Friday, September 11, 2020

The coronavirus is mutating — does it matter?

Researcher Thomas Nyalile at the U Mass Medical School tests D614G spike-protein variant on infectivity.  Image from Nature.

In March, David Montefiori, who directs an AIDS-vaccine research laboratory at Duke University in Durham, North Carolina, contacted Bette Korber, an expert in HIV evolution and a long-time collaborator. Korber, a computational biologist at the Los Alamos National Laboratory (LANL) in Sante Fe, New Mexico, had already started scouring thousands of coronavirus genetic sequences for mutations that might have changed the virus’s properties as it made its way around the world.

Compared with HIV, SARS-CoV-2 is changing much more slowly as it spreads. But one mutation stood out to Korber. It was in the gene encoding the spike protein, which helps virus particles to penetrate cells.  (Full Story)

New antiseptic kills antibiotic-resistant bacteria

A: Healthy bacteria. B: CAGE causes degradation after five minutes. C: Death after 60 minutes. LANL image.

To battle super-resilient bacteria, scientists at Los Alamos National Laboratory have developed a new topical ointment designed to kill what were once considered “unkillable” bacteria. Collaborating with Northern Arizona University and Dixie State University, Los Alamos scientists discovered what they have dubbed CAGE, a variation of something called a choline capable of penetrating the deepest skin layers to deliver antibiotics. Choline helps the body improve memory and cognition, protect the heart and boost metabolism, among other things.

To test the effectiveness of CAGE, Los Alamos scientists developed a skin ointment and applied it on 11 clinically isolated bacteria known to be strongly resistant to topical treatment.  (Full Story)

LANL scientists study impact of wildfires on health, environment

The wildfires burning across the western United States have been sending smoke across New Mexico.  Scientists at Los Alamos National Lab wanted to take a closer look, so they turned on their aerosol-gas forensics instruments. "Serendipitously to our surprise, one hour later the Medio Fire started by lightning,” said Manvendra Dubey, who runs the Laboratory’s Center for Aerosol-gas Forensics.

These scientists were able to track the Medio Fire from the start. The fire began in a dense, dry forest and spread rapidly.  It put out black smoke for a few days. "The way we measured the fire growth was by measuring black carbon in our lab,” Dubey said. (Full Story)

Mars 2020 mission looks to find signs of ancient microbial life

Scientists use patterns found in extreme environments on Earth to help them narrow their search for life on Mars. Dr. Nina Lanza, is a planetary scientist at Los Alamos National Laboratory. She helped create SuperCam, an instrument which identifies the chemical composition of rocks and soils, and whether or not it contains organic compounds. SuperCam is traveling to Mars as an attachment on NASA’s Perseverance rover for the Mars 2020 mission which launched on July 30, 2020.

According to Dr. Lanza, “living microbes play a role in forming rock varnish on Earth—one we don’t fully understand yet—so maybe they play a role in forming rock varnish on Mars, too. We know that microbes in varnish are well suited to the martian environment.  (Full Story)

The mystery of the neutron lifetime

Neutron decay diagram, from APS.

Scientists would like to have a solid number for the neutron lifetime to plug into these equations. They need the uncertainty of the lifetime down to less than a second. But getting this certainty is more difficult than it initially seemed. "The neutron lifetime is one of the least well-known fundamental parameters in the Standard Model," said Zhaowen Tang, a physicist at DOE's Los Alamos National Laboratory

"We cannot leave any stones unturned," said Tang. "There are so many examples of people who have seen something, just chucked something to a mistake, not worked on it hard enough, and someone else did and they got the Nobel Prize." (Full Story)

Nascent exascale supercomputers offer promise, present challenges

Roadrunner, the world’s first petascale supercomputer, included innovations to save electricity. LANL photo.

The transition to exascale will not be easy. “As these machines grow, they become harder and harder to exploit efficiently,” says Danny Perez, a physicist at Los Alamos National Laboratory. “We have to change our computing paradigms, how we write our programs, and how we arrange computation and data management.”

That’s because supercomputers are complex beasts, consisting of cabinets containing hundreds of thousands of processors. For these processors to operate as a single entity, a supercomputer needs to pass data back and forth between its various parts, running huge numbers of computations at the same time, all while minimizing power consumption. (Full Story)

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