Cracking the code of HIV; Providing an up-close view of the enemy

Supercomputer empowers researchers to answer the 64-million-atom question by running detailed simulations of HIV

2013-05-31

(Press-News.org) Researchers have determined the precise chemical structure of the HIV capsid, a protein shell that protects the virus's genetic material and is a key to its ability to infect and debilitate the human body's defense mechanism. Detailed simulations were achieved with the use of a supercomputer on a 64 million atom sample. The capsid has become an attractive target for the development of new antiretroviral drugs that suppress the HIV virus and stop the progression of AIDS.

The research paper describing these results is the cover story of this week's journal Nature (May 30, 2013).

This discovery was enabled by a recently-dedicated, new supercomputer called Blue Waters, one of the world's most powerful computers. Until the arrival of petascale supercomputers, scientists were unable to decipher in atomic-level detail the entire HIV capsid--an assemblage of more than 1,300 identical proteins forming a cone-shaped structure. The simulations that added the missing pieces to the puzzle were conducted during testing of Blue Waters at the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign (UIUC).

"The sustained petascale performance of Blue Waters is precisely what enabled these talented researchers to explore new methods combined with structural and electron microscopy data to reliably model the chemical structure of the HIV capsid in great detail," said Irene Qualters, NSF program manager for Advanced Cyberinfrastructure. "This knowledge will allow researchers to infiltrate that membrane with HIV-fighting drugs."

INFORMATION:

UIUC Physics Professor Klaus Schulten, his post postdoctoral researcher Juan R. Perilla, and NSF's Qualters discussed this discovery with reporters during an embargoed, webcasted press conference on May 28, 2013.

A video, Targeting the HIV Virus: Researchers Use Supercomputer to Solve the Structure, tells the story of this research.

More information is available in the UIUC press release, Wit, Grit and a Supercomputer Yield Chemical Structure of HIV Capsid.

-NSF-

ELSE PRESS RELEASES FROM THIS DATE:

Even with defects, graphene is strongest material in the world

2013-05-31

New York, NY—May 31, 2013—In a new study, published in Science May 31, 2013, Columbia Engineering researchers demonstrate that graphene, even if stitched together from many small crystalline grains, is almost as strong as graphene in its perfect crystalline form. This work resolves a contradiction between theoretical simulations, which predicted that grain boundaries can be strong, and earlier experiments, which indicated that they were much weaker than the perfect lattice. Graphene consists of a single atomic layer of carbon, arranged in a honeycomb lattice. "Our first ...

Lead acts to trigger schizophrenia

2013-05-31

Mice engineered with a human gene for schizophrenia and exposed to lead during early life exhibited behaviors and structural changes in their brains consistent with schizophrenia. Scientists at Columbia University's Mailman School of Public Health and the Johns Hopkins University School of Medicine say their findings suggest a synergistic effect between lead exposure and a genetic risk factor, and open an avenue to better understanding the complex gene-environment interactions that put people at risk for schizophrenia and other mental disorders. Results appear online ...

HIV treatment adherence and outcomes improving among HIV-positive transgender people

2013-05-31

PHILADELPHIA—HIV-positive transgender people are just as likely to stay in care, take their medication and have similar outcomes as other men and women living with the disease, according to new research from the Perelman School of Medicine at the University of Pennsylvania and published online May 30 in Clinical Infectious Diseases. The study—which looked at almost 37,000 patients at 13 HIV clinics from 2001 to 2011 in the US—suggests an encouraging shift from earlier work documenting poor retention in care and drug adherence in transgender people, a high risk group for ...

Circadian rhythms control body's response to intestinal infections, UCI-led study finds

2013-05-31

Irvine, Calif., May 31, 2013 — Circadian rhythms can boost the body's ability to fight intestinal bacterial infections, UC Irvine researchers have found. This suggests that targeted treatments may be particularly effective for pathogens such as salmonella that prompt a strong immune system response governed by circadian genes. It also helps explain why disruptions in the regular day-night pattern – as experienced by, say, night-shift workers or frequent fliers – may raise susceptibility to infectious diseases. UC Irvine's Paolo Sassone-Corsi, one of the world's leading ...

Pretesting cervical tumors could inform treatment

2013-05-31

Doctors at Washington University School of Medicine in St. Louis have shown that testing cervical tumors before treatment for vulnerability to chemotherapy predicts whether patients will do well or poorly with standard treatment. The study supports the future possibility of personalized medicine for cervical cancer, a tumor normally addressed with a one-size-fits-all approach. "Even though this is a small study, its strength is that it links a lab test of the tumor's chemotherapy response to survival outcomes for the patients," said Julie K. Schwarz, MD, PhD, assistant ...

Croaking chorus of Cuban frogs make noisy new neighbors

2013-05-31

Human-produced noises from sources such as traffic and trains can substantially impact animals, affecting their ability to communicate, hunt, or even survive. But can the noise made by another animal have the same detrimental effects? A new study presented at the 21st International Congress on Acoustics (ICA 2013) examines the calls made by an invasive species of tree frog and suggests the answer is yes. Ecologist Jennifer Tennessen, a graduate student at The Pennsylvania State University, and her colleagues recorded the calls of the Cuban tree frog (Osteopilus septentrionalis) ...

Texting proves beneficial in auditory overload situations

2013-05-31

During command and control operations, military personnel are frequently exposed to extreme auditory overload – essentially bombarded by multiple messages coming from radio networks, loudspeakers, and live voices in an environment also filled with high-level noise from weapons and vehicles. Adding a visual cue, such as texting, was explored by a team of researchers in Canada as a way to overcome this problem. Sharon Abel, defense scientist at Defence Research and Development Canada, will present her team's findings at the 21st International Congress on Acoustics (ICA ...

Native Ohioans' speaking patterns help scientists decipher famous moon landing

2013-05-31

When Neil Armstrong took his first step on the Moon, he claimed he said, "One small step for a man, one giant leap for mankind" – but many listeners think he left out the "a." A team of speech scientists and psychologists from Michigan State University (MSU) in East Lansing and The Ohio State University (OSU) in Columbus is taking a novel approach to deciphering Armstrong's quote by studying how speakers from his native central Ohio pronounce "for" and "for a." Their results suggest that it is entirely possible that Armstrong said what he claimed, though evidence indicates ...

New speaker system for cars creates separate 'audio zones' for front and rear

2013-05-31

Ever wish that your car's interior cabin could have separate audio zones for the front and rear seats? It soon may. A new approach achieves independent listening zones within a car by using small, modified speakers to produce directional sound fields and a signal processing strategy that optimizes the audio signals used to drive each of the speakers. The new design will be presented at the 21st International Congress on Acoustics (ICA 2013), held June 2-7 in Montreal. Today, car cabins often reverberate with the sounds of music, video soundtracks, navigation system ...

Ultrasound 'making waves' for enhancing biofuel production

2013-05-31

All chefs know that "you have to break some eggs to make an omelet," and that includes engineers at Iowa State University who are using high-frequency sound waves to break down plant materials in order to cook up a better batch of biofuel. Research by David Grewell, associate professor of agricultural and biosystems engineering, and his colleagues Melissa Montalbo-Lomboy and Priyanka Chand, has shown that "pretreating" a wide variety of feedstocks (including switch grass, corn stover, and soft wood) with ultrasound consistently enhances the chemical reactions necessary ...

Cracking the code of HIV; Providing an up-close view of the enemy

ELSE PRESS RELEASES FROM THIS DATE:

LAST 30 PRESS RELEASES: