PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

Gaming technology unravels 1 of the most complex entities in nature

Computational research unveils secrets in the human carbohydrate bar-code

2013-10-31
(Press-News.org) Contact information: Rob Dawson
rob.dawson@bbsrc.ac.uk
01-793-413-204
Biotechnology and Biological Sciences Research Council
Gaming technology unravels 1 of the most complex entities in nature Computational research unveils secrets in the human carbohydrate bar-code BBSRC-funded researchers at the University of Manchester's Institute of Biotechnology have used the power of off-the-shelf computer gaming technology to capture previously unobservable atomic movements. The research is helping to chart one of nature's most complex entities known as "glycomes" - the entire complement of carbohydrates within a cell.

This novel solution provides a new understanding of these vital biomolecules which play a role in everything from neuronal development, inflammation and cell structure, to disease pathology and blood clotting.

Understanding the shapes of major biological molecules has revolutionised areas like drug development and medical diagnostics, but the shape of complex carbohydrates has been largely ignored.

The research, reported in a series of six peer-reviewed scientific publications (see notes) with the most recent (published today) appearing in Carbohydrate Research, provides a new view of these biochemical barcodes and present new opportunities in the science of carbohydrates, such as designing drugs or biomaterials that mimic carbohydrate shape and interpreting burgeoning functional glycomics data.

Dr Ben Sattelle from the Faculty of Life Sciences said: "Carbohydrate activity stems from 3D-shape, but the link between carbohydrate sequence and function remains unclear. Sequence-function relationships are rapidly being deciphered and it is now essential to be able to interpret these data in terms of molecular 3D-structure, as has been the case for proteins and the DNA double-helix.

"By using technology designed for computer games, we have been able to investigate the previously unseen movements of carbohydrates at an atomic scale and over longer timescales than before. The insights relate carbohydrate sequence to molecular shape and provide information that will be vital for many industries.

"Carbohydrates remain extremely difficult to characterise in 3D using experiments and advances in computer technology, which exploit computer-gaming technology, have enabled us to use and develop methods that can routinely provide accurate 3D-data for this important class of biomolecules. The ability to model atomic motions in large carbohydrate polymers promises to transform our understanding of fundamentally important biological processes. For example, our approach has potential applications in the design of carbohydrate-based biomaterials, pharmaceuticals and foods."

Modelling carbohydrate motions in water is computationally demanding, meaning that simulations have been limited to short nanosecond timescales using conventional software and central processing unit (CPU) based computers. The team from Manchester achieved simulations ranging from one microsecond (the time it takes for a strobe light to flash) to twenty-five microseconds by exploiting the extra computational power of graphics processing units (GPUs) that are commonly used in game-play to produce moving images. Compared to CPU-based computers, or even supercomputing clusters of them, GPU technology allows many more simultaneous calculations to be performed.

The researchers produced the first predictions of microsecond molecular motions in glycomic building blocks and oligosaccharides. Previously unobservable atomic movements were predicted and found to be sensitive to the carbohydrate sequence. Building on these new insights, the researchers developed a new physics-based model and GPU software that allows far more realistic simulations of long carbohydrate sequences (polymers) - on microsecond and micrometer scales. Using heparan sulphate chains (Figure 1, see notes) the researchers showed that including both flexible degrees of freedom in their model, polymer linkage and ring motions, is crucial to reproduce experimental shape data and ring dynamics were implicated in sequence-dependent biological activity.

The research has culminated in a computational GPU-based method and protocol that can now be used by other researchers to explore the 3D-landscape of largely unchartered organismal glycomes in unprecedented detail.

### END


ELSE PRESS RELEASES FROM THIS DATE:

The secret's in the (robotic) stroke

2013-10-31
The secret's in the (robotic) stroke NYU-Poly researchers tease out cues that impact schooling fish behavior Brooklyn, New York— Recent studies from two research teams at the Polytechnic Institute of New York University (NYU-Poly) demonstrate ...

Increasing rate of knee replacements linked to obesity among young, researchers say

2013-10-31
Increasing rate of knee replacements linked to obesity among young, researchers say New data show younger adults have same or greater impairment than older patients BOSTON – Contrary to popular myth, it is not the aging Baby Boomer or weekend ...

Newly identified proteins make promising targets for blocking graft-vs.-host disease

2013-10-31
Newly identified proteins make promising targets for blocking graft-vs.-host disease Finding could help improve outcomes from bone marrow transplants ANN ARBOR, Mich. — Researchers from the University of Michigan Comprehensive Cancer Center have ...

