University of Alaska

A dime-sized fragment of dog bone — more than ten-thousand years old — has given researchers new clues about how domesticated dogs first made their way to the Americas.

Examining a pinto bean-sized bone fragment, the scientist thought she was analyzing an ancient bear bone.

“We have sort of a long standing project working on bear bones from these caves,” explained Charlotte Lindqvist. She’s an associate professor of biology at the State University of New York at Buffalo.

Caves dot the Alexander Archipelago in Southeast Alaska. The fragment of leg bone Lindqvist was examining came from a cave on the mainland just east of Wrangell Island. The cave is a marble tube, about the length of a standard swimming pool.

“This DNA, when we were looking at it and analyzing it, we realized: ‘This is not bear DNA,’” Lindqvist continued.

She and her colleagues realized the bone was from a dog and published their findings in a scientific journal in late February.

Turns out, the dog lived around 10,000 years ago.

“That is among the oldest dog remains that we have from North America,” Lindqvist said. Ancient dog remains are a rare discovery on their own, but Lindqvist explains that the location is also part of what makes this identification so exciting.

To understand why, it helps to look back to the Ice Age — which ended about 10,000 years ago.

“During the Ice Age most of North America was completely covered in these two big ice sheets. So there was no contact north and south of the ice sheet,” said Lindqvist.

Basically, a band of ice across Canada and the northern United States prevented the people living in northern Beringia — including what is now Alaska — from moving south into what’s now the Lower 48.

Lindqvist continued: “There has been this long-standing hypothesis that as soon as these two ice sheets started melting, it opened up a sort of continental or inland corridor. If you have seen the Disney movie ‘Ice Age,’ that’s sort of what is displayed in that movie. But more and more, we’ve started to believe that the coast probably started melting earlier and became viable earlier than this inland corridor.”

And as the adage goes: “A dog is a man’s best friend.”

“Finding a dog on the coast can tell us a lot,” Lindqvist continued, “not just about dog migration and where dogs have been — but also humans, because dogs follow alongside humans.”

And human remains and tools from various points in ancient history have been found in the same cave off Wrangell Island.

The dog bone Lindqvist and her colleagues — Flavio Augusto da Silva Coelho, Stephanie Gill and Crystal Tomlin — analyzed was collected in the late 1990s by a now-retired earth science professor at the University of South Dakota named Timothy Heaton.

“Back in the late 90s, and early 2000s, he did multiple trips, and excavated bones from a number of caves in Southeast Alaska,” Lindqvist explained.

The 50,000-odd bones now reside in the collections of the Museum of the North in Fairbanks.

The piece of dog femur may be tiny, but Lindqvist says it could still yield a lot of information.

“For now,” she said, “we have just isolated the DNA from the mitochondria in this bone, and that is inherited from the mother. So it only tells us the maternal history of this dog. If we can, from this tiny little bone that we have left, get some nuclear DNA — DNA from the genome, we might be able to get deeper insights into the history of this particular dog and the history of new world dogs.”

Lindqvist says she hopes for other discoveries in the thousands of bones from Southeast caves that are left to analyze.

“I’m sure it’s not the last [exciting discovery],” she said, “and it will be exciting as we hopefully will find older remains as well.”

The cave off Wrangell Island has only been partially excavated. That’s because it is a heritage site, protected by federal law. Human remains from the site have been repatriated to Wrangell’s Tlingit tribe, the Wrangell Cooperative Association, under the Native American Graves Protection and Repatriation Act.

Before the coronavirus pandemic, University of Alaska professors Devin Drown and Eric Bortz were studying African Swine Fever, a threat to the global supply of pork.

Lisa Smith was researching HIV’s effects on the brain. And Will George was studying coronaviruses in Alaska bats.

Now, all four are part of Alaska’s quickly intensifying hunt for new, more contagious variants of the coronavirus — the painstaking process of sequencing that state officials say is essential to keeping the virus in check.

Alaska already sequences a large proportion of its positive coronavirus tests compared to other states. But officials say they’re aiming to do even better, particularly after they ran into problems with a faulty sequencing machine a few weeks ago that delayed detection of Alaska’s first case of a more-contagious strain of the coronavirus originally found in Britain.

Now, the state health department has pulled together a group of researchers from Alaska’s public health labs and its university system in hopes of speeding up the process and expanding it dramatically.

Officials want to be sequencing some 20% of Alaska’s positives within a few weeks. That rate would far exceed the level of surveillance even by world leaders like Britain, which has analyzed some 6% of its cases.

“Among the state health departments, Alaska is definitely one of the leaders of the pack,” said Dr. Jay Butler, a former Alaska chief medical officer who’s now deputy director for infectious diseases at the CDC.

