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Cosmic Science

Antibody cocktail just might ward off COVID-19

An international research team led by University of Washington scientists has identified two kinds of “ultrapotent human antibodies” that could go into a drug cocktail for guarding against COVID-19.

  • UW’s David Veesler and Vir Biotechnology’s Katja Fink are the senior authors of the study published online today by the journal Science, which highlights two monoclonal antibodies known as S2E12 and S2M11. The antibodies were found to block SARS-CoV-2, the coronavirus that causes COVID-19, from latching onto molecular receptors on cells in hamsters.
  • An analysis of the antibodies’ molecular structure determined that they block the virus by gumming up its characteristic “spike” protein, which has been a target for many of the vaccines and therapies under development to fight COVID-19. Some of the researchers behind the newly published study, including Veesler, reported a similarly promising antibody called S309 in May.
  • Researchers say such antibodies could be combined in a drug cocktail to guard against the virus evolving to evade any single one of the ingredients. A drug that takes advantage of S309’s effect is already being tested in a phase 2/3 clinical trial launched by GlaxoSmithKline and Vir Biotechnology.

The principal authors of the Science study, “Ultrapotent Human Antibodies Protect Against SARS-CoV-2 Challenge Via Multiple Mechanisms,” are M. Alejandra Tortorici of the University of Washington and Martina Beltramello of France’s Pasteur Institute and CNRS. Other UW researchers among the 47 co-authors of the study include Ha Dang, Matthew McCallum and John Bowen.

This report was first published on GeekWire.

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Scientists design proteins that confound coronavirus

Imagine being able to ward off COVID-19 just by spritzing a nasal spray into your nostrils. It may not be just your imagination: Researchers at the University of Washington have designed a batch of synthetic proteins that could conceivably block the coronavirus behind this year’s pandemic from gaining a foothold.

“Although extensive clinical testing is still needed, we believe the best of these computer-generated antivirals are quite promising,” Longxing Cao, a postdoctoral scholar at UW’s Institute for Protein Design, said in a news release.

Cao is the lead author of a study about the protein-building experiment, published today by the journal Science. It’s the latest innovation to come from the emerging field of protein engineering, and the technique could revolutionize how drugs are developed to counter future pandemics.

It may not be too late to counter COVID-19 as well. “We are working to get improved versions … deployed to fight the current pandemic,” senior study author David Baker, the director of the Institute for Protein Design, told GeekWire in an email.

The technique involves creating small-molecule proteins, or mini-binders, that are custom-designed to latch onto the spiky molecular structures that are scattered around the surface of SARS-CoV-2, the virus that causes COVID-19.

The spikes on the virus do their dirty work by fitting into molecular-scale receptors on the surfaces of cells, much like fitting a key into a lock to gain entry to someone’s house. Once the virus “unlocks” a receptor, it gains entry to the cell, hijacks its chemical machinery and churns out more virus particles to spread the infection.

Baker, Cao and their colleagues used high-powered computers to design more than 2 million candidate proteins that could conceivably gum up the works for the virus’ spike protein. More than 118,000 of the most promising candidates were synthesized and tested on lab-grown cells.

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Northwest researchers get in on a quantum leap

Microsoft, the Pacific Northwest National Laboratory and the University of Washington are playing supporting roles in the White House’s $1 billion effort to advance research into artificial intelligence and quantum information science.

Those three organizations have already been working together through the Northwest Quantum Nexus to develop the infrastructure for quantum computers, which promise to open up new possibilities in fields ranging from chemistry to systems optimization and financial modeling.

The initiatives announced today are likely to accelerate progress toward the development of commercial-scale quantum computers, Chetan Nayak, Microsoft’s general manager for quantum hardware, said in a blog posting.

“Today marks one of the U.S. government’s largest investments in the field,” he said. “It is also a noteworthy moment for Microsoft, which is providing scientific leadership in addition to expertise in workforce development and technology transfer.”

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Synthetic proteins use logic to choose which cells to kill

The age of molecular-scale computing is entering a new era, thanks to the development of a system that uses synthetic proteins and Boolean logic to identify cancer cells.

The proteins can lock onto chemical markers on the surface of cells in predetermined combinations, performing the roles of logical AND, OR and NOT gates. It’s similar to the way binary computers do their thing, but with biochemistry rather than electronic bits.

“We were trying to solve a key problem in medicine, which is how to target specific cells in a complex environment,” Marc Lajoie, one of the lead authors of a study published today in the journal Science, explained in a news release.

“Unfortunately, most cells lack a single surface marker that is unique to just them. So, to improve cell targeting, we created a way to direct almost any biological function to any cell by going after combinations of cell surface markers,” Lajoie said.

Lajoie worked on the effort during his stint as a postdoctoral scholar at the University of Washington’s Institute for Protein Design. He’s now co-director for protein and cell engineering at Lyell Immunopharma, a California-based startup aiming to commercialize the technique.

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Mars mission puts working from home to the ultimate test

The launch of NASA’s Mars Perseverance rover marks the start of a seven-month-long journey involving tens of millions of miles of travel — but it also marks the end of an eight-year-long journey involving millions of miles of travel on the part of scientists and engineers across the country.

