Wednesday, June 27, 2012

Angel Investors and UAA: a plan to work together

UAA's Dr. Helena W. Wisniewski delivered  a talk at Anchorage's 49th State Angel Fund Forum, hosted by the Municipality of Anchorage and the Anchorage Economic Development Corporation on May 17, 2012.  (Thanks to the Mayor's office for recording her talk, which we share with you on UAA's INNOVATE blog.)

Wisniewski is UAA's Vice Provost for Research and Graduate Studies and Dean of the Graduate School. She brings an extensive background in higher education, industry and defense, and the entrepreneurial arena of start-ups.

Her talk covers infrastructure that UAA is establishing for investors to share in the development of patents and intellectual property created through research at UAA. She touched on many examples of current work funded with INNOVATE money in January, 2012 including: the Arctic squirrels use in the study of human obesity, the special compounds in Alaska blueberries that may provide intervention in demensia and Alzheimer's research, cheap solar-powered sensors to monitor distant infrastructure and an instrumented mouthguard that can detect impact to the brain -- useful in athletics and war-time situations where head trauma is a potential, among others.

The Municipality's receipt of $13.2M from the U.S. Department of Treasury's Small Small Business Credit Initiative prompted the summit. This fund is known as the 49th State Angel Fund. UAA Chancellor Tom Case is on the 49th State Angel Fund Advisory Committee.


Wednesday, May 30, 2012

Getting a better fix on head injuries with a "smart" mouthguard

Paris with undergraduate research assistant Grant Birmingham.
When I tracked down mechanical engineer Anthony Paris in late May to catch up on an engineering INNOVATE project, we quickly migrated from his office over to a nearby conference room. The whiteboard there was covered with a lacy blue scrawl, an eruption of calculations that drew the eye and held it. But we didn’t talk about those at first. 

Instead, every few minutes he’d dash back to his office and return with something mechanical: a curved spine with an embedded rod on the side to reinforce it; two big white plastic blocks attached to one another by curved rods, simulating the lumbar spine attached to the pelvis; or a mouthpiece with three sugar cube-sized attachments that looked like something a dentist might try and shove into an unwilling mouth.

His current INNOVATE award will further research on the instrumented mouthguard. The funding bought him two portable force plates to continue testing the latest-generation device.

Paris is quick to point out that credit for his recent successes is shared with his INNOVATE Co-PIs, engineering professors John Lund and Jennifer Brock. Lund engineered the electronics and Brock wrote proposals and synthesized data, including high-speed video analysis.

First UAA iteration of a "smart" mouthguard.

A process of constant refinement

On the first iteration created at UAA, the team used an 18-year-old veteran soccer player to head balls with the mouthguard in place, recording impact to skull. ME undergraduate Tessa Kara was funded through the Office of Undergraduate Research and Scholarship (OURS) for this first round of testing.

Now, with a more compact second generation mouthpiece — the wireless transmitter and data logger are separate from the mouthpiece, so it’s slim and more compact — he’s just finished a round of testing with another subject, this time a young man. Over the course of two sessions, the test subject headed soccer balls 10 times at five different velocities, ranging from 8 to 28 miles per hour.

The testing went well. “We got great data!” Paris said, sounding both excited and relieved. “The device worked flawlessly."

Birmingham with the slimmer second-gen model.
The next step comes this summer, when he’ll position a third tester on the portable force plates so that when he maneuvers to head the ball, the force plates will also be gathering data on the interaction between the body and the ground. He’ll then have a complete loop, soccer ball to head, feet to floor.

The force plates echo earlier work with a biomedical team in Boise, Idaho on the biomechanics of soccer heading. There, a single force plate was permanently installed in a gym floor, and Paris dropped a soccer ball 35 feet onto a bowling ball positioned on the force plate, the curves of which duplicated those of the human head and simulated the impact between ball and head.

Increasing concern over concussive head injuries

All this effort is in service of getting detailed and accurate measurement of impact on the human skull. There is much public debate about appropriate treatment for sports concussions, from The New York Times topics page on football and head injuries to a story this April in the Anchorage Daily News about a local teen who experienced a serious concussion during an indoor flag football practice. New York University even hosted a debate earlier this month on banning college football due to head injuries.

