Support & Acknowledgements
We would never have been able to proceed on our iGEM journey without the input and immeasurable expertise of our supervisors and advisors. Given the novelty of this field we have relied on the insight of a huge range of individuals, and we extend our gratitude to every single one of them.
Professor Anil Wipat is a Professor of Bioinformatics at the School of Computing Science. He co-directs Newcastle's Interdisciplinary Computing and Complex BioSystems (ICOS) research group and is also affiliated with the Centre for Bacterial Cell Biology and co-director of the Centre for Synthetic Biology and Bioexploitation. Anil's experience in both biology and computing science proved extremely useful in guiding the project through to completion.
Dr Thomas Howard is a senior lecturer in microbiology in the School of Biology and led the inaugural University of Exeter entry into the iGEM competition and has been involved in iGEM ever since. He is now hosting the wet-lab aspects of the Newcastle iGEM 2016 team, and his extensive microbial knowledge informed the feasibility and development of our ideas.
Dr Jem Stach is a senior lecturer in microbiology in the School of Biology and worked on discovering the novel antibiotic abyssomycin that can potentially be used to treat MRSA. Jem's expertise in microbial genetics was instrumental in developing our biobrick submissions.
Dr Dana Ofiteru is a lecturer in the School of Chemical Engineering and Advanced Materials and secured use of COMSOL finite element analysis modeling software for our team and delivered training therein, as well as facilitating use of equipment for measuring specific heat capacity.
Dr Martin Sim is a research associate in the Centre for Bacterial Cell Biology working as part of the ICOS group, using molecular & synthetic biology for wastewater treatment. He has mentored and advising the team on molecular biology techniques, experimental design and in silico construct design and part synthesis.
Dr Matthew Peake is a research technician in the Devonshire Building, and is involved in and supports molecular, microbial & synthetic biology projects. He has mentored and advised the team on microbiology and demonstrated practical laboratory techniques.
James Skelton is a PhD student in the School of Computing Science at Newcastle University, he develops bioinformatics pipelines and methods to facilitate the development of synthetic biology approaches to wastewater treatment. He has mentored the team in rule-based modelling approaches.
Michael Martyn recently graduated from MSc Synthetic Biology at Newcastle University and is a Research Assistant in ICOS working on the Newcastle University Frontiers in Engineering Biology (NUFEB) project. He has mentored the team on in silico modelling and wiki design.
Professor Angharad Gatehouse has the Chair of Invertebrate Molecular Biology at Newcastle University and was ranked third in the world ratings for her citations on GM crops. She discussed ethics and human practices with the team, commenting on public opinions on genetically modified organisms.
Dr Jon Marles-Wright is a senior lecturer at Newcastle University and assisted the team with their part characterisation for the Edinburgh overgraduate team, as well as lending plate readers and providing general experimental advice to the wet lab team.
Professor Martin Hanczyc is head of Hanczyc Lab and is a Principal Investigator at the University of Trento. He graciously shared his knowledge of microbial fuel cells with us and gave insight into the future of these technologies.
Dr Lucy Eland of the ICOS Research Group supervised and instructed Ollie and Jake in the preparation and moulding of PDMS microfluidic devices, which became an integral part of the project.
Dr Patrick Degenaar consulted us on integration of biology and electronics and assisted us with circuit diagrams of some of our constructs.
Dr John Hedley advised the team on suitability of materials to use as electrodes in their microfluidic devices.
Dr Jochen Friedl, postdoc researcher of batteries for providing us with the equipment and expertise to facilitate our conductivity testing.
Dr Ed Milner, Dr Paniz Izadi and Professor Ian Head for showing us their work on microbial fuel cells, explaining best practice for their manufacture and providing us with the materials to build our own cell.
Dr Goksel Misirli met with team to discuss standard virtual parts and simulator architecture.
A huge thank you to Carl and Tony at FabLab Sunderland for providing expertise on 3D printing and product manufacture and teaching us the fundamentals of design work.
MakerSpace Newcastle for offering practical 3D manufacture advice from the local community.
Open Lab is a cross-disciplinary research centre at Newcastle University, and is one of the world’s leading research centres into human-computer interaction (HCI) and ubiquitous computing. The group consists of doctoral and post-doctoral researchers and academics from a wide range of disciplines, including computer science, electrical engineering, fine arts, psychology, sociology, education, clinical sciences and design. Tom Nappey and Jekaterina Maksimova, a design intern from the University of Dundee helped us bring our designs to life and manufacture the breadboard.
Lorraine Ward from John Adams Customer Services and the Product Designer team for providing feedback on their design rationale and strategy when producing electronics kits for children.
As you'll see from our team page we are an interdiciplinary group, consisting of Biologists, Computer Scientists and Biomedical Scientists. This brought a number of different and unique perspectives to our project. Although every team member has played a part in every aspect of the project, in order to manage our time effectively we divided our team into a number of different sub-teams. Each of these were responsible for working on a different part of our project.
The breadboard team, consisting of Ollie and Rupert was responsible for the design and construction of the plug 'n' play style kit we produced to serve as a demonstration of our technology. This involved making CAD desgins of the various parts, sourcing materials and ultimately fabricating our kit using 3D printing and laser cutting. Along the way, they engaged with members of the local maker community to seek expertise on the design anc construction of our kit. The kit was developed iteratively so that this expertise could be incorporated along the way.
The component team of Jake and Ollie were responsible for the design and construction of the chamber at the heart of our kit. That is, the part which integrates the bacteria with the electronics. This required modelling, construting, and testing various containers. Of which there were many. Informed by our modelling we eventually settled on a microfluidics chamber design which was best suited to producing the heating effect we required. As well as testing the chamber design to avoid leaks and so forth this team was also responsible for deciding upon the best growth medium to use, which required conducting heating experiments, and electrochemical impedence spectoscopy work. This team also investigated ways that we could measure the output of our system electronically using photoresistors.
In addition to our bilogical lightbulb constructs, we also worked on a number of other components combining bacteria and electronics. Our variable resistor parts, including our light dependent resistors and our biological 'capacitor' were researched and designed by this team of Lauren and Jake. This involved a mixture of reasearching suitable BioBrick parts and assembling them into genetic circuits, and lab work to process our synthesised parts and verify that they worked, or didn't work, as we expected them to. For example, our Zinc sequestering experiment.
Our wiki team, lead by Rupert and assisted by Jake and Kerry was responsible for the design and construction of our iGEM wiki and the related task of documenting our various constructs on the parts registry. The team designed the overall structure and style of the wiki as well as producing the various graphics you see here today whilst the content was supplied by the other individual sub-teams.
Kristina and Jake worked on our modelling. The team used modelling to explore potential uses of our technology beyond the summer, and to inform our design process. This involved a number of different modelling tools, both for designing our biological constructs (rule bender and ODE modelling) as well as our physical hardware (multiphysics modelling). This subteam was responsible for taking the valuable insights from our models and incorporating them into the rest of the design process. For instance, after we conducted multiphysics modelling of our original chamber designs we found they were too large. Our modelling showed us that we needed to switch to microfluidics scale hardware. The modelling team also worked on our circuit builder which gives us a way to showcase how bacteria and electronics might be integrated in the future and allows wiki users to build hybrid bacterial-electronic circuits themselves.
Kerry and Rupert worked on the research, design and programming of our human practices 'thought experiment'. This is a game aimed at challenging people's perceptions of synthetic biology projects in order to engage them with our new technology and collect feedback. As part of this the team met with a number of people to gather ideas for content, particularly the Policy & Ethics in the Life Sciences research group at our University. They also researched existing uses of thought experiments in the physical and social sciences and used this to inform the design of our game today. Beyond that they set out to record some thoughts and feedback of users on the game to ensure that it was suitable for achieving our aim of encouraging users to think about the potential impacts of our technology.
Josh, Ollie and Kristina worked on our microbial fuel cell, or 'battery', parts. As this work builds directly on that of a previous iGEM team, Team Bielefeld in 2013 this sub-team had to do a lot of research to understand their work and how it could be improved. They were then responsible for designing and running experiments to evaluate how our porin constructs worked in practice, in the process constructing several microbial fuel cells following a protocol by the University of Reading's National Centre for Biotechnology Education.
Our lightbulb sub-team of Lauren & Josh were responsible for the experiments surrouding our various bacterial 'lighbulb' constructs. From using existing registry parts like the htpG promoter, this team branched out into researching alternative heat-shock promoters we could use in our designs which lead to our dnaK promoter part. As well as designing our bulb constructs this team designed and ran all the experiments we needed to perform to see if our parts were working correctly and then processing this into a format suitable for putting on our wiki, and on the parts registry.
As with any large project, iGEM requires a lot of administration work. From arranging the travel to the different meet-ups we attended at home, in Edinburgh and London, and abroad in Paris. As well as making sure we all ended up going to Boston for the giant jamboree. All of which was handled seamlessly by Emilija in the admin sub-team. Also a big thanks to Claire Smith in the ICOS group for aiding with travel booking, ordering and Aaron Bolt at Selective Travel for dealing with the group travel booking
We are proud to have participated in the Third International InterLaboratory Measurement Study in synthetic biology. We originally completed the InterLab study as part of our laboratory induction course. However, over the course of the summer, as we gained more confidence in our wet lab work we repeated the InterLab two further times to improve the quality of the data we collected. This responsibility fell to the members of our InterLab team Emilija and Josh. They even expanded on our original goal of completing the plate reader measurements and chose to conduct the plate reader protocol as well!
Outreach & Funding
Kerry & Ollie worked hard on reaching out to companies to source the materials we required for our project at as low a cost as possible as well as sourcing local expertise on parts of the project which were entirely new to us, like physical fabrication. They are responsible for most of the sponsors you can see on our home page. The sub-team also co-ordinated our crowdfunding campaign and made the marketing materials like pictures and video which helped us spread the word about our project, and got us in the local paper.