And perhaps the biggest marvel is that, in the end, most of them got the rover and its scientific instruments ready for launch while working from home.

Working from home has been a tough thing to manage for many of the businesses affected by the coronavirus pandemic and social-distancing restrictions. It’s been tough for NASA as well.

“Putting a spacecraft together that’s going to Mars, and not making a mistake — it’s hard, no matter what. Trying to do it during the middle of a pandemic, it’s a lot harder,” Matt Wallace, the mission’s deputy project manager at NASA’s Jet Propulsion Laboratory in Pasadena, Calif., said during a pre-launch briefing.

Fortunately, NASA and its partners could draw upon decades’ worth of experience in remote operations. “When the pandemic came along, it didn’t make that much difference in the way I operate, because I was already used to working remotely with JPL,” said the University of Washington’s Tim Elam, who’s part of the science team for the rover’s X-ray fluorescence spectrometer.

Once the rover is on its way, working remotely will become even more routine. “Pasadena is about the same distance away from Mars that Seattle is,” Elam joked.

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Physics professor tackles another quantum mystery

The University of Washington physicist who once ran a crowdfunded experiment on backward causation is now weighing in with a potential solution to one of the longest-running puzzles in quantum mechanics.

John Cramer, a UW physics professor emeritus, teamed up with Caltech electrical engineer and physicist Carver Mead to put forward an explanation for how the indefinite one-and-zero, alive-and-dead state of a quantum system gets translated into a definite observation — a phenomenon known as wave function collapse.

“Up to now, the mechanism behind wave function collapse has been considered a mystery that is disconnected from established wave mechanics. The result has been that a large number of attempts to explain it have looked elsewhere,” Cramer told GeekWire in an email.

“In our work, we have discovered that wave function collapse, at least in a simple case, is implicit in the existing formalism,” he said, “as long as one allows the use of advanced as well as retarded electromagnetic potentials.”

In other words, the explanation requires accepting the possibility that time can flow backward as well as forward. And for some physicists, that might be too big of a quantum leap.

“Most people just don’t like the idea of having the kind of time symmetry that sort of implies that time isn’t strictly speaking a one-way street,” Cramer acknowledged during a phone interview.

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Award recognizes research on DNA data storage

Strauss and Ceze
Microsoft’s Karin Strauss and the University of Washington’s Luis Ceze have earned the 2020 Maurice Wilkes Award from the Association for Computing Machinery’s Special Interest Group on Computer Architecture. (UW Photo)

University of Washington computer science professor Luis Ceze and Microsoft principal research manager Karin Strauss have won a prestigious award from the Association of Computing Machinery for their work on DNA-based data storage systems.

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COVID-19 projections show higher death tolls ahead

Coronavirus models
This chart shows the daily U.S. death toll due to COVID-19 as a solid red line on the left, with a dotted line that traces the seven-day rolling average. To the right, the gray area shows the range of uncertainty in today’s projection from the Institute for Health Metrics and Evaluation, with a dashed trend line that stabilizes and then rises sharply. The pink area shows the range of uncertainty for Youyang Gu’s C19Pro projection, with a dotted trend line that gradually rises and then falls. (IHME / COVID19-Projections.com Graphics)

The latest projections for the course of the coronavirus pandemic in the U.S. suggest that there’s going to be an upswing in the daily death toll, but they differ in how that upswing will develop.

If you go by the University of Washington’s Institute for Health Metrics and Evaluation, whose computer models have been closely watched since the early days of the pandemic, the trend appears likely to stabilize at somewhere between 650 and 750 COVID-related deaths per day nationwide through the start of September. Then the model calls for a steady rise to more than 1,400 daily deaths by October.

The institute’s best guess is that the cumulative U.S. death toll will exceed 200,000 on Oct. 1. The current U.S. death toll, according to Johns Hopkins University’s coronavirus dashboard, is just over 116,000.

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Coronavirus contact tracing is ramping up

Contact tracing
Contact tracing is a key part of the strategy for corralling coronavirus. (University of Washington Photo)

The Washington State Department of Health is in the early stages of a massive effort to interview COVID-19 patients and track down those who might have been infected by those patients.

Contact tracing is a tried and true technique, typically used to stem the spread of infectious diseases ranging from tuberculosis to measles to gonorrhea. Now it’s part of the strategy for getting the coronavirus pandemic under control.

“Contact tracing is going to be an essential part of our reopening and containment efforts moving forward,” said Janet Baseman, an epidemiologist at the University of Washington’s School of Public Health. “We need to trace every contact possible, because every contact counts in stopping this disease.”

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UW to host institute on climate and oceans

Beluga whales
The beluga whales that make their home in Alaska’s Cook Inlet have been the subject of studies by researchers at the National Oceanic and Atmospheric Administration and the University of Washington’s Joint Institute for the Study of the Atmosphere and Ocean. (JISAO Photo / Manuel Castellote)

The National Oceanic and Atmospheric Administration has selected the University of Washington to host a Pacific Northwest research institute focusing on climate, ocean and coastal challenges, supported by a five-year award worth up to $300 million.

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