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How genomics can revolutionize public health

Coronavirus evolutionary tree
A phylogenetic tree tracks the evolution of SARS-CoV-2, the virus that causes COVID-19, as it spread throughout the United States. An orange dot at lower left indicates WA-1, the first confirmed case in the U.S., which was detected in Washington state. (Nextstrain / GISAID Graphic)

From the early days of the coronavirus pandemic, genetic sleuths have been at the forefront in the global effort to monitor SARS-CoV-2, the virus that causes COVID-19. By comparing the molecular fingerprints of different virus samples collected in Washington state, they were able to track down the first signs of community spread in the U.S.

In a paper published today by Nature Medicine, some of the pioneers of genomic epidemiology have laid out a 10-point plan for creating a well-supported scientific ecosystem — not only to fight COVID-19, but to head off future pandemics as well.

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Artist pays tribute to DNA pioneer Rosalind Franklin

Artist Kate Thompson with Rosalind Franklin portrait
Artist Kate Thompson worked samples of synthetic DNA into the ink and acrylic coating for her portrait of DNA pioneer Rosalind Franklin. (University of Washington Photo / Dennis Wise)

On one level, multimedia artist Kate Thompson’s work shows the black-and-white visage of Franklin — the late biochemist whose famous “Photo 51” revealed the double-helix structure of life’s most vital molecule, even though she didn’t get her full share of credit for it.

Look more closely, and you’ll see a mosaic of 2,000 images submitted by the general public as part of UW’s #MemoriesInDNA project.

And if you were to scrape off a few flakes of paint and process them in a DNA lab, you could read out the pixels that make up all of those images and more, translated from the four-letter genetic code of life to the ones and zeroes of digital data.

“This portrait is not only preserving Franklin’s memory, but preserving the data as well, in a form that will be accessible to future generations,” Karin Strauss, co-director of UW’s Molecular Information Systems Laboratory and principal research manager at Microsoft Research, said today in a news release about the art project.

Thompson’s portrait arguably ranks as the most visual and publicly accessible demonstration of mass data storage in DNA, which has been the focus of study at MISL for years.

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Bill Gates touts AI and gene editing for global health

Margaret Hamburg and Bill Gates
Microsoft co-founder Bill Gates makes a point during a Q&A with Margaret Hamburg, board chair for the American Association for the Advancement of Science. (GeekWire Photo / Alan Boyle)

Microsoft co-founder Bill Gates has been working to improve the state of global health through his nonprofit foundation for 20 years, and today he told the nation’s premier scientific gathering that advances in artificial intelligence and gene editing could accelerate those improvements exponentially in the years ahead.

“We have an opportunity with the advance of tools like artificial intelligence and gene-based editing technologies to build this new generation of health solutions so that they are available to everyone on the planet. And I’m very excited about this,” Gates said in Seattle during a keynote address at the annual meeting of the American Association for the Advancement of Science.

Such tools promise to have a dramatic impact on several of the biggest challenges on the agenda for the Bill & Melinda Gates Foundation, created by the tech guru and his wife in 2000.

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Scientists crack the code of mystery DNA

Evolutionary DNA tree
It’s been 80 million years since our our evolutionary branch diverged from mice — so why do we share some fragments of DNA that are essentially unchanged? (Fred Hutch News Service Illustration / Kim Carney)

Why do some strings of genetic code remain virtually unchanged despite tens of millions of years of evolutionary divergence? A newly published study that takes advantage of the gene-editing technique known as CRISPR has found that at least some of those DNA strings are essential to keep healthy cells growing and block the growth of tumor cells.

The research, published today in Nature Genetics, is the “first study finding large-scale importance of these highly conserved elements,” senior author Rob Bradley of Seattle’s Fred Hutchinson Cancer Research Center said in a news release.

Bradley and his colleagues say unraveling the mysteries of those ultra-conserved elements could lead to new avenues for cancer treatment.

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Chinese gene-editing scientist goes to prison

He Xiankui
Chinese researcher He Jiankui discusses his lab’s effort to produce babies whose genes have been altered to protect them from future HIV infection. (The He Lab via YouTube)

Chinese researcher He Jiankui, who stirred up a global controversy last year when he said his experiment produced twin baby girls with gene-edited traits, has been sentenced to three years in prison and ordered to pay a $430,000 fine, the state-run Xinhua news agency reported today.

