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Students design award-winning superbug 'eater'

The concept of a new bacteria-eating virus designed to fight the modern-day superbug Clostridium difficile, has been developed by a team of University of Nottingham students in a global competition.

The ‘bacteriophage’ was devised by the team as part of their synthetic biology project that recently won a prestigious Gold Medal at the International Genetically Engineered Machine (iGEM) competition in Boston, USA.

C. difficile infection is the most common cause of antibiotic-associated diarrhoea in the western world and is a big problem in hospitals and healthcare facilities. The disease symptoms are caused by the release of two major toxins by the bacterium. 

Under normal circumstances, a healthy gut microbiome prevents the proliferation of C. difficile. However, when these good bacteria are obliterated by the use of broad-spectrum antibiotics, the bug proliferatesand causes disease. One way to counter the expansion in numbers of toxin-producing C. difficile is to use competing strains that are not producing toxin as a probiotic. 

The aim of the Nottingham iGEM team’s project, called Clostridium dTox; it’s not so difficile was to engineer a C. difficile bacteriophage (phage), to produce factors that would suppress toxin production. They demonstrated that the latest gene-editing techniques could be used to repress expression of both toxin genes (tcdAand tcdB) by targeting their mRNA. The ultimate goal is a C. difficile-specific bacteriophage therapeutic which stops toxin production in those cells that are infected with the phage, converting them into health-promoting probiotics. Unlike antibiotics, phage cause no collateral damage to the native gut microbiome.

The team was also nominated at iGEM for ‘Best New Composite Part’. A composite part is a functional unit of DNA consisting of two or more basic parts assembled together. These must include all characterisation information and be added to the Registry.

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Around 400 teams of more than 5,000 undergraduate and postgraduate students from 45 countries competed at iGEM. They were tasked with using the principles of synthetic biology, the ‘Engineering of Biology’, to design biological parts, devices or systems to address a real-world problem or to perform a novel, previously unseen function. The best ‘parts’ of every project are then submitted in the form of a ‘BioBrick’ to the iGEM BioBrick registry for use by others.

Director of the University of Nottingham’s Synthetic Biology Research Centre, Professor Nigel Minton, said: “This was a tremendous achievement considering the short time that the team had to design, build and test the parts needed for the innovative project they devised. We broke new ground for iGEM by engineering a strict anaerobic bacterium, rather than the more traditional chassis other teams focus on. This was made possible by the extensive skills and expertise available through the involvement of SBRC researchers who gave so much of their free time to supervise the team.”  

The University’s Gold-winning team members were; Lucy Allen, Hassan Al-ubeidi, Ruth Bentley, Sofya Berestova, Eun Cho, Lukas Hoen, Daniel Partridge, Varun Lobo, Fatima Taha and Nemira Zilinskaite.  For the duration of their project they were embedded within BBSRC/EPSRC Synthetic Biology Research Centre (SBRC)  at Nottingham, under the overall guidance of Nigel P Minton and Philippe Soucaille and under the close supervision of a dedicated multidisciplinary team comprising Louise Dynes, Daphne Groothuis, Dr Christopher Humphreys, Dr Carmen McLeod, Dr Michaella Whittle and Dr Craig Woods.

Human Practices and Public Engagement

The team devised a number of activities that explored how their creation, Clostridium dTox, could impact society. This included mining and carrying out a sentiment analysis of data from hundreds of social media comments on an online phage therapy video and exploring the current legislation surrounding phage therapy. They also researched what makes C. difficile such an important issue to society and how their project can help make a positive impact on communities by working towards the development of a novel therapy for its treatment. Finally, they held a discussion group with non-scientists, and interviewed five leading scientific experts in the field, including the UK Public Health England lead on C. difficile infection, to understand how the team could make their project as effective as possible.

Public engagement was an important focus for the team, which developed hands-on workshops to communicate the project in local schools, libraries, the media and to staff and students at the University. 

What the Judges said

Great project, great wiki!! You just light up so many questions in my mind and actually this is the key of synthetic biology! Thank you so much for your effort and all hard work!”

Super interesting idea to use temperate phages for this! …. You are clear on your achievements and reasoning throughout, which is super refreshing. Great effort!”