For Paris, the cause of impact is less important than accurately measuring the accelerations of the head due to impact. In fact, improvised explosive devices (IEDs) deployed against soldiers in war are another critical application.

“Do accelerations of the head determine the type of brain injury someone has,” he asks. “Can they help determine how you would treat it?”

Consider a blow to the head during snowboarding. “How do you decide on return to play?" Paris asks. "How do you treat them? The same questions are true for boxing, IED blasts in the military and head-to-head impact in soccer or football."

 “Our goal is to continue development and make the instrumented mouthpiece small enough to be useful and practical in all these situations." Birmingham and two other undergraduate research assistants,  Lilan Smith and Kaelin Ellis, have joined Paris in data gathering.

Deriving angular accelerations: 'There's a bit of math there.'

What they measure

Paris and the INNOVATE team use accelerometers on the mouthpiece to measure linear accelerations. From those, they are able to mathematically determine angular accelerations. (That’s the poetic blue scrawl on the conference room whiteboard. Yes, “There’s a little bit of math there,” Paris quips.) 

What’s the difference between the two types of accelerations? For linear, think of the head moving forward and backward, side to side or up and down. For angular accelerations, think of the top of the head tipping backward, the chin coming up. In aviation, this is known as roll, pitch and yaw.

                                      Research includes video analysis of ball-to-head impact.

A visual Paris employs to explain the difference is a glass half-full of iced tea. Push it side to side and ice and liquid moves with the glass. That’s linear movement. 

Spin the glass, and the ice and liquid stay immobile while the glass moves around it. That’s angular movement. 

The accelerometers he’s using, by the way, are similar to what you’ll find in your iPhone, car airbags or Wii handheld devices. Even runners use them in their shoes. Part of what’s making the development of an instrumented mouthpiece possible is the decreasing size and cost of accelerometers.

Sports where helmets are common have an advantage, Paris says. The data logger and transmitter can be installed in the helmet; even football helmets with mouth guards attached offer an advantage because wiring to the transmitter could pass through the attachment mechanism. 

Boxing, like many sports performed without a helmet, offers more challenge.

But since lots of contact sports require mouthguards anyway, why not use them more fully to measure impact to the skull? Paris aims to refine the mouthguard into a smaller and smaller device.

“John Lund said it best,” Paris recalls. “ ‘In 20 years, nobody will be putting a dumb piece of plastic in their mouth.’ ” 

Why would you, when you could use a “smart” mouthguard that delivers nuanced information about the impact status of your brain?

Paris is enthusiastic about the capabilities of the new mouthguard and the acceleration data his team is collecting. He’s exploring patent opportunities now. 

Honored with an Exemplar Award for student mentoring 

This spring, Paris was singled out for a special honor given to faculty who do an exceptional job mentoring students outside the traditional classroom setting. The presentation took place during the Undergraduate Research Symposium this spring; Brock accepted the award for Paris, who was obligated to attend committee meetings for engineering curriculum updates at the time. 

It was at least fitting that she received it for him; she had nominated him after witnessing his work with undergraduates. In her letter, she wrote, "He encourages his students to set high goals, and it is worth noting that two of his research mentees have been accepted at top graduate programs, one at Columbia University in New York and another at the University of Oxford in England."

One of the groups he mentored developed a spinal rod bender, used during back surgery, for which a patent application has been filed. 

“He’s a one-man undergraduate research program!” Brock said when she happened by the conference room where we were talking. She even arranged to frame the award so it could hang on his wall instead of compete for space on a jam-packed desk.
Julia DelSignore, left.

Andrew Cochrane, right,Tessa Kara, center.
Two students also nominated him for the Exemplar. One was Andrew Cochrane, who double majored in mechanical and electrical engineering and received the $2,000 Discovery Award for his academic achievements. 

The other was Julia DelSignore, who collaborated on early soccer impact testing and received a Discovery grant to help with travel expenses to present research at the 12th Pan American Congress of Applied Mechanics in Port of Spain, Trinidad. DelSignore is pictured at left with professors Paris and Brock during the Trinidad conference. You can download a PDF of their paper here.

