Tag: Biology

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Biologists use AI to flesh out cell’s inner workings

3-D cell model
A 3-D view of human cells is color-coded to highlight substructures. (Allen Institute for Cell Science)

What happens when you cross cell biology with artificial intelligence? At the Allen Institute for Cell Science, the answer isn’t super-brainy microbes, but new computer models that can turn simple black-and-white pictures of live human cells into color-coded, 3-D visualizations filled with detail.

The online database, known as the Allen Integrated Cell, is now being made publicly available — and its creators say it could open up new windows into the workings of our cells.

“From a single, simple microscopy image, you could get this very high-contrast, integrated 3-D image where it’s very easy to see where all the separate structures are,” Molly Maleckar, director of modeling at the Seattle-based Allen Institute, told GeekWire.

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How families will help shape the future of health

Future of Health panel
Panelists discuss the future of health during a Town Hall Seattle forum at the Institute for Systems Biology. From left: GeekWire’s Clare McGrane, the panel’s moderator; Leroy Hood of Providence St. Joseph Health; Howard Frumkin of the University of Washington School of Public Health; and John Aitchison of the Center for Infectious Disease Research. (GeekWire Photo / Alan Boyle)

It’s no secret that a rising flood of data, from the results of sophisticated genetic tests to the vital signs recorded by your smartphone, is transforming the way we approach health and wellness. But one of the pioneers of that trend says big data could well shift the focus of the quest for wellness from the hospital to the home.

“I think the most powerful unit for scientific wellness is the family,” Leroy Hood, co-founder of Seattle’s Institute for Systems Biology and chief science officer at Providence St. Joseph Health, said during a March 7 forum on the future of health.

The forum was hosted by the Institute for System Biology’s headquarters as part of Town Hall Seattle’s science lecture series.

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How are gut microbes connected to memory?

Bacteria and brain
Researchers at the Pacific Northwest National Laboratory are studying how bacteria in the gut can affect the brain’s memory function. (PNNL Illustration)

AUSTIN, Texas — Can probiotic bacteria play a role in how well your memory works? It’s too early to say for sure, but mouse studies have turned up some clues worth remembering.

Preliminary results suggest that giving mice the kinds of bacteria often found in dietary supplements have a beneficial effect on memory when it comes to navigating mazes or avoiding electrical shocks.

One such study, focusing on mazes and object-in-place recognition, was published last year. And researchers from the Pacific Northwest National Laboratory in Richland, Wash., are seeing similarly beneficial effects on memory in preliminary results from their experiments.

PNNL’s Janet Jansson provided an advance look at her team’s yet-to-be-published findings here today at the annual meeting of the American Association for the Advancement of Science.

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How mosquitoes associate scents with swats

Mosquito
A mosquito flies on the end of a tether during an experiment to study responses to a swat-like shock. (Kiley Riffell Photo via University of Washington)

Does it do any good to swat at a mosquito if you miss? Yes, according to a newly published study.

A novel experiment conducted primarily by biologists at the University of Washington found that mosquitoes seem to associate the shock of the swat with the swatter’s scent, and learn to stay away.

“Once mosquitoes learned odors in an aversive manner, those odors caused aversive responses on the same order as responses to DEET, which is one of the most effective mosquito repellents,” senior author Jeff Riffell, a UW biology professor, said in a news release.

“Moreover, mosquitoes remember the trained odors for days,” he said.

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Chinese team clones monkeys from fetal cells

Zhong Zhong
Zhong Zhong is a cloned monkey. (Chinese Academy of Sciences / Qiang Sun and Mu-ming Poo)bio

Researchers at the Chinese Academy of Sciences Institute of Neuroscience in Shanghai have produced identical primate clones using the same procedure that brought Dolly the sheep into the world more than two decades earlier.

The procedure, known as somatic cell nuclear transfer, involves removing the nucleus of an egg cell and replacing it with nuclear material from a body cell.

Chinese researchers described the experiment in a research paper published today by the journal Cell.

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Biologists sniff out another way to make methane

R. palustris
Rhodopseudomonas palustris, shown in this photomicrograph, is a type of bacteria that can use iron-only nitrogenase to convert nitrogen and carbon dioxide into methane as well as ammonia and hydrogen gas in a single enzymatic step. (UW / Harwood Lab)

Every year, microbes produce hundreds of millions of tons of methane, a greenhouse gas that’s more potent than carbon dioxide. Scientists had thought the job was done exclusively through methanogenesis. But in the journal Nature Microbiology, a research team led by the University of Washington’s Caroline Harwood lays out an alternate method that makes use of a backup enzyme called iron-only nitrogenase.

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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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