Supercomputer Models Ribosome

Scientists at Los Alamos National Lab have successfully created an in silico molecular simulation of the ribosome, the cell's biological machine that "reads" RNA to create proteins.

Using 768 processors of the 8192 available on “Q,” the Los Alamos supercomputer, the researchers simulated 2.6 million atoms in motion for a computer model of the ribosome at work.

A paper describing the effort will appear in the Oct. 24 edition of Proceedings of the National Academy of Sciences.

This success has implications for drug discovery as well as for systems biology, a multidisciplinary and emerging scientific effort which, in part, has biologists and computer scientists cooperating to construct computer models of biological processes at the molecular level.

"The methods and implications lie at the interface between biochemistry, computer science, molecular biology, physics, structural biology and materials science," Kevin Sanbonmatsu, leader of the Los Alamos team, said in a statement. "I believe the results serve as a proof-of-principle for materials scientists, chemists and physicists performing similar simulations of artificial molecular machines in the emerging field of nano-scale information processing.

The study identified a corridor, a new region inside the ribosome, through which the transfer RNA must pass in order for the RNA decoding process to occur, potentially offering new targets for antibiotics.

While this study modeled the ribosome, researchers at Lawrence Livermore National Lab are working to join the Blue Gene supercomputer and the Purple supercomputer, formerly housed at IBM's Poughkeepsie Development Center, to model the human brain, a long-term effort conservatively estimated to cost $100 million.

S. 1873 Adds Protection for Vaccine Makers

While President Bush was at the National Institutes of Health on Tuesday outlining a plan to ask Congress for $7.1 billion to defend against a potential influenza pandemic he was also asking Congress to grant vaccine manufacturers protections against civil lawsuits.

I'm also asking Congress to remove one of the greatest obstacles to domestic vaccine production: the growing burden of litigation. In the past three decades, the number of vaccine manufacturers in America has plummeted, as the industry has been flooded with lawsuits. Today, there is only one manufacturer in the United States that can produce influenza vaccine. That leaves our nation vulnerable in the event of a pandemic. We must increase the number of vaccine manufacturers in our country, and improve our domestic production capacity. So Congress must pass liability protection for the makers of life-saving vaccines,” the President said.

The US Senate is considering legislation (S. 1873) that will establish a lead federal agency that will oversee the development of countermeasures against bioterrorism and create incentives for the domestic manufacturing of vaccines and countermeasures, and provide liability protections for those that develop vaccines against biological weapons.

The bill would give the US Secretary of Health and Human services power over what information the public can know about the drugs people could be made to take if the bill is enacted. It would also shield manufacturers, universities and other drug research institutions against liability when drug products lead to illness, disability or death. It also would exempt the new agency from standard Freedom of Information Act and Federal Advisory Committee Act requirements for public transparency and would exempt certain federal cost oversight requirements.

The bill, the Biodefense and Pandemic Vaccine and Drug Development Act of 2005, was introduced by Sen. Richard Burr (R) of North Carolina on Oct. 17, and approved by the Senate's health committee and is now on the Senate calendar.

It would establish the Biomedical Advanced Research and Development Agency, and an advisory group, the National Biodefense Advisory Board, composed of the director of the agency, the assistant to the president for homeland security and counterterrorism, the director of the Office of Science and Technology Policy, the assistant secretary for public health emergency preparedness, the director of the National Institutes of Health, the director of the Centers for Disease Control and Prevention, the FDA commissioner, the assistant secretary of defense for health affairs, the assistant secretary of homeland security for science and technology, and the secretary of agriculture.

Additionally, the secretary of HHS would appoint four representatives from pharma and biotech, four academicians, and five other members, all serving for three-year terms.

The National Vaccine Information Center (NVIC), an advocacy group, is calling the bill "a drug company stockholder's dream and a consumer's worst nightmare."

John Hanchette, a journalism professor whose bio says he was a former editor at USA Today, is in full attack mode on the bill, as seen on an editorial published on the website of the Niagara Falls Reporter.