Really terrific modelling efforts! I really liked how thoroughly your work was documented on your wiki; everything was very clear.”

Overall the project idea was very innovative, and you have great characterization on your parts. Good job!” 

Very impressive! It is very inspiring that your project used phage therapy, RNA interference and the extended application of CRISPR/Cas technology.”

Amazing job, I hope that you continue this project.”

Sponsors

Nottingham’s iGEM team was generously supported by the University of Nottingham’s Research Priority Area in Industrial Biotechnology, through grant funding from the Wellcome Trust, the Biotechnology and Biological Sciences Research Council (BBSRC) and the National Institute for Health Research (NIHR) via the Nottingham Digestive Diseases Centre, by generous cash donations from Don Whitley Scientific Ltd, LanzaTech and  Seres Therapeutics and through in-kind support from Qiagen, Millipore Sigma, Promega, Eppendorf, New England Biolabs, LabFolder and Snapgene.  

Collaborators

The team is also grateful for the support given by the following collaborators: Team Biomarvel Korea and the teams from Imperial College London and the University of Warwick. 

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SBRC - Nottingham returns to New Scientist Live 2018

For the second year in a row, The Synthetic Biology Research Centre – Nottingham (SBRC) and its associated BBSRC NIBB - C1net hosted an exhibition stand which highlighted the great research we do here at the centre. The exhibition stand included an interactive computer model of a biochemical pathway displayed on an iPAD, developed by members of the SBRC computational team. This gave visitors the opportunity to decide how they would alter a metabolic pathway to produce the required end-product. Following from the success of having an anaerobic microbiology cabinet last year, Don Whitley Scientific very kindly loaned one of their anaerobic cabinets once again for us to display as part of our exhibition. We gave visitors an idea of what is like working in these cabinets through a fun task. This required them to transfer ‘knitted bacteria’ from falcon tubes into Petri dishes using tweezers against the clock! 

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We developed a Raspberry Pi sequencer for NSL to demonstrate how we check DNA sequences for errors. With assistance from Dr Michael Wilson of the Advanced Data Analysis Centre (ADAC), programming languages Python and Java were used to convert data generated by coloured beads (representing DNA nucleotides) passing an LED and colour sensor into the corresponding 4-letter DNA sequence.    

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Then we had several display cases showing Petri dishes and microscope images of the bacteria we use in the SBRC, plus a mini-bioreactor to help us explain how fermentation processes could be scaled up. Accompanying this we had some examples of potential products, such as a model tyre and a fuel tank, to demonstrate where the C1 compounds could end up after the bacteria have converted them into useful chemicals.      

“The new Scientist Live was a unique experience, as it offered the opportunity to communicate and explain the benefits of our scientific research to a wide range of people, aged between 9yrs and 40yrs. Not only were we able to inspire the young generation but also inform and address the concerns of many adults and older people. Of course such a huge event attracted people from different scientific fields, which gave us a good insight into what is happening in other universities and companies around the globe. I am really grateful for the opportunity to be part of the SBRC’s NSL team and I would definitely volunteer for that again.” Stylianos Grigoriou, SBRC PhD Student.

The final section of our stand was part of a collaboration set up with ARUP, a multinational professional services firm which provides engineering, design, planning and consulting services for aspects of the built environment. ARUP’s digital technical team designed a Virtual Reality Lab for us to use on the stand. Visitors were able to play the Virtual Reality demonstration and get the full feeling (visual and sound) of what it’s like to work in a lab, without having the risks of being in a full working lab environment. This included a serial dilution experiment and an explanation to why we do this technique as part of our synthetic biology research. With many people queuing up for this exhibit over the weekend, it was certainly a major draw to the stand.

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Over the 4 day event we were helped by many brilliant volunteers from the SBRC, who all demonstrated their enthusiasm and passion for science in their conversations as well as convincing possible sceptics about the benefits of our research. This was a great chance for them to inspire and motivate young people, adults and family audiences in which they all did an amazing job.

New Scientist Live was an enjoyable and valuable experience, interacting with the public and talking about our work in the SBRC at a range of levels, from the very young to adults as well as more experienced and knowledgeable members of the public. I was very impressed with what our outreach team put together for the SBRC exhibit; a virtual reality lab experience, Don Whitley Scientific anaerobic cabinet and Raspberry pi benchtop sequencer which all drew large crowds. I was proud to be part of the team and to represent SBRC Nottingham at such a high profile event.” Dr Andrew Dempster, SBRC Post-Doctoral Researcher.

