Tag: Genetics

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DNA sequenced in space for the first time

Image: Kate Rubins with DNA experiment
NASA astronaut Kate Rubins sequenced DNA using the MiniON device at lower right. (Credit: NASA)

NASA biologist-astronaut Kate Rubins performed the first DNA sequencing experiment in space over the weekend, using a miniaturized device that was delivered to the International Space Station just last month.

The palm-sized MiniON DNA sequencer, built by Oxford Nanopore Technologies, could eventually open the way for full-fledged experiments studying how space radiation might scramble the genes of earthly organisms. This time around, the experiment was aimed merely at finding out whether the device worked.

Rubins used the MiniON sequencer to analyze prepared DNA samples from a mouse, bacteria and a virus. The same analysis was done with equipment down on the ground, with the aim of reading out and matching up the chemical letters of genetic code – that is, adenine, guanine, cytosine and thymine.

The outcome? In today’s status update, NASA reported that the experiment demonstrated for the first time that DNA sequencing could indeed be done in an orbiting spacecraft. That wasn’t a sure thing. Some researchers worried that air bubbles could have gummed up the works in zero-G.

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How evolution played a role in autism genes

Image: Human and Neanderthal skulls
These skulls of a modern human and a Neanderthal are from the Cleveland Museum of Natural History. (Credit: DrMikeBaxter / HairyMuseumMatt via Wikimedia)

One of the biggest genetic differences between humans and other members of the primate family tree, including Neanderthals, predisposes people to a type of autism. The stretch of DNA appears to be an important piece of the human genome, but why?

University of Washington genome scientist Evan Eichler and his colleagues on an international research team focus on that question in a study published today by the journal Nature.

The key genetic structure consists of 95,000 molecular base pairs in a region on chromosome 16 that’s known as 16p11.2. The structure includes 28 genes, flanked by blocks of DNA with duplicated sequences of genetic code known as copy-number variants.

Eichler’s team compared the genomes of modern humans with the genetic code for chimps, gorillas and orangutans, as well as the code for Neanderthals and another strain of extinct pre-humans known as Denisovans. Humans were the only ones to have the structure in the 16p11.2 region.

The researchers’ analysis indicates that the structure appeared in our ancestors’ genome relatively suddenly, about 280,000 years ago. That time frame is about 80,000 years before anatomically modern humans – that is, Homo sapiens – show up in the fossil record.

“Most duplications in our genome are millions of years old, and the speed at which this structure transformed our genome is unprecedented,” Eichler said in a news release.

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Monkey genes shed light on brain mysteries

Image: Monkey brain
A cross-section of the neocortex and cerebellum from an adult rhesus monkey brain has been labeled with a stain that highlights brain cells. (Credit: Allen Institute)

A project led by Seattle’s Allen Institute for Brain Science has mapped out how genes get fired up in key areas of a rhesus monkey’s brain as it develops – and the results could help researchers unlock the mysteries surrounding autism, microcephaly, schizophrenia and other neurological conditions.

The gene expression map, laid out today in research published by the journal Nature, shows that rhesus macaque monkeys are much better models than the usual mice for humans when it comes to brain development. It also confirms the view that different neurological disorders follow dramatically different genetic pathways.

“The sets of genes that turn on early, and the sets of genes that turn on in the adult, shift dramatically,” Allen Institute neuroscientist Ed Lein, the study’s senior author, told GeekWire.

The gene map follows up on earlier work that Lein and his colleagues have done with mice, to track how the brain develops from its fetal stage to adulthood. The Allen Institute has done similar work with adult human brains and fetal brains as well.

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How health care will change in 10 years

Genetics pioneer Leroy Hood is furthering his agenda for what he calls P4 medicine through a commercial venture called Arivale as well as a collaboration between his Institute for Systems Biology and Providence Health & Services. (Credit: ISB)
Genetics pioneer Leroy Hood is furthering his agenda for what he calls P4 medicine through a commercial venture called Arivale as well as a collaboration between his Institute for Systems Biology and Providence Health & Services. (Credit: ISB)

Good news: Arivale co-founder Leroy Hood says he can “almost guarantee” there’ll be ways to keep yourself physically and mentally fit into your 90s.

“You’re going to have to decide on your own what to do after that,” he jokes.

That near-guarantee was one of the predictions Hood delivered today as the keynote speaker for Life Science Innovation Northwest, an annual biotech conference presented this week by Life Science Washington at the Washington State Convention Center in Seattle.

About 800 attendees are getting acquainted with the latest ventures in the life sciences – including Arivale, which was named Startup of the Year at last month’s GeekWire Awards.

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Cancer gene research wins White House honors

University of Washington geneticist Mary-Claire King gets set to receive her National Medal of Science from President Barack Obama at the White House on Thursday. (Credit: National Science and Technology Medals Foundation)
University of Washington geneticist Mary-Claire King gets set to receive her National Medal of Science from President Barack Obama at the White House on Thursday. (Credit: National Science and Technology Medals Foundation)

A quarter-century after her discovery of the BRCA1 breast cancer gene, University of Washington geneticist Mary-Claire King has received the nation’s highest scientific honor – and high praise from President Barack Obama – for her achievements.

King’s status as a winner of the National Medal of Science was announced last December, but after some delays on account of weather, Obama finally put the gold medal around her neck during a White House ceremony on Thursday.

The president said “every single American should be grateful” for the career path that King, 70, chose back in the late 1960s when she was starting out in college.

“At a time when most scientists believed that cancer was caused by viruses, she relentlessly pursued her hunch that certain cancers were linked to inherited genetic mutations,” Obama said. “This self-described ‘stubborn’ scientist kept going until she proved herself right. Seventeen years of work later, Mary-Claire discovered a single gene that predisposes women to breast cancer.”