Anthony Paris
Anthony Paris joined UAA's faculty as an assistant professor of engineering in 2007. He was a research assistant professor at Boise State University in Idaho before that. He earned his B.S.  and M.S. in mechanical engineering at Washington University in St. Louis, and his doctorate in theoretical and applied mechanics from University of Illinois at Urbana-Champaign.

When he’s not in the lab gathering data or working calculations on the whiteboard, Paris can be found practicing yoga at a local Anchorage studio.

Tuesday, May 8, 2012

Funding story: A novel encompassing Alaska's three whaling eras

New England whalers like the one above sailed Alaska waters in the 1800s.
Novelist and UAA professor Don Rearden received INNOVATE funding this year to support research for his latest creative endeavor, a novel about whales that traverses the three great epochs of Alaska whaling history – pre-contact, commercial whaling of the 1800s, and modern-day subsistence whaling under the governance of the Alaska Eskimo Whaling Commission.

“The good thing about getting this award is that it allowed me to say, ‘I have this project I am working on, and the university is sponsoring me,' ” Rearden says.

That support helped him secure a Scholar in Residence position for a week this summer at the New Bedford Whaling Museum in Massachussetts, where he begins gathering some of the historical detail that will color his work.

Why a novel for such an epic history? And, frankly, is there room for another after Melville’s Moby-Dick? And just how gutsy was it to go after INNOVATE funding for creative writing in a competitive field choked with scientists anxious for laboratory research space and time.

Rearden says that for the most part, he chose fiction because the documentary non-fiction work on whaling already had been done. He cites John Bockstoce and his 1986 work from University of Washington Press, Whales, Ice & Men: The History of Whaling in the Western Arctic, among others.

But the idea of a fictionalized history had been alive in him for some time. For one thing, he and close friend and colleague Shannon Gramse had tossed around the idea of a screenplay that would cover Alaska’s great whaling eras. He’s moving ahead on a novel because the story is just so big, he says, and novels reach a wider audience than screenplays. And besides, “We’ll probably still do a screenplay once the novel is done,” he says. And he hopes to convince poet Gramse to provide some poems for the novel.

Power of story

But for Rearden, there is an even more personally compelling reason to choose fiction over non-fiction. In his view, it contains the power of story – elements of character, voice and predicament that can reel an audience in  -- right through to the last page.

Herman Melville
Certainly Melvillle knew that, and yes, his famous Moby-Dick intimidates Rearden.

“That’s an amazing work, so yes it’s scary,” Rearden acknowledges. That’s why Rearden plans to give Melville a nod right upfront in his own novel.

But Rearden brings something unique to this Northern whale writing adventure. His boyhood spent in rural Alaska with his schoolteacher mother and law-enforcement dad exposed him to the hold that an active spirit life can have among villagers. He found it magical and life changing.

He arrived in Akiak as a second grader. And while some of the boys were compelled to box him about when he first arrived, he found village life not just satisfactory, but wholly engaging. He was thrilled to be out riding dog sleds and learning how to set fish traps under the ice.

But, even more, there were the mythical stories everyone told,  “…that idea of ghosts and spirits -- this other world that is just really real for everyone.” Remote communities then had fewer distractions … “we had just one phone in the whole village,” he remembers. The spirits and monsters that peopled local stories thrived, and quickly turned Rearden into a serious student of the culture.

Even in elementary school, he knew he would be a storyteller. “I read a lot. And even before I could be, I knew I wanted to be a writer.”

His family returned to his birth state, Montana, but they were back in Alaska by the time Rearden hit eighth grade. His affection for the relationships and shared village culture – transmitted in stories -- only grew.

“I am a firm believer that all that was right with humanity up to 10,000 years ago was because of story. The way to be a human being. We have lost that.

“We don’t tell stories that are meaningful anymore, that people can learn how to be better people from. That’s why I am drawn to fiction, and I’ll try to do that.”

