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Geometry goes viral: Researchers use maths to solve virus puzzle

Geometry goes viral: Researchers use maths to solve virus puzzle

Researchers have developed a new mathematical framework that changes the way we understand the structure of viruses such as Zika and Herpes.

The new mathematical framework changes the way we understand the structure of viruses such as Herpes.

The discovery, by researchers at the University of York (UK) and San Diego State University (US), paves the way for new insights into how viruses form, evolve and infect their hosts and may eventually open up new avenues in anti-viral therapy.

Viruses look like tiny footballs because they package their genetic material into protein containers that adopt polyhedral shapes.

The new theory revolutionises our understanding of how these containers are shaped, solving a scientific mystery that has endured for half a century.

High resolution

For more than fifty years, scientists have followed the Caspar-Klug theory (CKT) about how the protein containers of viruses are structured. However, improvements in our ability to image viral particles at high resolution have made it apparent that many virus structures do not conform to these blueprints.

Published in the journal Nature Communications, the new theory accurately predicts the positions of proteins in the containers of all icosahedral (or twenty-sided) for the first time. It simultaneously works for viruses that conform to CKT and for those that posed an unresolved problem to that theory.

Professor Reidun Twarock, mathematical biologist at the University of York’s departments of Mathematics and Biology and a member of the York Cross-disciplinary Centre for Systems Analysis, said: “Our study represents a quantum leap forward in the field of structural virology, and closes gaps in our understanding of the structures of many viruses that are ill described by the existing framework.

Anti-viral strategies

“This theory will help scientists to analyse the physical properties of viruses, such as their stability, which is important for a better understanding of the mechanism of infection. Such insights can then be exploited for the development of novel anti-viral strategies.

“In particular the structures of larger and more complex viruses that are formed from multiple different components were previously not well understood.

“Our over-arching scheme reveals container architectures with protein numbers that are excluded by the current framework, and thus closes the size gaps in CKT.

Viral evolution

“The new blueprints also provide a new perspective on viral evolution, suggesting novel routes in which larger and more complex viruses may have evolved from simple ones at evolutionary timescales.”

Dr Antoni Luque, theoretical biophysicist at San Diego State University and their Viral Information Institute, said: “We can use this discovery to target both the assembly and stability of the capsid, to either prevent the formation of the virus when it infects the host cell, or break it apart after it’s formed. This could facilitate the characterization and identification of antiviral targets for viruses sharing the same icosahedral layout.”

Materials provided by the University of York

Majority of social media users are happy for their data to be used for research, study reveals

Majority of social media users are happy for their data to be used for research, study reveals

Social media users are generally positive about their personal data being used for research purposes, a study by the University of York has revealed.

Social media platforms have often been used by researchers to gather data on so-called “adverse events” from drugs and medical procedures, with adverse events often being under-reported in studies.

Social media users cited the potential benefit for medical research as the most influential factor for them to consent to their data being used for research.

Concerns

However, the study revealed concerns around regulation and the ethics of using personal data for research purposes.

The qualitative study used interviews, virtual discussions and focus groups to explore views and attitudes towards the use of social media to monitor adverse events.

Some of those taking part had suffered adverse reactions to medicines themselves.

Safety

Lead author Dr Su Golder, NIHR Postdoctoral Research Fellow from the University of York’s Department of Health Sciences said: “We found it interesting that social media users were happy for their data to be used for research, but as researchers it’s important to take into account their concerns and make sure we assure people that their data will be used appropriately and safely.

“It is clear that social media users are in favour of some sort of overarching guidance for all institutions to follow and that further work is required to establish when consent is required for individual’s social media data to be used.”

Dr Golder said researchers were already aware of the huge potential benefits of using social media for research purposes.

Helping researchers

“It could be argued that some health scandals of the past could have been averted or discovered earlier if social media was around then as the adverse effects would probably have been highlighted,” she added.

“Social media has a part to play in helping researchers and our study has revealed that people are willing for it to be used under the right circumstances.

“Our findings will not only help direct future research but will also provide people managing social media websites, universities, ethics boards, pharma companies and policymakers with evidence to inform policy and guidance on the use of social media data for research. “

Climate change ‘disrupts’ local plant diversity, study reveals

Climate change ‘disrupts’ local plant diversity, study reveals

Researchers have discovered that the numbers of plant species recorded by botanists have increased in locations where the climate has changed most rapidly, and especially in relatively cold parts of the world.

