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Scientists build proteins into molecular capsules

Nucleocapsid
This cutaway view shows the protein design for a synthetic nucleocapsid known as I53-50-v1. (Nature / UW Graphic / Butterfield, Lajoie et al.)

University of Washington researchers have taken a page from the viral playbook to create microscopic assemblies for packaging genetic material — with the goal of using the system for targeted drug delivery.

The assemblies, known as synthetic nucleocapsids, work like viruses to protect their payloads as they enter cells. They can even evolve over time. That may sound like the start of a science-fiction novel, but  the authors emphasize that their plot doesn’t have a scary ending.

“Our nucleocapsids are not viruses, because they have no way to get into cells, out of cells, or replicate on their own without our direct intentional assistance,” they said in an email sent to GeekWire by UW biochemist Marc Lajoie.

Lajoie is one of the authors of the study, published today by the journal Nature.

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Semi-synthetic bacteria make ‘alien’ protein

Semi-synthetic bacteria
Bacteria express a green fluorescent protein that’s produced from DNA instructions with unnatural chemical “letters” added. (Scripps Research Institute Photo / Bill Klosses)

Researchers have reached a new milestone in their effort to expand the genetic alphabet of life by designing a strain of E. coli bacteria that creates proteins unlike anything cells can produce naturally.

The technique, detailed in a paper published today in the journal Nature, could lead to the production of totally new types of protein-based medicines, plastics and biofuels.

It could also stretch the definition of natural vs. artificial life.

“I would not call this a new lifeform — but it’s the closest thing anyone has ever made,” study leader Floyd Romesberg, a biochemist at the Scripps Research Institute, said in a news release.

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Meet the Mariana snailfish, the sea’s deepest fish

Mariana snailfish
The Mariana snailfish is the deepest fish collected from the ocean floor. (UW Photo)

They look like ghosts of the abyss, but the wispy, pinkish-white, smooth-skinned creatures at the bottom of the Pacific Ocean’s Mariana Trench have a distinction of substance: They’re the deepest fish ever brought up from the deep sea.

Now the species known as the Mariana snailfish has its official scientific name: Pseudoliparis swirei, a Latin-inspired designation paying tribute to Herbert Swire, a navigator on the 19th-century expedition that discovered the Mariana Trench.

A researcher at the University of Washington’s Friday Harbor Laboratories played a key role in Pseudoliparis swirei’s discovery. UW’s Mackenzie Gerringer is the lead author of a paper on the species’ discovery, published today in the open-access journal Zootaxa.

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AI2’s search engine gets a biomedical boost

AI2's Marie Hagman
AI2’s Marie Hagman drew upon person experience during her work on Semantic Scholar. (GeekWire Photo / Alan Boyle)

As senior product manager at Seattle’s Allen Institute for Artificial Intelligence, or AI2, Hagman played a key role in figuring out how to incorporate documents from PubMed and other biomedical databases in the academic search tool.

She drew upon her personal experience from 15 years earlier, when she was a software engineer suffering from two stomach ulcers and gastritis. Her specialist gave her a prescription to deal with the issue, but told her she’d probably have to keep taking pills for the rest of her life.

“I was thinking, ‘Hmm … I’m young and healthy. That just doesn’t sound right,’” Hagman recalled. “They still couldn’t tell me why I had this problem. So I decided to be my own advocate.”

She searched through the medical literature on stomach ulcers, and found a study in which researchers pointed to a type of bacteria known as Helicobacter pylori as a potential cause. Armed with that knowledge, she persuaded another specialist to put her on a two-week round of antibiotics.

“I’ve been cured ever since,” Hagman told GeekWire.

Now her objective is to help researchers, and even regular folks, find the most relevant studies that address the medical questions they want to answer.

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Biomedical labs get $10 million boosts

Jay Shendure
University of Washington geneticist Jay Shendure will direct one of the newly created Allen Discovery Centers. (Allen Institute Photo)

The Paul G. Allen Frontiers Group, created by Microsoft co-founder Paul Allen to speed the pace of biomedical breakthroughs, is adding two more research centers to its lineup – including one at the University of Washington.

Each of the Allen Discovery Centers will receive $10 million in grants over the next four years, with the potential for a total $30 million boost over eight years.

