From genes to DUST - a data revolution

Rob James examines how the University of Derby's College of Science and Engineering is preparing to spearhead two major new projects which will help to shape how we view our health and our environment in the future, harnessing computer science and augmented reality to convert data and ideas into new possibilities to improve the quality of our lives.

Science and scientists have come to dominate the national conversation over the past 12 months.

The role of the experts on the SAGE (Scientific Advisory Group for Emergencies) committee in guiding the government’s response to the coronavirus pandemic has come under widespread scrutiny.

The continuing advances in artificial intelligence, a notable addition to the UK’s new defence strategy, and the thirst for data from companies who want to sell us products and services seems unrelenting.

At the University of Derby, two significant science projects are about to take off which have the potential to make a real impact on how we look after the health of our bodies, our cities and planet.

Imagine having a prescription that was truly tailored to your health needs. We’re not just talking about generic antibiotics or a treatment that has been known to work on other people, but remedies that are specifically designed for each of us.

Personalising healthcare has become the holy grail for the pharmaceutical and wellness industries. Just as every individual’s DNA code is unique, it stands to reason that our bodies should respond to food and drugs in different ways.

Already the University of Derby is working on metabolomic research for conditions such as Covid-19, diabetes and obesity. But later this year, FORM (Facility for Omics Research in Metabolism), backed by £850,000 from the D2N2 Local Enterprise Partnership – and matched by the University -  will open at the Kedleston Road site, to bring together biomedical and data science expertise that could revolutionise our diet and medication.

The FORM provides the University with the capability of universal detection of genes (genomics), mRNA (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in biological samples. This will not only help advance understanding of diseases, but also identify new and innovative solutions to improve health and reduce disease. 

“Genes are responsible for how we are and what we are. In addition, there are other factors which equally contribute towards our health, such as our environment, diet and lifestyle including what our mother ate during her pregnancy,” explains Professor Gyan Tripathi, the Head of the University of Derby’s Human Sciences Research Centre.

“A lot of things go can wrong on the gene itself. Our DNA sequence remains the same, yet genes can become modified, known as epigenetic changes, and that can affect how genes are expressed and manifest their function.

“All of us are unique in our own way. We metabolise each food intake differently. This facility gives us a holistic capability to look at these individual factors.”

Professor Gyan Tripathi smiling at the camera, with a computer in the background.

Our DNA sequence remains the same, yet genes can become modified, known as epigenetic changes, and that can affect how genes are expressed and manifest their function.

Professor Gyan Tripathi
Head of Human Sciences Research Centre

Making sense of biomedical data

Covid-19 is already providing an interesting example of how our genetics affect our susceptibility to disease, according to Professor Tripathi.

“South Asian populations in the UK are highly susceptible to the virus, yet in India it is slightly different. There they are able to mitigate the effects and resist much better, and one of the reasons, we think, is probably the vitamin D levels [from exposure to sunlight] because that controls the inflammation.

“For me to get the level of vitamin D I need I have to be in the sun for a minimum of 20 minutes, but for a white Caucasian five minutes is enough. That’s a huge difference.”

The desire to understand the factors which make us more or less likely to contract an illness, or to suffer from it to a greater degree than someone else, is what is driving the push towards personalised ‘medicare’, where our genetic code and metabolism will be used to determine how each of us would react to different treatments in order to find the right one – in the right quantity – to restore us to health.

To identify those things, however, we need data and the means to assess what that information can tell us about an individual. Research elsewhere has already shown that artificial intelligence can be used to predict cancer, using imaging and genetic data. So, what else could it have potential to do?

Professor Tripathi adds: “Omics is basically a technique which will generate a lot of data. Data science and bioinformatics has a big role because they are what make data usable.”

Helping business to innovate

The University’s Data Science Research Centre, led by Professor Farid Meziane, will be heavily involved and the project has already created a buzz among companies in Derbyshire who lent their support to the bid to D2N2, having identified how having this research and data close at hand can help them to enhance potentially life-saving treatments.

OMICS isn’t just useful for helping prevent illness or aid recovery. It has the capacity to develop forensic investigation work undertaken by police forces, to boost the performance of elite athletes and to support new forms of sustainable agriculture, such as vertical farming.

Dr Chris Bussell, Pro Vice-Chancellor Dean of the College of Science and Engineering, says: “Companies can identify new drug delivery systems and new causal traits to conditions and potentially help put personalised medical care in place earlier, or help to create new interventions, to offset any medical conditions that might be prevalent in particular populations for particular reasons.

“So, the outcome of this is not only better scientific understanding and knowledge, but also the way in which companies will be able to use the facility as part of their own R&D and innovation for meditech, personalised treatments and better understanding of disease conditions.”

The facility will begin to take shape at the University’s Kedleston Road campus through the spring and early summer, with it being fully operational by the autumn.

Dr Chris Bussell wearing a suit and tie, smiling while in conversation.

Companies can identify new drug delivery systems and new causal traits to conditions and potentially help put personalised medical care in place earlier.

Dr Chris Bussell
Pro Vice-Chancellor Dean of the College of Science and Engineering

Making the city of the future an (augmented) reality

Computer science is also at the heart of the DUST (Derby’s Urban Sustainable Transition) project, which could help to create Derby’s future cityscape with the help of Augmented Reality (AR).

Made possible by a £640,000 donation by the late Professor Richard Horsley Osborne, who was among the trustees to pave the way for the city’s University status, the three-year research project will lay the groundwork for the long-term development of Derby, addressing issues of climate change, human and nature habitat management, sustainable mobility transport, and integrated connectivity.