Alaska has several advantages over other states in its push to boost its sequencing infrastructure, Butler said in an interview. It has a centralized public health infrastructure in Gov. Mike Dunleavy’s administration; it also has a relatively small population, making it easier to sequence a larger proportion of its positive tests.

Then, Butler added, there’s the potential for “cross-fertilization” between the state’s public health efforts and Alaska’s university system.

A complex process

Butler’s agency has issued sharp warnings about the new coronavirus strains, which arise from naturally-occurring mutations in its genetic code.

One of the strains known as B.1.1.7, originally found in Britain, could be 50% more contagious, and the CDC projects that it will be responsible for most new cases of COVID-19 in the U.S. by March. Another variant originally found in South Africa is also more contagious and, scientists say, appears to be able to evade at least one vaccine.

The state has found just one case of these variants so far, in a traveler infected with the B.1.1.7 strain who officials say followed isolation guidelines and likely did not spread it to others. But those officials also say they expect more cases soon, given the strains’ rapid spread outside Alaska.

“Alaska is doing very well, compared to other states. But it’s very important that we don’t let our guard down, especially as we start to see these new variants emerge,” Dr. Joe McLaughlin, the state epidemiologist, said at a news conference last week.

Sequencing individual strains is more complicated than testing for the existence of the coronavirus itself. The process requires researchers to document each individual piece of the virus’ genetic code, which contains some 30,000 pieces.

First, Alaskans must be identified as carrying the virus through a standard COVID-19 test, with positive tests shipped to the state virology lab in Fairbanks on dry ice.

Not every positive sample can be sequenced, though. Certain types of tests use up the entire sample to identify a person as positive for COVID-19, leaving none left to sequence. Others are processed at out-of-state labs.

“Sequencing has become more of a detective game, where I have to search out specimens and figure out where they are in the world, and how to get them back to the lab,” said Jayme Parker, a top state lab official.

The state is trying to sequence positive tests from across Alaska, which Parker said is aimed at providing a representative view of the different strains of virus spreading in different areas. The state also wants to sequence COVID-19 cases from travelers, and a new Anchorage commercial lab, Beechtree Molecular, is providing the state with samples collected at Alaska’s major airports.

Other samples prioritized for sequencing are COVID-19 cases from coronavirus outbreaks or clusters and those in vaccinated people, Parker said.

Experts say sequencing capacity is critical in allowing the state to track variants as they enter Alaska. But they also note that the technology can be used to retroactively trace how the coronavirus is spreading around the state.

In Britain, scientists used sequencing to trace a cluster of cases of the same strain to a dialysis clinic. And university researchers in Alaska have analyzed sequencing data to examine whether the state’s COVID-19 surges stemmed from homegrown strains of the virus, or ones brought from Outside.

‘The run is failing’

Lisa Smith, the former HIV researcher, was finishing her doctorate at University of Alaska Fairbanks at the start of the pandemic when she got pulled into working at the virology lab. She’s now leading the state’s sequencing program.

Scientists at the virology lab have been sequencing strains of the coronavirus for much of the past year. But the rise of the new, more contagious variants has made the work more urgent, and an incident in December prompted state officials to make a new push to expand their sequencing bandwidth.

That month, workers at the Fairbanks lab were trying to sequence about 300 samples that they suspected could be the B.1.1.7 strain.

But as they prepared to sequence one of their last batches, they encountered a cascade of failures, including a broken machine. Ultimately, one of the samples popped up as a hit for B.1.1.7 — but by that point, it was weeks after the swab was collected.

University researchers could have picked up the slack while the state’s machine was offline. But the state didn’t have a formal system to transfer the specimens, Parker said.

“People were saying, ‘The run is failing,’ and I kept seeing these emails,” Parker said. “I started looking at what we were really dealing with and felt like this was the moment I needed to get everyone together and make sure that we have a consolidated plan.”

Now, the state’s public health labs have formed what Parker calls a sequencing “consortium” with university labs in Fairbanks and Anchorage run by the two professors, Drown and Bortz.

Rather than sequencing solely at the Fairbanks virology lab, the state aims to expand its bandwidth by also sending samples to Drown’s lab at University of Alaska Fairbanks, and to Anchorage’s state-run public health lab.

The state will look to Bortz’s lab, at University of Alaska Anchorage, when it needs sequencing results urgently, since scientists there use a different machine that can handle fewer samples but generates data more quickly.

Once the system is in place within a few weeks, Parker said she expects to be able to sequence more than 300 samples weekly, up from the roughly 100 that are being processed now — though she added that it could be difficult to secure that many positive samples.

“I want to get decent visibility on what’s circulating,” Parker said. “I don’t want to over-sequence, to the point where we’re just sequencing the same viruses over and over again.”