Biochemists find incomplete protein digestion is a useful thing for some bacteria

2013-10-31
Biochemists find incomplete protein digestion is a useful thing for some bacteria To the authors' surprise, 1 specialized replication factor was partially digested or trimmed, physically cut into shorter fragments, by an energy-dependent protease ...

Long-term use of prescription-based painkillers increases the risk of depression, SLU researcher finds

2013-10-31
Long-term use of prescription-based painkillers increases the risk of depression, SLU researcher finds ST. LOUIS – Opioid analgesics, or prescription-based narcotic pain killers, have long been known to reduce pain, but reports of adverse effects and addiction continue ...

Houston we have a problem: Microgravity accelerates biological aging

2013-10-31
Houston we have a problem: Microgravity accelerates biological aging New research in The FASEB Journal suggests that gravitational unloading significantly impairs the function of endothelial cells, as evidenced by gene expression ...

Primary GOES-R instrument ready to be installed onto spacecraft

2013-10-31
Primary GOES-R instrument ready to be installed onto spacecraft A key instrument that will fly on the Geostationary Operational Environmental Satellite – R (GOES-R) spacecraft, NOAA's next-generation of geostationary satellites, is cleared for installation ...

Lefties more likely to have psychotic disorders such as schizophrenia: Yale study

2013-10-31
Lefties more likely to have psychotic disorders such as schizophrenia: Yale study Being left-handed has been linked to many mental disorders, but Yale researcher Jadon Webb and his colleagues have found that among those with mental illnesses, people with psychotic ...

Direct link established between stimulus-response learning and substance abuse

2013-10-31
Direct link established between stimulus-response learning and substance abuse Findings from Douglas Institute neuroscientist Véronique Bohbot, PhD, neuroscientist at the Douglas Mental Health University Institute, found ...

Could a milky way supernova be visible from Earth in next 50 years?

2013-10-31
Could a milky way supernova be visible from Earth in next 50 years? Advances in cameras, new strategies for detection make it possible COLUMBUS, Ohio—Astronomers at The Ohio State University have calculated the odds that, sometime during the next 50 years, a supernova ...

LAST 30 PRESS RELEASES:

Breathable yet protective: Next-gen medical textiles with micro/nano networks

Frequency-engineered MXene supercapacitors enable efficient pulse charging in TENG–SC hybrid systems

Developed an AI-based classification system for facial pigmented lesions

Achieving 20% efficiency in halogen-free organic solar cells via isomeric additive-mediated sequential processing

New book Terraglossia reclaims language, Country and culture

The most effective diabetes drugs don't reach enough patients yet

Breast cancer risk in younger women may be influenced by hormone therapy

Strategies for staying smoke-free after rehab

Commentary questions the potential benefit of levothyroxine treatment of mild hypothyroidism during pregnancy

Study projects over 14 million preventable deaths by 2030 if USAID defunding continues

New study reveals 33% gap in transplant access for UK’s poorest children

Dysregulated epigenetic memory in early embryos offers new clues to the inheritance of polycystic ovary syndrome (PCOS)

IVF and IUI pregnancy rates remain stable across Europe, despite an increasing uptake of single embryo transfer

It takes a village: Chimpanzee babies do better when their moms have social connections

From lab to market: how renewable polymers could transform medicine

Striking increase in obesity observed among youth between 2011 and 2023

No evidence that medications trigger microscopic colitis in older adults

NYUAD researchers find link between brain growth and mental health disorders

Aging-related inflammation is not universal across human populations, new study finds

University of Oregon to create national children’s mental health center with $11 million federal grant

Rare achievement: UTA undergrad publishes research

Fact or fiction? The ADHD info dilemma

Genetic ancestry linked to risk of severe dengue

Genomes reveal the Norwegian lemming as one of the youngest mammal species

Early birds get the burn: Monash study finds early bedtimes associated with more physical activity

Groundbreaking analysis provides day-by-day insight into prehistoric plankton’s capacity for change

Southern Ocean saltier, hotter and losing ice fast as decades-long trend unexpectedly reverses

Human fishing reshaped Caribbean reef food webs, 7000-year old exposed fossilized reefs reveal

Killer whales, kind gestures: Orcas offer food to humans in the wild

Hurricane ecology research reveals critical vulnerabilities of coastal ecosystems

[Press-News.org] Gaming technology unravels 1 of the most complex entities in nature
Computational research unveils secrets in the human carbohydrate bar-code