 Another one of the highlights of the event was an amazing Cupriavidus necator bacterium costume (or Cooper as he was named) hand-made by SBRC post-doctoral researcher Dr Christian Arenas. This was a superb addition to the stand bringing in frequent curious visitors!! Many younger visitors were very interested in Cooper and Dr Christian explained that Cupriavidus necator is not a harmful bacteria but a helpful one which can turn waste gases into something useful!


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The event was extremely successful not only as a fantastic opportunity to highlight the wonderful cutting edge research taking place at SBRC–Nottingham but also for the researchers to raise public awareness and practice their science communication.

It was great seeing how people reacted when some of the things that might seem unreal and the products of imagination were mentioned. In some way we showed there that the weirdest ideas can come true with work and will. We, researchers, sadly live in a bubble difficult to break in the working environment. In my opinion, it is necessary to break it once upon a while, and these events are a perfect occasion for it. Seeing some of these surprised faces, especially the children’s, made the event worthy and left me a very good sensation at the end. Diego Orol Gomez, SBRC PhD Student.

 ARUP photo

A very big special thanks goes to everyone involved in the organisation and delivery of this event including:

SBRC Committee members: Louise Dynes (Project Manager), Dr Christian Arenas, Dr Ruth Cornock, Michelle Kelly and Dr Pippa Strong

SBRC Volunteers: Dr Andrew Dempster, Dr Muhammad Ehsaan, Stylianos Grigoriou, Diego Orol Gomez, Dr Patrick Ingle, Dr Carmen McLeod, Jacque Minton, Claudio Tomi Andrino and Federico Turco

Sponsors:

ARUP – Simon Blakeney, Dominic Evans, Tammy Strong and all the volunteers from ARUP who came to help with the VR

Don Whitley Scientific

Synthetic Biology Research Centre, Nottingham 

Network in Industrial Biotechnology and Bioenergy, C1net

BBSRC and EPSRC

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RCUK Global Challenges Research Fund (GCRF) Hub

The last few weeks have been busy with reports and experimental work, but also with proposals. In particular we are working on a full proposal for an RCUK Global Challenges Research Fund (GCRF) Hub. The topic is Industrial Biotechnology for Sustainable Development, and we were awarded an RCUK GCRF travel grant for a trip to meet with partners and stakeholders in India and work on developing the bid.

We managed to meet a wide range of organisations including large and small companies in the waste management, biotech and chemicals sectors, and also social enterprises, NGOs and government funded agencies. We can’t mention everyone, but particularly good sessions with companies Tata Chemicals, Praj Industries, Godavari Biorefineries, String Bio, Waste Ventures and Noval Ltd; NGOs Saahas and Toxic Link; the Biotechnology Industry Research Assistance Council and the National Solid Waste Association of India who all gave excellent advice.

As well as Prof Banks and Dr Heaven from BORRG, the UK visitors included Dr Joseph Gallagher and Dr David Bryant from Aberystwyth University’s Biomass Conversion and Biorefining group, Prof Nigel Minton from the University of Nottingham’s Synthetic Biology Centre, Prof Patricia Thornley from the Tyndall Centre at the University of Manchester, and Dr Pathik Pathak who directs Southampton’s Social Impact Lab. The host team included Prof Arvind Lali and Dr Annamama Odaneth from ICT Mumbai, Dr S Venkata Mohan from CSIR-IICT Hyderabad and Dr Shams Yazdani from ICGEB Delhi.

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If anyone offers you the chance to organise a trip involving visits by 10 senior academics to 5 separate cities on different days, the best advice is – duck. But in fact the visit was amazingly effective, allowing us to meet as a team and also to gather information, views and ideas from other stakeholder that will significantly strengthen the proposal. One particularly good feature was the round table sessions run by Pathik Pathak and Patricia Thornley at the end of the week.

Special thanks to Uma Patil of the UK Foreign and Commonwealth Office, the Science and Innovation Adviser at the British Deputy High Commission in Mumbai, who worked miracles to make it a really profitable trip.