Therein lies a hint to the novel’s characters that he’s currently searching out. What voice will be the storyteller? And what role will a whale play?

The oldest mammals 

Conceivably, says Rearden, a whale that spanned all three of these eras could still be swimming gracefully through the ocean. Some whales are commonly thought to live at least 100 years.

But in a 2001 column, science writer Ned Rozell cited research that proposed lifespans much longer than that. In, “Bowhead Whales May be the Oldest Mammals,” scientists aged whales through chemicals in their eyes and from embedded ivory harpoons discovered by hunters. The oldest whale they studied could potentially have been 245 years old – a survivor through early indigenous whaling and the East Coast industrialized fleets of the 1800s.

Abandonment of the Whalers in the Arctic in 1871, from an old print.
Then, questing after lucrative whale oil, whaling fleets ventured farther and farther north, until September, 1871, when 32 of some 41 ships got stuck hard fast in the Arctic ice.  More than 1,200 people survived, but the catastrophe -- and the simultaneous discovery of kerosene as an alternative fuel -- delivered a crippling blow to that whaling era.

Not lost to Rearden’s fertile imagination is the circling back to the Arctic that the current Beaufort and Chukchi Sea oil exploration means. The collapse of the fishing fleets of the 1800s coincided with the discovery of fossil fuels and the rapid industrialization of modern times.

Now that same enormous appetite for energy has brought us back to the home of the bowheads, home of that once sought-after lamp oil.

The draw for Rearden to a whaling novel includes a fascination for what science is currently learning about whales – their intelligence and the capacity some have for language and culture.

But there is more: the power of the whale in Alaska Native culture.

“Some of it just fascinates me,” Rearden says, “How story  affects behavior. So, when it’s whaling season, everyone gets along in the village. There are no bad thoughts, no arguments, because the whale would be able to sense that. There are stories about that, and I’ll definitely work with that idea.”

The notion of an old whale that has survived both pre-contact and industrialized whaling, a whale that has lived that long and then allows itself to be taken in the third, subsistence era – “it’s because something was right about that,” Rearden says, “for the whale to give itself. “

Perhaps we are coming full circle, he thinks, “to where we advance enough that we have the understanding of whales that these ancient people did. Maybe we are regaining something that was lost.”

'There was an asterisk'

And finally, what about that question of hutzpah, a creative writer going after research funds from the INNOVATE awards.

Rearden smiles. “There was that asterisk on the application, and it said the research could be for creative works. And I thought, could I get that?” He decided to try.

But he also did it for his students. He teaches newcomers who need help with the writing process through the College Preparatory and Developmental Studies. He also teaches the novel Ishmael by Daniel Quinn in the University Honors College.

And he sits on a committee that awards undergraduate research grants. Sometimes awards in the humanities go unasked for, and un-awarded.  “I am always telling my students they really should apply, for their creative work. I couldn’t be a hypocrite myself, and not apply.”

To Rearden, his INNOVATE award signals that UAA, which prides itself in being a home for research, definitely casts its support to work in the creative arts.
Don Rearden

Don Rearden is a new dad this year, father to young Atticus. His wife, Annette, is a professor in the School of Nursing. After his long stays in rural Alaska sharing and enjoying Native foods, he confesses a fondness for Akutaq, Eskimo ice cream, and being an accomplished hunter of moose and caribou. He has worked at UAA seven years, and has his master's degree in Creative Writing. His first novel, The Raven's Gift, was published in 2011.

Thursday, February 2, 2012

When less is more: New image compression success could save millions

We all know the pain of sending a too-large photo via email, only to have it bounce back into our can’t-send file.

Or how about on the other end -- the agony of pasting a too-small photo into a too-big web hole, and ending up with a fun-house pixelated version of the image.  The photo was so compressed, too much of its visual information disappeared.

Now imagine you are NASA, trying to capture high-resolution images of the Martian landscape and then transmit them across millions of miles of space over limited bandwidth channels – losing as little information as possible while achieving as much compression as possible.  Even with our narrow experience doing Earth-bound photo transmission, we can tell this is complex and really hard.