The discovery has had a huge impact on cancer diagnosis and prevention, highlighted by actress Angelina Jolie’s decision to undergo a preventive double mastectomy in 2013 because she carried the BRCA1 gene.

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Experts weigh in on genetically engineered crops

Image: Genetically engineered crops
Corn is one of the best-known genetically engineered crops. (Credit: NIEHS)

A scientific analysis backed by the National Academies finds no evidence that genetically engineered crops pose heightened health risks or environmental problems, but points up subtler concerns about the technology.

Today’s 420-page report says the impact of genetic engineering for resistance to insects and herbicides has been mostly positive, due to a decrease of pests and crop losses. The outcomes vary widely, however. If proper pest management practices aren’t followed, insects and weeds can evolve to overcome the crops’ built-in resistance. That presents a “major agronomic problem,” the report says.

“Genetically Engineered Crops: Experiences and Prospects” was drawn up by a committee comprising more than a dozen experts, with the support of the National Academy of Sciences, the National Academy of Engineering and the National Academy of Medicine. The experts delved into nearly 900 publications about genetically engineered corn, soybeans and cotton, which account for almost all of today’s commercial genetically engineered crops.

The experts also heard from 80 speakers during a series of public meetings, and read through 700 comments from members of the public.

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BioViva makes progress in anti-aging quest

Image: Telomeres
Telomeres, highlighted in green, serve as protective DNA caps for the cell’s chromosomes. (Illustration courtesy of BioViva USA)

The way BioViva founder Elizabeth Parrish sees it, biological aging is a disease – and she’s willing to bet her life on a cure.

Last fall, the 45-year-old Seattle-area woman underwent an experimental type of gene therapy aimed at addressing some of the big effects of aging, including loss of muscle mass and a shortening of the chromosomes’ telomeres. The procedure was reportedly done in Colombia, to get around U.S. regulations.

The idea of having gene therapy done on yourself raised eyebrows in the biotech community, but Parrish was unfazed.

“I 100 percent believe that it will work, or else I wouldn’t have done it,” Parrish told GeekWire during an interview in February. “I didn’t try to flame out in glory. The research shows that it should absolutely work.”

Now BioViva is reporting that it does seem to work, at least on Parrish’s telomeres. And that’s likely to fuel a debate over the widening scientific quest for greater longevity – conducted not only by BioViva, but by other ventures such as Human Longevity Inc. This week, Human Longevity announced a 10-year deal with AstraZeneca to analyze 500,000 DNA samples for anti-aging clues.

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‘Genetic superheroes’ shielded from diseases

Resilence Project
A graphic illustrates how some rare individuals seem to be shielded from childhood diseases for which they carry the genes. (Credit: The Resilience Project)

Hundreds of diseases have been linked to genetic factors, but now scientists say they’ve found some people who stay healthy even though they have disease-causing genes.

So what’s their secret?

If researchers could answer that question, they might be able to come up with new treatments and even cures for gene-linked maladies such as cystic fibrosis, Huntington’s disease or sickle-cell anemia.

The good news is that researchers have identified 13 adults who are resilient to severe childhood diseases that are in their genes. In a study published by Nature Biotechnology, researchers report that the 13 were found by analyzing genetic data from nearly 600,000 individuals.

The bad news is that it’s impossible to get back in touch with those lucky 13. When they gave their DNA samples to be analyzed, they didn’t give their consent to be recontacted. As a result, they’ll have to remain anonymous.

“It’s almost as if you got to take the wrapping off the box, and you couldn’t open the box up,” said study co-author Stephen Friend, president of Seattle-based Sage Bionetworks.

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LOL! Cat photo data stored in DNA molecules

Image: DNA in test tube
All the movies, images and other data from more than 600 basic smartphones (10 terabytes) can be stored in the pink smear of DNA at the end of this test tube. (Credit: Tara Brown Photography / UW)

Researchers at the University of Washington and Microsoft are developing a digital storage system that can archive data in DNA molecules, with the random-access readability and error correction protocols that’d be required for real-world applications.

Once they’ve overcome those hurdles, they just have to figure out how to make the technology affordable. Eventually, such research could help open the way for data storage devices that can pack information millions of times more tightly than current silicon-based methods.

“Life has produced this fantastic molecule called DNA that efficiently stores all kinds of information about your genes and how a living system works — it’s very, very compact and very durable,” Luis Ceze, UW associate professor of computer science and engineering, said in a news release. “We’re essentially repurposing it to store digital data — pictures, videos, documents — in a manageable way for hundreds or thousands of years.”

Ceze and his colleagues describe their work in a paper presented this week in Atlanta at the ACM International Conference on Architectural Support for Programming Languages and Operating Systems, or ASPLOS.

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Scientists take gorilla genome to next level

Image: Susie the gorilla
Researchers sequenced and assembled an updated gorilla genome using a DNA sample from a gorilla named Susie. (Credit: Lincoln Park Zoo)

A team led by University of Washington researchers has taken a second turn at sequencing the gorilla genome, putting together puzzle pieces that didn’t match up the first time around.

The results are likely to bring about revisions in the evolutionary tale of the western lowland gorilla, and where it fits in the primate family tree that includes us humans.

“I believe there is far more genetic variation than we had previously thought. The first step is finding it,” UW geneticist Evan Eichler, the senior author of a research paper on the project published by the journal Science, said in a news release.

One of the co-authors from UW, Christopher Hill, told GeekWire in an email that the new research is part of an effort to create a comprehensive catalog of the genetic differences between humans and other great apes.

“The differences between species may aid researchers in identifying regions of the human genome that are associated with cognition, behavior and neurological diseases,” Hill said. “Having complete and accurate reference genomes to compare allows researchers to uncover these differences.”

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