“We were ready”

On Monday, Bortz’s lab at UAA was bustling with students, some of whom have shifted their work to COVID-19 in the past year.

Among the researchers was George, who was previously studying bat coronaviruses.

On Monday, he was manipulating samples of SARS-CoV-2, the virus that causes COVID-19, to test a new protocol for identifying concerning strains. The idea is to sequence specific areas of the virus’ genetic code, rather than the whole thing, George said.

If the protocol works, it could allow for quicker detection of the strains, along with analysis of lower-quality samples that otherwise wouldn’t be adequate for sequencing.

While it was hard to interest friends in harmless bat coronaviruses, it’s been exhilarating to shift his focus to a global public health crisis, George said.

“It’s kind of cool to see things come to life, and to see people actually care about your research,” he said.

In addition to studying new sequencing protocols, the university researchers also want to develop methods that would allow the work to be done in remote locations, like rural villages or hub communities. That could speed up the identification of coronavirus strains, since currently samples have to be shipped to the virology lab in Fairbanks before they can be sequenced.

Drown, the Fairbanks professor, argues that the university labs’ contributions to coronavirus sequencing underscores the value of investing in academic research in the state — even as Alaska lawmakers have sharply reduced the university system’s budget in recent years.

“Being able to transfer our skills quickly to this pandemic is what the university is for,” he said. “We were ready to do it.”

One of the National Science Foundation’s flagship initiatives for the past few years is called Navigating the New Arctic. It looks at the effects of a warming climate on Arctic communities. However, some in the field believe NSF isn’t doing enough to involve Indigenous people who live there.

More than 200 researchers from around the country signed an open letter to the foundation last month, requesting more Indigenous input within the initiative.

Margaret Anamaq Rudolf is a doctoral candidate at the University of Alaska Fairbanks. An Inupiaq woman originally from Fairbanks, her area of study is cross-cultural science education — which she says involves trying to answer the question, “How do we improve working relationships between researchers and Indigenous communities?”

Rudolf is one of the people who authored the letter to the National Science Foundation. While she welcomes the foundation’s initiative, she says it falls short of its potential to include the people who live in the Arctic.

“NSF is still centering researchers in Navigating the New Arctic, instead of centering Indigenous people in what they want and they need,” Rudolf said.

The letter from researchers was formed in solidarity with another letter sent last year from four Native organizations — Kawerak Inc., the Association of Village Council Presidents, the Bering Sea Elders Group and the Aleut Community of St. Paul Island.

The letter from Native groups outlines several issues that would have been studied more comprehensively if traditional knowledge was included from the start. Those include food security and community infrastructure. The letter also highlighted problems with requests for proposals.

Henry Huntington is an Eagle River-based independent researcher who’s worked with the initiative. He’s also one of the main authors of the open letter. He says that requests for research proposals from the National Science Foundation are geared to traditional academic knowledge.

“The forms that you fill out work pretty well if you have a bunch of university degrees and you have some scientific publications and all the standard things that you’d expect of someone with academic training,” Huntington said.

Comparatively, Huntington says it’s harder to list the traditional knowledge of Alaska Natives, who often are much more informed about their communities and will contribute as much if not more to the research.

“They confirm what we already know, instead of investigating what we want to know,” said Cana Uluak Itchuaqiyaq, one of the more than 200 scientists who signed the letter.

Itchuaqiyaq is a PhD candidate in technical communication and rhetoric at the University of Utah. An Inupiaq woman from Kotzebue and Noorvik, she says growing up, researchers coming into her community often would form questions that Alaska Native people already knew the answers to.

“And so, it’s taken tons of time for academia and the sciences to catch up to us,” Itchuaqiyaq said. “They’re just catching up.”

Kawerak social science program director Dr. Julie Raymond-Yakoubian helped write last year’s letter. She says oftentimes when Arctic researchers are making research proposals, one of their last steps is to ask for collaboration with tribal organizations, instead of including them from the start.

“When tribes and tribal organizations and Alaska Native organizations are brought into the process so late in the game, there’s really no way to effectively collaborate on a truly equitable level,” Raymond-Yakoubian said.

NSF Arctic sciences program director Colleen Strawhacker says a major initial issue with Navigating the New Arctic was that many researchers were eager to compete for grants and proposals, making tribal outreach a lower priority.

“Given the feedback from communities, that’s clearly … quite frankly a disrespectful approach to including Indigenous communities in NNA-type science,” Strawhacker said.

While NSF officials are still working on a formal response to the letter from the Arctic researchers, Strawhacker says she values the feedback. She says building and strengthening tribal relationships is key moving forward with Navigating the New Arctic.