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Cyrus Biotech and CRISPR gene pioneers team up

Feng Zhang
MIT researcher Feng Zhang will be the principal investigator for the Broad Institute’s collaboration with Cyrus Biotechnology. (HHMI Photo)

Seattle-based Cyrus Biotechnology says it’ll collaborate with the Broad Institute of MIT and Harvard on ways to optimize CRISPR gene-editing techniques for use in developing novel human therapeutics.

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Scientists publish a ‘parts list’ for the brain

Rebecca Hodge with brain
Rebecca Hodge, a senior scientist at the Allen Institute for Brain Science and one of the principal authors of a research study outlining a “parts list” for mouse brains and human brains, holds a section of postmortem human brain that was used in the study. (Allen Institute Photo)

A study led by researchers at Seattle’s Allen Institute for Brain Science lays out a “parts list” for the brain, including a detailed look at the differences between the parts for human brains and mouse brains.

They say the genetic results, published today in the journal Nature, suggest that relying on mice to study how the brains of men and women work could lead neuroscientists down blind alleys.

“The answer may be that you have to go to species that are more similar to humans,” Ed Lein, an investigator at the Allen Institute who’s also affiliated with the University of Washington, told GeekWire.

It’s not that the basic parts list is all that different: The researchers found that most of the 75 different cell types identified in the human brain, based on genetic makeup, are found in the mouse brain as well.

That commonality applies even to cells that the scientists had previously thought might be uniquely human, such as the “rosehip neurons” discovered last year.

But there are significant differences in the way those genes are expressed — differences that have developed over 75 million years of evolution. “The genes themselves haven’t really changed, but their regulation can change a lot,” Lein said.

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Year in Science: Genetic hopes and fears come true

He Xiankui
Chinese researcher He Jiankui discusses his lab’s effort to produce babies whose genes have been altered to protect them from future HIV infection. (The He Lab via YouTube)

In science, it was the best of times, and the worst of times.

2018 was a year when researchers focused in on ways to head off disease by reprogramming a patient’s own cells, but also crossed what many thought were ethical red lines in genetic experimentation. It was the first year in which women won a share of the Nobel Prize for physics as well as for chemistry, but also a year when the #MeToo issue came to the fore in the science community.

And it was the year that marked the passing of British physicist Stephen Hawking, who was arguably the world’s best-known living scientist.

As I look back at 2018, I’m seeing some stories that I missed but ended up featuring prominently in other folks’ year-end recaps. So, to even things out, my top-ten list focuses on five developments that we featured in the course of the last 12 months, and five more that didn’t get much play at the time.

Feel free to use the comment section to cast write-in ballots for the year’s science highlights and low lights. (For example, the sad tale of Tahlequah and the Southern Resident orca population tops The Seattle Times’ year-end list).

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Human gene-editing experiment put on hold

He Jiankui
Chinese researcher He Jiankui addresses the Second International Summit on Human Genome Editing in Hong Kong. (National Academies via Twitter)

The Chinese researcher behind a controversial experiment to produce gene-edited children took the stage at a Hong Kong conference to explain his work, and acknowledged that the international outcry has brought a halt to the experiment.

“The clinical trial was paused due to the current situation,” He Jiankui, a biomedical researcher at the Southern University of Science and Technology in Shenzhen, said today at the Second International Summit on Human Genome Editing.

The university says He (pronounced “Heh”) has been on unpaid leave since January, and today Chinese news outlets reported that his lab on campus has been shut down and sealed off for investigation.

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Reports of gene-edited babies spawn investigations

CRISPR mechanism
CRISPR-Cas9 technology uses “molecular scissors” to cut and splice DNA. (UC-Berkeley Graphic)

Multiple investigations are being sought in the wake of reports that a Chinese laboratory facilitated the birth of twin girls whose genes had been edited to protect them against the HIV virus that causes AIDS.

The first-of-its-kind experiment, which took advantage of the CRISPR gene-editing technique, came to light in reports published late Sunday by MIT Technology Review and The Associated Press. The researcher in charge of the project, He Jiankui of the Southern University of Science and Technology in Shenzhen, also published a series of videos explaining the gene-editing project.

There has been no outside confirmation of He’s claims, but geneticists and health policymakers say such claims raise grave ethical issues — including the prospect of creating designer babies, enhancing traits and even introducing exotic new traits.

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