Human activity has been responsible for substantial declines in biodiversity at the global level, to such an extent that there are calls to describe the modern epoch as ‘The Anthropocene’.

But although the total number of plant species on the planet may be in decline, the average number of plant species found locally – the so-called local or alpha diversity of a site – seems to be stable, or even increasing in places.

Scientists at the University of York think that the ‘disruption’ of these local plant communities by rapid climate change, especially changes in rainfall, may be allowing new species in and fuelling these local diversity increases.

Substantial implications

Lead author, Dr Andrew Suggitt from the University of York’s Department of Biology, said: “We used a large dataset of over 200 studies in which botanists had counted the number of plant species present in survey plots situated all around the world.

“We tested for the influence of climate change alongside other well-known drivers of diversity change, finding that the local differences in climate, and exposure to climate change, were responsible for a substantial part of the change in plant species numbers found in these surveys”.

“Our models suggest that typical rates of climate change in cooler regions of the world are driving an increase in local species richness of 5% per decade. This is really quite a large number if it continues for 13 decades or more, given that humans have already been changing the climate for over half a century, and climate change is set to continue until the year 2100, at least. What we are observing has substantial implications for future ecosystems”.

Pervasive effect

Co-author Professor Chris Thomas added:  “This does not mean that the botanical world gets a clean bill of health. We are living in ‘The Anthropocene’ epoch, and some plant species have become globally extinct.  Many, many more are endangered.

“However, there is a disconnect between what is happening at that global level and the average change to plant diversity that can be observed in, say, a one metre square plot of ground.

“The effect of climate change may not be as dramatic as a meadow being turned into a car park, or a forest being cut down, but it’s a pervasive effect that is already evident over vast areas of the Earth’s land surface.

“For example, warmth-loving bee orchids (Ophrys apifera) have started arriving at a much wider variety of sites across the north of England, taking advantage of the changing climate.

“The data we have analysed tells us that colonists are tending to arrive faster than incumbents disappear, giving rise to slight increases in plant diversity in places where the climate is changing the most”.

Shuffling the deck

Dr Suggitt added: “The recent global assessment report by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services highlighted worrying declines in plants and animals around the world.

“But it also highlighted the sore need for greater clarity over how climate change is shuffling the deck of plant species found in particular locations – especially in under-sampled areas such as the tropics, Africa and Asia.

“We hope our study opens the door to a fuller understanding of how climate change is affecting plant communities, and what this means for the conservation of nature and its contribution to people”.

Materials provided by the University of York

new tree

New species of tree discovered in Tanzania mountains

Researchers have discovered a new species of tree in the Usambara Mountains in Tanzania.

The tree, which grows up to 20m tall and has white flowers, was discovered in the Eastern Arc Mountains, a globally important region for species in need of conservation.

It has been categorised as endangered due to its restricted population range at only 8km-sq. It is as yet unknown what kind of wildlife might rely on the tree, but it is most likely pollinated by a species of beetle.

Researcher Dr. Andy Marshall, from the University of York’s Department of Environment and Geography, discovered the tree when carrying out a survey of the forest to understand the environmental factors that influence the amount of carbon that forests can store.

Botanist George Gosline, from Kew Gardens, recognized that this is a new species related to a group previously thought to be restricted to western Africa.  This in turn led to recognition of three new species in the group.

Reducing numbers

Dr. Marshall said: “The tree is in a particularly beautiful part of the world – up high in the clouded mountains and surrounded by tea estates.  Now that we know it exists, we have to look at ways to protect it.

“With such a small population, it is important that it does not become isolated from other forests in the region, due to increasing agriculture. Small forests need to be connected to others to ensure seed dispersal and species adaptation to climate change.”

The forests of these mountains have been reduced in size by thousands of square kilometres over the past hundred or so years and are now threatened by climate change. The researchers argue that it is essential to look at conservation methods in order to maintain or increase the tree population.

Human intervention

Research shows that forests that have been restored with the help of human intervention rarely achieve the same number of species that would have occurred naturally. This means that conservation efforts should begin before any further damage occurs.