“I think it’s critical if we want to fund the best science in the Arctic, we need those perspectives,” Strawhacker said. “We need perspectives from multiple scientific disciplines, but we need perspectives from Indigenous elders and the knowledge that they’ve acquired. I think if we don’t do that, we are doing a disservice to the science and understanding the changes in the Arctic.”

At the beginning of February, NSF announced that the Navigating the New Arctic community offices would be hosted at three universities, including the University of Alaska Fairbanks and Alaska Pacific University, a tribal college in Anchorage.

APU president Valerie Nurr’araaluk Davidson, a Yu’pik woman, described the office as a “hub for Indigenous engagement.”

Raymond-Yakoubian from Kawerak says she’s hopeful that outreach like this, the solidarity between Native groups and researchers shown by both letters, and a push for more Indigenous researchers will produce better outcomes in Arctic research.

A Pribilof Island community of fewer than 400 people has received more than $250,000 in federal funds to train locals to work at its commercial aircraft test range.

The Aleut Community of St. Paul Island announced last week that it was one of seven recipients nationwide to receive the Economic Development Administration’s STEM Talent Challenge grant.

The ACSPI’s aircraft test range will be through a partnership with Sabrewing Aircraft Company, a California drone manufacturer.

The test range is expected to begin operations in the fall, according to project manager Dylan Conduzzi. He says this grant will give tribal and community members access to technical training.

“[It] is really meant to bring in the resources that bring onsite training into the community,” Conduzzi said. “And to make them accessible to tribal members and community members so that when these jobs open up in the test range — which are high-paying, high-tech, STEM-related jobs — they’re able to jump into and immediately assume those roles.”

Historically, local jobs in the STEM field have not been given to residents, according to Conduzzi.

“Many of the technical roles are filled by folks that are not from St. Paul,” he said. “And that gap is created really from a capacity issue in terms of education and expertise. So the goal of this grant is to be able to provide training that addresses that gap.”

Programs will be offered through the island’s University of Alaska Fairbanks Bering Sea Campus. They will range from hazmat courses and drone pilot certification to tribal management degrees.

The funds also provide an opportunity for the island to diversify its largely fishing-based economy, Conduzzi said.

Eighty organizations applied for the federal STEM Challenge grant last summer, according to the Economic Development Administration. Other recipients include a Maryland community college, the University of Michigan and a non-profit in Hawaii.

The University of Alaska’s interim president will serve at least another year.

At a Friday meeting, the UA Board of Regents decided to extend Pat Pitney’s contract as interim president until the spring of 2022, when it will resume searching for a permanent president. The board cited the need for stability during ongoing budget cuts and the COVID-19 pandemic.

Pitney, a former budget director for Gov. Bill Walker, took over as the university system’s president in August after the previous president, Jim Johnsen, resigned.

A new study from the University of Alaska Fairbanks uncovers how arctic ground squirrels recycle nutrients to stay healthy during their long hibernations.

Sarah Rice is the lead author of the paper and a Ph.D. student at UAF’s Institute of Arctic Biology. She says during the winter, arctic ground squirrels enter a state of extreme hibernation.

“They can take their body temperature below freezing,” Rice said. “When they’re in hibernation their heartbeats five times a minute, and they breathe once a minute. They’re just this incredible animal. It’s almost like in a suspended state of animation.”

Arctic ground squirrels can hibernate for up to eight months — and they appear to wake from their winter sleep without starvation or muscle loss. Rice wanted to know how they stayed in such good shape without exercise or food.

The study found that the squirrels’ bodies transformed existing nutrients into resources that could be used to build back tissue that atrophied during hibernation.

To do the study, Rice and her colleagues collected squirrels, brought them to a lab, and introduced them to the cold, dark conditions that induced hibernation. Then the scientists sampled the hibernating animals’ blood to track how nutrients in their bodies changed over time.

“We go into this cold chamber with a little headlamp on,” Rice said. “And we run our experiments on the animal, just going super slow, and super carefully, so we don’t wake them up. And then we put them back on the shelf, and you’re just in this dark room surrounded by like 30 hibernating animals the entire time. It’s just dead quiet.”

If people stayed long enough in one very cold place without food or exercise, they wouldn’t survive the starvation or muscle atrophy that would occur. But if people could recycle nutrients like arctic ground squirrels do, it could keep people on bed-rest healthier or allow astronauts to travel to space with fewer resources.

According to Rice, researchers think they may be able to borrow some of the science of animal hibernation to benefit people.

“Hibernation is a model that has found solutions to problems in the world,” Rice said. “It’s able to survive extremely long fasting at extremely cold temperatures. And so if we can understand some of these mechanisms of resilience, maybe we can take that and apply it to human medicine.”