Postgrads and postdocs are no doubt envious: actually this type of visit is more hard work than glamour and I don’t think anyone had time to see a single cultural artefact or historic site. On the other hand, these guys are all big names in their fields and were talking to some really expert groups on the subjects they love best – I guess you can’t ask for anything more enjoyable than that!

Links:
GCRF Hubs call www.rcuk.ac.uk/…/interdisciplinary-research-hubs-to-address…
UK FCO Science and Innovation Network www.gov.uk/…/organisations/uk-science-and-innovation-network
ICT Mumbai www.ictmumbai.edu.in/EMPBiodata.aspx
CSIR IICT Hyderabad www.iictindia.org
ICGEB Delhi www.icgeb.org/home-nd.html

 

Robots in the Synthetic Biology Research Centre - Nottingham

A state of the art robotics suite has been installed at the Synthetic Biology Research Centre (SBRC) Nottingham. The equipment, worth over £1.1m will enable world leading synthetic biology research. Scientists will use the robots to engineer large numbers of bacterial strains to turbo-charge their work towards creating chemicals for industry and transport fuels from waste materials. For example one of the foci of the SBRC is the creation of Cupriavidus necator strains capable of producing chemicals such as 3-Hydroxypropionic acid from waste single carbon gases, such as carbon monoxide and carbon dioxide. Furthermore the robots will be used to help advance our understanding of native bacterial CRISPR systems. This technology will play an important role in helping us modify pathways to improve the metabolic flux towards chemical products such as ethanol or 2,3 butanediol. 

Thanks to its modular construction our robotics platform is also well suited to help each of our researchers at different stages of their work. For example, a researcher may need to test hundreds of primer pair combinations to select a desired PCR product; or they may need to screen hundreds of bacterial colonies in their search for a desired DNA fragment or gene with required properties. Currently these types of experiments can take weeks or even months to accomplish. Using the robotic platform these types of work will take less than a week. Additionally, thanks to built-in Data Acquisition, Reporting Tools and a barcoding system, the scientists can easily access and extract all the necessary information about protocols or samples at any future time point.

The robotic platforms enable automation of common pipelines in molecular biology including plasmid assembly, transformation of bacteria, colony picking and screening. The SBRC-Nottingham will work with other researchers in the University and the wider area in order to fully utilise the high-throughput capabilities of the equipment. The platforms contain liquid handling robots, thermocyclers, a colony picker and spreader, incubators, shakers and a plate reader, connected by a robotic arm.

Robot 1Gene assembly, PCR, DNA size selection, cherry picking & quality control.

Rocot 2Colony picking, culture plating, sample collection, inoculation, & analyte purification.

 

Nigel Minton, Director of the SBRC-Nottingham said: ‘This is a fantastic addition to our research capability. The robots will allow us to not only automate many routine procedures but carry out 100s of experiments in parallel –something we can’t do currently. This will free up our specialist and highly-skilled research teams to focus on the more academically challenging aspects of their research and enhance our progress towards using bacteria to make chemicals and fuels for us sustainably’.

More information is available from:

Professor Nigel Minton, Director BBSRC/EPSRC Synthetic Biology Research Centre, University of Nottingham nigel.minton@nottingham.ac.uk  

The SBRC Nottingham is a BBSRC/EPSRC joint funded research centre led by Professor Nigel Minton and employs approximately 120 researchers including academics, research and technical staff and PhD students. The main location for the SBRC is the University’s flagship CBS Building on the University Park campus, Nottingham. In the UK, six synthetic biology research centres have been funded by the government in Bristol, Cambridge/Norwich, Manchester, Edinburgh, Warwick and Nottingham. These centres are part of a £200m investment in Synthetic Biology by the UK government.

Beckman Coulter was selected as the supplier of the robotic platform after a competitive tender process.

They are working closely with the SBRC during the installation of the equipment. Contact Magdalena Jonczyk (Magdalena.Jonczyk@Nottingham.ac.uk) for more information about the robots and to arrange a tour of the facility.

Contact Alan Burbidge (Alan.Burbidge@Nottingham.ac.uk) for more information about the SBRC Nottingham.

 

 

SBRC Newsletters

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