A research project, led by Dr Marshall, in another part of Tanzania, the Magombera Forest, should provide researchers with further understanding of the best methods to employ for protecting these secluded rare species. The project includes working with local villagers to develop new methods for restoring forests and to find alternative sources for wood, and how local people can help to reduce wildfires and invasive vines that can kill trees.

With local support, thousands of small trees have grown back in areas once lost, suggesting that a similar approach could be used in other areas where species are at risk of becoming extinct through human activity and climate change.

Irreplaceable

George Gosline, botanist from Kew Gardens, said: “The discovery of this extremely rare species reaffirms the importance of the Eastern Arc Mountains as one of the most important reservoirs of biodiversity in Africa.

“The area is a refuge for ancient species from a time when a great forest covered all of tropical Africa.  These forest remnants are precious and irreplaceable.”

The discovery is not the first to be made in the region by Dr Andy Marshall; other discoveries in the Eastern Arc Mountains include a new chameleon species and the Polyceratocarpus askhambryan-iringae tree, which was discovered by chance whilst Dr Marshall was researching one of the world’s rarest primates, the kipunji monkey.

Materials provided by the University of York

A close up of human eye

Breakthrough in understanding how human eyes process 3D motion

Scientists at the University of York have revealed that there are two separate ‘pathways’ for seeing 3D motion in the human brain, which allow people to perform a wide range of tasks such as catching a ball or avoiding moving objects.

The new insight could help further understanding into how to alleviate the effects of lazy eye syndrome, as well as how industry could develop better 3D visual displays and virtual reality systems.

Much of what scientists know about 3D motion comes from comparing the ‘stereoscopic’ signals generated by a person’s eyes, but the exact way the brain processes these signals has not been fully understood in the past.

Scientists at the Universities of York, St Andrews, and Bradford have now shown that there are two ways the brain can compute 3D signals, not just one as previously thought.

Fast and slow signals

They found that 3D motion signals separate into two ‘pathways’ in the brain at an early stage of the image transmission between the eyes and the brain.

Dr Alex Wade from the University of York’s Department of Psychology said: “We know that we have two signals from our visual system that helps the brain compute 3D motion – one is a ‘fast’ signal and one is a ‘slow’ signal.

“This helps us in a number of ways, with our hand-eye coordination for example, or so that we don’t fall over navigating around objects. What we didn’t know was what the brain did with these signals to allow us to understand what is going on in front of our eyes and react appropriately.

“Using brain imaging technology we were able to see that these two 3D motion signals are separated out into two distinct pathways in the brain, allowing information to be extracted simultaneously and indicating to the visual system that it is encountering a 3D moving object.”

Lazy eye syndrome

The research team had previously shown that people with lazy eye syndrome might still be able to see ‘fast’ 3D motion signals, despite them having very poor 3D vision in general.  Now that scientists understand how this pathway works, there is the potential to build tests to measure and monitor therapies aimed at curing the condition.

Dr Milena Kaestner, who conducted the work as part of her PhD at the University of York, said: “We were also surprised to see a link between 3D motion signals and how the brain receives information about colour. We now believe that colour might be more important in this type of visual processing than we previously thought.

“The visual pathways for colour have been thought to be independent of signals about motion and depth, but the research suggests that there could be a connection in the brain between these three visual properties.”

Dr Julie Harris, from St Andrews University, said:  “Knowing more about our visual system, and particularly how motion, depth and colour could all be connected in the brain, could help in a number of research areas into what happens when these pathways go wrong, resulting in visual disturbances that impact negatively on people’s quality of life.”

Materials provided by University of York

watching tv

Study reveals everyday technology helps fight loneliness

The research, co-produced by the University of York and the loneliness charity WaveLength, looked at data collected from 445 people over two years and found that they rated their health more positively after being given new technology.

The study participants had an average age of 44 and over 50% had been homeless and experienced poor mental health.

Positive influence

Lead author of the study, Professor Marin Webber, from the Department of Social Work and Social Policy at the University of York, said: “The research shows that technology can have a positive influence on the life of someone who is lonely.

“The benefits of everyday technology are heightened for people who are at the greatest risk of suffering from loneliness. This includes people who are in a bad financial situation and experiencing poor physical and mental health.”