Dr Bussell, who will oversee the project as its principal investigator, said: “We are enormously grateful to the Osborne family for their generosity and support, and this project in many ways will reflect Professor Osborne’s own expertise in economic regeneration of towns and cities within the East Midlands, particularly in Derbyshire and Nottinghamshire. 

“It will bring together researchers from many different disciplines to, ultimately, produce an augmented reality of a reimagined city.”

The potential is almost limitless. For example, imagine stripping away the streets that cover the Markeaton Brook as it flows into the River Derwent to show how it could be a functional ‘blue’ route into the city, reviving the redundant canal infrastructure, or even picturing what it would be like to walk into Derby on a walkway high up among the trees, as just one of many new ‘green routes’, lined with plants and promoting a connection with nature that enhances wellbeing.

It’s all possible to create and experience these visions of Derby using the immersive technology that the project will bring on board. Additional expertise in areas of computer programming, game visualisation, urban planning and ecology in urban environments, will be brought into the University to adapt an existing virtual model of the city to give it the texture and imagery to show how the city can one day appear to residents and visitors.

A three-dimensional illustration of the city of Derby, as seen from the air.
The 3D model of Derby which will be used as a base for the augmented reality imaging of the city.

The first ‘fly-through’, along the route of the brook, could be achieved by the end of this year, says Kay Walker, Project Co-ordinator, but it will more than just a flight of fancy.

“I don’t want this to be something that looks good but has no function. We could create any visual of the city, but I want to make sure that behind it we’ve got the data to prove that there will be an improvement resulting from the intervention, be that a net positive construction, or improvement in biodiversity and habitats, or better transportation links.

“Over the life of the project I also want to be able to demonstrate that there is a nature connectedness benefit, associated mental health improvement, and that fitness levels could potentially increase. I’m very much driven by having that science behind it, and that will probably take three to five years to come to fruition.”

Black and white image of Kay Walker smiling at the camera

It allows that immersive experience within the city so that we can see existing features, but managed and altered in a certain way to bring out that sustainable transition

Kay Walker
DUST Project Co-ordinator

Testing the possibilities in a virtual space

The project will also allow students to be involved through a multi-disciplinary ‘Big Challenge’, in which they are given a live brief and must consider the implications for elements such as transport, human activity and biodiversity, and come up with solutions which could be factored into the actual project work.

Transport and connectivity within Derby will be a significant area of focus, so the involvement of Toyota, which has had its main UK manufacturing plant just outside Derby, at Burnaston, for the past 30 years, will provide an added dimension of technical expertise.

Tim Freeman, Deputy Managing Director, Toyota Motor Manufacturing (UK) Ltd, said: “Towns and cities require sustainable, accessible mobility to remain attractive and liveable.

“Toyota is making the transition from “vehicle manufacturer” into “mobility company”.  That’s why we are excited to be contributing to this important project led by the University. We hope that not only will it help create a vision for the future of Derby, but ultimately help inform Toyota’s vision for the future of urban mobility.”

Kay Walker adds: “One of the interesting things about Derby and why it makes a great case study is that it does have pockets of very poor air quality associated with transport. We can reimagine those areas, and that can provide the impetus for addressing that issue.

“As part of the project we can make an assumption, for example, that to address the removal of diesel and petrol vehicles from the city centre we replace it with more sustainable, zero-emission mobility solutions, which is where there is opportunity to collaborate with Toyota. It is an opportunity for them to use the local city as a testbed in a virtual space.

“We can place images of new transport technologies in the virtual space showing the viewer a driverless car, or a tram in the street scene. It gives it that element of reality and what’s actually possible. We then have an opportunity to test public behaviour towards those things when they see it in augmented reality.

“Whilst planning an intervention we can re-examine connectivity on a city scale.

“For example if you’re putting a tram route all the way around [the city] it could change people’s desire line, their chosen route from point A to B. Likewise, if you are opening up the Markeaton Brook you are effectively creating a barrier through the city centre, which might be very beneficial, but is also disruptive for day to day activities such as commuting, deliveries, etc. and requires new infrastructure to allow the city to function.”

Kay anticipates that the city’s heritage groups, businesses and residents’ focus groups can also play a part in the process, by feeding into the discussion about how certain changes may affect the cityscape or the ease of movement. Much of that activity is likely to be made possible thanks to Derby City Council’s enthusiastic support for the project.

“The DUST project is a really exciting opportunity for the city – even more so in the context of Covid-19, as its lasting impact will shape how the city functions and operates in the future,” says Councillor Matthew Holmes, Deputy Leader of Derby City Council and Cabinet Member for Regeneration, Planning and Transportation.

“The project will lay the foundations for the long-term development of Derby; informing our key plans and programmes, including the development of Derby’s own Climate Change Strategy – led by the city’s Climate Change Commission (chaired by Dr Bussell).

“In order to get to a place of change we need to understand what that place could look like, and how it operates.”

Urban sustainability transition is a global challenge, which is taking place in locations as varied as Newcastle and Singapore.

“Different cities are taking different approaches and doing different things,” says Kay, “but I think where we are different for Derby is the use of the Augmented Reality approach on a city-wide scale. It allows that immersive experience within the city so that we can see existing features, but managed and altered in a certain way to bring out that sustainable transition, while still feeling as though you’re connected to that sense of place.”

Councillor Matthew Holmes, wearing glasses and a suit, looking at the camera.

The project will lay the foundations for the long-term development of Derby; informing our key plans and programmes, including the development of Derby’s own Climate Change Strategy.

Councillor Matthew Holmes
Deputy Leader, Derby City Council