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Posts Tagged ‘C. difficile’

Nottingham iGEM Team Win Gold Medal!

Words and pictures provided by the University of Nottingham:

iGEM Team

The University of Nottingham’s 2018 iGEM team have been awarded a prestigious Gold Medal and were nominated for ‘Best New Composite Part’ at the recent International Genetically Engineered Machine (iGEM) competition in Boston, USA.

It is the first team from Nottingham to win a Gold Medal, which was awarded at the iGEM Jamboree event in Boston on Sunday 28th of October 2018.

iGEM

The iGEM competition began in January 2003 and currently attracts over 400 teams, from more than 45 countries and annually exceeds 5000 global undergraduate and post-graduate student participants. Teams use 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.

University of Nottingham's iGEM team

University of Nottingham’s iGEM team

The Team

Nottingham’s team was composed of ten undergraduate students drawn from the Schools of Life Sciences, Biosciences, Computer Science, Mathematics and Social Sciences. 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.

Clostridium dTox

The team’s innovative synthetic biology project, Clostridium dTox; it’s not so difficile, aimed to develop a novel therapy for the treatment of disease caused by the superbug Clostridium difficile, colloquially known as C Diff.

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

The project’s aim was to engineer a C. difficile bacteriophage to produce factors that would suppress toxin production. The strategy adopted was to repress expression of both toxin genes (tcdA and tcdB) by targeting their mRNA using either antisense RNA (asRNA) or CRISPR interference (CRISPRi) technology (dCas9). The ultimate goal is a C. difficile-specific bacteriophage therapeutic which ablates toxin production in those cells that are infected with phage, converting them into health promoting probiotics. Unlike antibiotics, phage cause no collateral damage to the native gut microbiome.

The team was also nominated 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.

Human Practices and Public Engagement

The team devised a number of activities that explored how 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 and to staff and students at the University. The team members have also been busy promoting their project via a range of social media platforms as well as by publishing articles in a local newspaper and in the University of Nottingham’s Impact Magazine.

Gold Medal

All of these aspects enabled the team to produce a project of high enough quality to win a Gold Medal at the Giant Jamboree, recognising the fulfilment of all the competition criteria. The 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.

“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”. – Nigel P Minton, SBRC Director, Nottingham

“Doing iGEM has given me a holistic understanding of the synthetic biology process. Coming from a Computer Science background, I had no knowledge of the science prior to iGEM, but working alongside talented team-mates meant that I left with a much better understanding of our project. I feel that my communication skills have improved since starting iGEM, as it has allowed me to interact with students and experts from many disciplines”. – Hassan Al-ubeidi, UG Computer Science.

“iGEM was an exciting challenge. As the sole modeller for our team, I improved my ability to work independently to research and solve problems. I learnt how to communicate my work in a way such that those with less technical knowledge can understand. Attending the Jamboree and seeing other projects made me appreciate the power of synthetic biology to build a better world”. – Ruth Bentley, UG Mathematics.

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 also wishes to acknowledge support provided by the following collaborators: Team Biomarvel Korea and the teams from Imperial College London and the University of Warwick.

sponsors for Nottingham iGEM

dw-weiss

Interview with Dr. William Weiss from University of North Texas

Our US distributor Microbiology International carried out this in-depth interview with Dr. William Weiss, a Whitley Workstation user from University of North Texas. 

Dr. William Weiss is the Director of Pre-Clinical Services at University of North Texas in Fort Worth, working to develop animal models in infectious disease for the evaluation of new and novel therapies in antibacterial, antifungal and antiviral research. He has been using a Don Whitley Scientific DG250 and an A35 anaerobic workstation for about two decades.

Read more about his research on novel antibiotics for the treatment of Clostridium difficile infection here.

Q: What manner of specimens are you working with and which bacteria do you cultivate in the anaerobic workstation?

A: Here in the Pre-Clinical Services group, we are essentially a contract research organization, and the majority of our work in the A35 anaerobic workstation involves C. difficile. We are carrying out various research projects for different pharmaceutical companies, and biotechnology companies, here in the US, as well as Europe and South America. There are various experimental models for reproducing C. difficile disease, for example, the “gold standard” model involving the hamster, and there is also one that involves mice.

Basically, in this model, spores from C. difficile are introduced into the animal, and they colonise in the gut. C. difficile spores come from the environment and are ubiquitous, but because they are held in check by the normal gut flora, they never proliferate and they never cause disease. It’s only when patients are treated with broad spectrum antibiotics that healthy bacteria are destroyed and C. difficile then proliferates and causes disease. That’s why often, people going into the hospital and receiving multiple antibiotics can develop C. difficile disease.

Q: So what is the role of the A35 workstation in your C.diff. research?

A: The model we are using to test novel therapies designed to combat this disease depends strongly on the A35: we grow the C. difficile culture by streaking the frozen cultures onto appropriate media, incubate them in the A35 chamber at 0% oxygen, and then harvest the vegetative cells and treat them to form spores, which we store. The spores are then introduced into the animals, the animals are treated with a broad-spectrum agent, they develop the disease, and we try different forms of therapy. The end-points in terms of efficacy are increased survival, as well as the amount of C. difficile that can be found in the fecal pellets of the hamsters, or in the contents of the cecum. We process the fecal pellets or a cecal sample and plate it, then we place those plates inside the chamber to incubate for about 48 hours. An animal that might have the disease could have 6 logs of C. difficile in their gut, whereas one that has seen successful treatment, such as with vancomycin, the gold standard right now, might be reduced from 6 logs to 2 logs or even less. All that incubation is being done inside the A35.

Q: The A35 isn’t your only workstation though, tell us about that.

A: With C. difficile being a larger problem than it used to be, we are seeing a real uptick in the number of companies interested in it, thus explaining our need for the A35 workstation. The C. difficile in the environment is very hardy, because it can form spores, but in order to count the spores, they have to germinate into the vegetative state, and that’s what you need the workstation for. Prior to the A35, we had the smaller DG250 model, and at the time, when we were just working with some bacteroides, not a lot, it sufficed. But when we started working with C. difficile, the amount of studies and the type of studies we did really expanded. So at that time, we contacted Microbiology International since we needed a larger workstation in order to accommodate all those studies. The A35 is now our second Whitley workstation, but we are still using the DG250, too. We’ve converted the DG250 to a microaerophilic environment, because we do Helicobacter pylori work in there. It’s a facultative anaerobe, so when we need to grow up plates or process samples, we use that smaller workstation with a 5% oxygen mix.

Read the full interview here

Read more about Dr Weiss’ work here