Clare, who is living in Kilburn, recently received a television from WaveLength after she left prison. Experiencing several health issues and disabilities means that she is now often housebound. Commenting on the difference her television has made, she explained: “I have found the TV to be invaluable as it is a real companion to me when I am bedbound and stops me from feeling lonely. I really enjoy tuning into my favourite programmes for entertainment and learning. The TV has made such a positive difference to my life.”

Connect

The report calls on policy makers to make funding available so that vulnerable people can purchase everyday technology and for free access to a minimum standard of broadband in order to connect greater numbers of people via smart televisions and tablet computers.

CEO of Wavelength, Tim Leech, said: “Our latest report shows that everyday media technology has a real role to play in helping people to feel less lonely. The research shows a statistically significant relationship between technology usage, a reduction in loneliness, and an increase in self-rated health. The results of this study should lead to a greater recognition of the valuable role technology can play in fighting loneliness, alongside other forms of support.”

Materials provided by Univerity of York

Extinct and living sloths. Image

Scientists get a grip on sloth family tree

Scientists have solved the evolutionary puzzle of how sloth went from enormous ground-dwelling giants to the small, famously-laidback tree-climbers of the modern day.

The study, by an international team of researchers led by academics at the University of York, challenges decades of scientific opinion concerning the evolutionary relationships of tree sloths and their extinct kin.

The two living types of sloth – two and three toed – seem remarkably similar, but the new research published in Nature Ecology and Evolutionestimates they last shared a common ancestor more than 30 million years ago.

Extinct giants

The researchers unexpectedly discovered that the three-toed sloth is related to two giant ground sloths – the elephant-sized Megatherium and the pony-sized Megalonyx, which last roamed the earth around 10,000 years ago.

Megalonyx

The pony-sized Megalonyx last roamed the earth around 10,000 years ago. Credit: AMNH

The researchers used cutting-edge techniques to extract ancient protein sequences from the fossilised bones of extinct sloths held in the collections of the American Museum of Natural History in order to map their relationship to living species of sloth.

Protein analysis allowed researchers to analyse fossilised sloth bones that were between 120,000 and 400,000 years old.

Fossilised bones

Lead author of the study, Samantha Presslee, a PhD student in the Department of Archaeology at the University of York, said: “Scientists have long been perplexed by the fact we used to have huge ground sloths and have ended up with modern, small, tree-dwelling ones.

“Previous analysis of the sloth family tree has been done by looking at the anatomy of extinct sloths from often-fragmented skeletons in the fossil record, but protein analysis gives us quite a different picture. Structural proteins in bone such as collagen encode information that can last up to around 3.8 million years.”

The study is published at the same time as another piece of related research is reported in the journal Current Biology. The second study analysed ancient DNA found in well-preserved fossilised sloth bones and, while the two research teams used different molecular methods, they produced the same results, verifying the family tree findings of both studies.

Deeper time

While in this case scientists were able to use both methods to examine the evolutionary history of the sloth, protein analysis has the potential to take researchers further back into the evolutionary past of a wider range of animals than ever before.

Dr Kirsty Penkman from the Department of Chemistry at the University of York, who was also involved in the protein study, said: “We now have the potential to extract and interpret protein evidence from a wide range of extinct species well beyond the current reach of ancient DNA, which is a relatively fragile molecule.

“Looking at DNA offers amazing insights, particularly into remains that have been preserved in permafrost, but this obviously limits the range of species you can look at. This method allows scientists to go back into deeper time and look at species that lived and died in warmer climates.”

Materials provided by University of York

Quantum network

Establishing the ultimate limits of quantum communication networks

At the moment, sensitive data is typically encrypted and then sent across fibre-optic cables and other channels together with the digital “keys” needed to decode the information. However, the data can be vulnerable to hackers.

Quantum communication takes advantage of the laws of quantum physics to protect data. These laws allow particles—typically photons of light —to transmit the data using quantum bits, or qubits.

Superior capabilities

Multinational corporations, such as IBM and Google, are now building intermediate-size quantum computers with increasing number of quantum units or qubits.

Once they scaled up to larger sizes, these devices will have far-superior capabilities than current classical computers. For instance, they may process extremely large numbers in just a few seconds, speed-up many fundamental mathematical operations, and perfectly simulate molecular and biological processes.