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Allen Frontiers Group boosts biomedicine

Molecular structure
Three Allen Distinguished Investigator projects focus on epigenetics, or how genes are turned on and off. Researchers will study how the 3-D shape of the genome and the presence of regulatory molecules impact the behavior of cells.(Molekuul.be via Paul G. Allen Frontiers Group)

Epigenetics, aging and microbial evolution: Those are the latest words in biomedical research for the Paul G. Allen Frontiers Group, backed up with $7.5 million in awards for five teams of scientists.

Each of the teams will receive $1.5 million over the next three years to boost early-stage studies that have the potential to yield medical breakthroughs.

“It’s part of Paul Allen’s growing commitment to the idea that this is the century of bioscience,” Tom Skalak, executive director of the Seattle-based Frontiers Group, told GeekWire. Allen, one of the founders of Microsoft, launched the Frontiers Group last year with a $100 million commitment.

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Big data helps scientists solve protein puzzles

Protein models
The molecular diagram at left is a representation of a protein molecule known as DMT superfamily transporter YddG, generated by Rosetta@Home software. The diagram at right is a representation of the molecule as determined by experiments. (Sergei Ovchinnikov et al. / UW via AAAS / Science)

Molecular biologists have enlisted cutting-edge trends in genomics and big data to get a grip on one of the grand challenges of biotech: figuring out how protein molecules fold.

But they couldn’t have done it without the help of tens of thousands of volunteers.

The fruits of all that crowdsourced computer labor went public today in the journal Science. Researchers from the University of Washington and other institutions say they’ve solved more than 600 protein-folding mysteries – which represents a fair proportion of the estimated 5,200 protein families whose molecular structure was unknown.

Still more solutions are in the works, and solving those puzzles could lead to new types of medicines and synthetic molecular machinery.

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Complex life may have gotten a false start

Stromatolite
This is a 1.9-billion-year-old stromatolite — or mound made by microbes that lived in shallow water — called the Gunflint Formation in northern Minnesota. Such formations provide evidence of oxygen-rich settings on ancient Earth.. (UW Photo / Eva Stüeken)

Researchers say multicellular life could have arisen in Earth’s oceans more than 2 billion years ago, only to fall victim to a drop in oxygen levels.

That scenario is based on a study of concentrations of the element selenium of sedimentary shale, led by researchers at the University of Washington. The findings – published online in the Proceedings of the National Academy of Sciences – shed light not only on the origins of life on Earth, but on the potential for detecting life on distant planets.

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Wild-haired moth named after Donald Trump

Neopalpa donaldtrumpi
Two views of the moth now known as Neopalpa donaldtrumpi highlight the yellowish-white scales on its head. (Vazrick Nazari Photo via ZooKeys / Pensoftbiolo

Donald Trump isn’t even sworn in as president yet, but he already has a species named after him: a micro-moth with a bushy head of yellowish-white scales.

Neopalpa donaldtrumpi is found in a habitat that, ironically, stretches across the U.S.-Mexico border – from California to Baja California. Biologists have long known that twirler moths inhabited the region, but until recently, they thought there was only one species in the genus.

Canadian evolutionary biologist Vazrick Nazari discovered that wasn’t the case when he examined insect specimens from the Bohart Museum of Entomology at the University of California at Davis. A few of the moth specimens didn’t match the description for Neopalpa neonata.

Among the distinguishing features for the outliers were yellowish-white scales on the moth’s head, and an orange-yellow coloration on the upper side of the forewing. The scales reminded Nazari of Trump’s signature comb-over, and led him to go with “donaldtrumpi” as the species name.

Nazari’s findings were published online today by the open-access journal ZooKeys.

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Scientists find ways to pick a protein’s pockets

Folded protein
This graphic shows the structure of a computationally designed protein that incorporates sheet-like structures with pockets, known as beta sheets. The beta sheets are the wavy “noodles” in the diagram. The structure also incorporates curled-up molecular spirals. (UW Institute for Protein Design / AAAS)

Researchers at the University of Washington have cracked the code for producing molecular structures with tiny pockets – structures that are likely to expand the repertoire for custom-designed proteins.

The structures, technically known as beta sheets, are thought to have an effect on metabolic pathways and cell signaling. Knowing how to produce them synthetically in precise configurations could lead to new treatments for maladies such as AIDS, cancer and Alzheimer’s disease.

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