejohn provided feedback and guidance on the graphic design aspect of the project, as well as general advice about our wiki.
Natalie Garrett was kind enough to take our team and individual photographs, even at the top of the biosciences building on a windy day!
Oliver Carney, Applications Specialist, and Sarah Dickinson, Product Specialist, of BMG Labtech delivered and set up the FLUOstar Omega microplate reader. They were patient and understanding with the lab team during the setup and demonstration of the microplate reader we were kindly lent by BMG Labtech. Their in-depth explanation of the device and promise of continued support was much appreciated.
Peter Winlove, offered various support and advice throughout the project. This included a detailed meeting discussing the rate constant of our toehold system, and the design of our prototype.
Paul Hughes of Galloways Ltd., who printed our free business cards in record time - a generous offer and one we very much appreciated in the final weeks of the project!
Dale Cook of Affinity, who provided us with a copy of Affinity Designer, a fast, clean piece of graphics software. We relied on the program for most of our graphical work, and are extremely grateful to Dale for his generosity.

Attributions within the team:

A huge strength of our team is its interdisciplinary nature; having biologists, physicists, natural scientists, and biochemists allowed us to tackle the problem of bTB from different perspectives. We harnessed the diverse nature of our team and gave equal weighting to the three main areas of the project: the lab work, the modelling work, and the outreach (human practices) side of the project. Although every team member had input in all sections of the project, each of us had preferences in the area in which we worked. These are briefly outlined:

Todd, Amy, Dan, and David worked on the modelling section of the project. This included creating a simulation of our system with complex toehold-trigger interactions in a 3D environment, researching real world values for properties such as binding distances, viscosities, temperatures, etc., and solving problems such as confinement into a low binding affinity microcentrifuge tube.
We were all present in the laboratory at various stages of the project but the key laboratory members were Bradley, Emilia, Jasmine, Georgina and Joe. Lab duties included making up antibiotic plates and glycerol stocks (using liquid nitrogen), using the FLUOstar Omega microplate reader to gain accurate quantitative fluorescence readings, and running and extracting agarose gels.
Bradley, Emilia, Jasmine, and Georgina were all involved in toehold research and design during the early stages of the project. This included searching for a piece of target RNA present in a Mycobacterium bovis infection but not present in the BCG vaccine, and using tools such as NUPACK and UGENE to design a toeholds with a variety of chromoproteins and other markers. Yemi also created a detailed schematic of TB infection.
A small team comprised of David, Todd, and Rachel worked on the wiki design and implementation. This included coding, scripting, and styling the wiki, as well as designing layouts, templates, and making the carousel on the main page. In particular, Todd scripted the sliding logo in the navigation menu.
Joe, Amy, and Yemi handled the outreach side of the project - a monumental task. Their duties included meeting with various farmers, vets, and any other people involved with bovine TB in our local area and beyond. Their research informed our project and experimental design and proved invaluable to prototype design. In addition, Joe was in charge of creating a video to raise awareness of bovine TB in the local area.
A lab team composed of Bradley, Emilia, Jasmine, Georgina and Joe tackled the interlab study we volunteered to take part in. This included procedures such as miniprep, ligation, transformation, preparing overnight cultures, digestion, and sequencing.
Joe, Amy, Dan, and Bradley were all very involved in graphic design and produced some high-grade work including the TB infographic (by Amy), the carousel slides (various contributors), and an article (by Joe). Rachel and David contributed to layout design of wiki templates, presentations, and other such documents. Dan made some intricate graphics for the presentation. Georgina and Jasmine designed our Exeter stash for Boston - hoodies and t-shirts.
The presentation material was worked on as a team with some long nights involved! The main design was thought up as a group, building on the work Amy had done in her infographic. The implementation of this design was undertaken by Todd using the Affinity software kindly provided. This included making standard designs for the banner, poster and presentation. Todd and Dan put some hard work into writing our official abstract and title.
Our project involved much collaboration, and various members of our team were in contact with other iGEM teams. Emilia was communicating with the Bielefeld iGEM team by coordinating Skype calls and email exchanges. Dan and Rachel contacted Oxford iGEM to discuss modelling and collaboration. We all attended the UK iGEM meetup hosted by iGEM Westminster, where Bradley, Todd, Dan, and Yemi presented. Joe managed the Exeter iGEM twitter account, (as well as other social media) which resulted in a group skype of several teams, including iGEM Warwick, iGEM Manchester, and iGEM Sydney. Joe also sent an article to be published in a newsletter arranged by iGEM Amoy. In fact, Joe was a real hero on the collaborations part of the project and lead most of our Skype meetings with other teams, as well as being in charge of the team diary.
Our presentation in Boston is to be presented by Joe, Dan, and Todd. We wish them luck and all the best!

References

Please see the modelling page for references relating to the simulation created.

Please see the design page for references relating to our proposed testing methods.

Team:Exeter/Attributions