One challenge will be to connect quantum computers together, in order to create a quantum-version of the Internet or " quantum Internet".

However, an important but unanswered question remains: what is the ultimate rate at which one can transmit secret messages or quantum systems from one remote quantum computer to another?

Notoriously difficult

Writing in the journal Communications PhysicsProfessor Stefano Pirandola, from the University of York’s Department of Computer Science, said scientists have answered the question.

Prof Pirandola studied the optimal working mechanism of a future quantum Internet, and also provided the ultimate secret-key capacities that can potentially be achieved.

He said: “Studying quantum networks is notoriously difficult, but recent mathematical tools developed in quantum information theory have allowed us to completely simplify the analysis.

Qubits

“An outstanding question was to compute the maximum number of elementary quantum systems (known as qubits) that could be reliably transmitted from one user of the network to another, or similarly, the maximum number of completely secret bits that these remote users could share.

“This number has now a precise analytical formula.”

Furthermore, the study reveals that the classical-inspired strategy of simultaneously sending qubits through multiple routes of the network can remarkably boost the rate, i.e., the speed of the quantum communication between any two remote users.

Materials required University of York

trimethoprim

Antibiotics found in some of the world’s rivers exceed ‘safe’ levels, global study finds

Concentrations of antibiotics found in some of the world’s rivers exceed ‘safe’ levels by up to 300 times, the first ever global study has discovered.

Researchers looked for 14 commonly used antibiotics in rivers in 72 countries across six continents and found antibiotics at 65% of the sites monitored.

Metronidazole, which is used to treat bacterial infections including skin and mouth infections, exceeded safe levels by the biggest margin, with concentrations at one site in Bangladesh 300 times greater than the ‘safe’ level.

In the River Thames and one of its tributaries in London, the researchers detected a maximum total antibiotic concentration of 233 nanograms per litre (ng/l), whereas in Bangladesh the concentration was 170 times higher.

Trimethoprim

The most prevalent antibiotic was trimethoprim, which was detected at 307 of the 711 sites tested and is primarily used to treat urinary tract infections.

The research team compared the monitoring data with ‘safe’ levels recently established by the AMR Industry Alliance which, depending on the antibiotic, range from 20-32,000 ng/l.

Ciproflaxacin, which is used to treat a number of bacterial infections, was the compound that most frequently exceeded safe levels, surpassing the safety threshold in 51 places.

Global problem

The team said that the ‘safe’ limits were most frequently exceeded in Asia and Africa, but sites in Europe, North America and South America also had levels of concern showing that antibiotic contamination was a “global problem.”

Sites, where antibiotics exceeded ‘safe’ levels by the greatest degree, were in Bangladesh, Kenya, Ghana, Pakistan and Nigeria, while a site in Austria was ranked the highest of the European sites monitored.

The study revealed that high-risk sites were typically adjacent to wastewater treatment systems, waste or sewage dumps and in some areas of political turmoil, including the Israeli and Palestinian border.

Monitoring

The project, which was led by the University of York, was a huge logistical challenge – with 92 sampling kits flown out to partners across the world who were asked to take samples from locations along their local river system.

Samples were then frozen and couriered back to the University of York for testing. Some of the world’s most iconic rivers were sampled, including the Chao Phraya, Danube, Mekong, Seine, Thames, Tiber and Tigris.

Dr John Wilkinson, from the Department of Environment and Geography, who co-ordinated the monitoring work said no other study had been done on this scale. He said: “Until now, the majority of environmental monitoring work for antibiotics has been done in Europe, N. America and China. Often on only a handful of antibiotics. We know very little about the scale of problem globally.

“Our study helps to fill this key knowledge gap with data being generated for countries that had never been monitored before.”

Antimicrobial resistance

Professor Alistair Boxall, Theme Leader of the York Environmental Sustainability Institute, said: “The results are quite eye opening and worrying, demonstrating the widespread contamination of river systems around the world with antibiotic compounds.

“Many scientists and policy makers now recognise the role of the natural environment in the antimicrobial resistance problem. Our data show that antibiotic contamination of rivers could be an important contributor.”

“Solving the problem is going to be a mammoth challenge and will need investment in infrastructure for waste and wastewater treatment, tighter regulation and the cleaning up of already contaminated sites.”

Material provided by University of York