If you are Frank Moore, a computer science professor at UAA, this is your problem to solve, which you happen to be quite excited about.

That’s because Moore has had recent success “squeezing” images through compression, but retaining high resolution, results that promise to go beyond the best NASA has ever seen.

First, a brief lesson in compression. To compress an image, you begin by substituting a coefficient for every pixel. Nothing is compressed at this stage, just transformed. Next these coefficients can be compressed in waves so that the information is statistically concentrated in fewer and fewer coefficients. The result is smaller files that are easier and cheaper to store or transmit.

But, there is a trade off. On the other end, when you receive the image, it needs to be reconstructed as accurately as possible. Somewhere, there’s a sweet spot between high-resolution images and file size, and Frank Moore has found it.

State-of-the-art methods use “wavelet transforms” for compressing and reconstructing images. NASA created its own family of wavelets called ICER.  They use “lossy” compression (that’s right, you intentionally lose some of the visual information in exchange for a smaller file).

Notice the pixelation in this ICER transformed Mars detail.
Moore’s work has shown that you can use an evolutionary algorithm to optimize new sets of numbers that correspond to new transforms capable of outperforming these contemporary wavelets.

He started out by showing that --  for an equal amount of compression --  you can significantly reduce the error when reconstructing the image. Then, he showed that -- accepting a given amount of error -- you can reduce the compressed file size further.

His most recent work has, for the first time (drum roll here...), reduced both the compressed file size AND the error rate. Better still, file size and error rates only improve with additional levels of compression. "That's not something that happened with earlier results," Moore said.

He has numbers to demonstrate how his error rate and file size evolve with added levels of compression.
  • The best single-level compression yields a 26.8 percent reduction in resolution error, but only a 3.3 percent reduction in file size.
  • At three levels of compression, the best-evolved transform yields a 45.9 percent error reduction, with file sizes 13 percent smaller.
  • But the big success came with five levels of resolution. Here, errors were reduced by 50 percent and the file size was 28 percent smaller.
Moore's version shows less error in image reconstruction.
The worldly applications for this compression and reconstruction success are huge. Smaller files that still effectively reconstruct an accurate image mean cheaper storage and transmission costs, something government and industry need and want.

Medical imaging is a good example. The price of storage and transmission has been billowing at an annual rate of 50 percent; billions could be saved with cheaper but still accurate compression methods.

Other applications, for us mere Earthlings? Moore says his new transforms could produce higher-quality mp3s, instead of the hollow-sounding versions we can now cost-effectively create.

He’ll use his recently awarded INNOVATE funds to further his evolutionary computations, applying his NASA success to an international compression standard.

Read more about his work in his own words; five projects are posted on his faculty website.

Frank Moore with "The Great One."
Frank Moore is an Associate Professor of Computer Science at the University of Alaska Anchorage. He has taught computer science, computer engineering and electrical engineering courses since 1997, and has more than six years of industry experience developing software for a wide variety of military research and development projects.

His current research uses evolutionary computation to optimize transforms for lossy image compression and reconstruction, funded by a NASA EPSCoR CAN for Research award. Moore has published more than 75 peer-reviewed journal articles, conference papers and technical reports.

Tuesday, January 17, 2012

When you can't be there: Cheap, solar-powered sensors to monitor remote Alaska infrastructure

Solar-powered sensors already exist, but are expensive and lack the capabilities of a new monitoring device that electrical engineering professor John Lund is now designing.

His wireless device would likely be used along remote roads in Alaska, keeping an eye on culverts, telephone poles, bridges and other essential infrastructure.  The sensor could be programmed to measure a feature like light, lean or orientation – some indicator of change, and constantly transmit that data whenever the device has the solar power to do so – which would be about every 30 seconds.

Circuit board for solar-powered sensor
Lund won an INNOVATE award in December 2011 to design and create the sensors over the next six months. He intends to pursue a patent and publish in a peer-reviewed journal.

The cool part of Lund’s design is that – because these devices have FRAM, or special memory qualities – each sensoring device receives and stores all data from every other device in its same network; if one fails, every other monitor in the system contains all the data for the entire network.

Imagine an Alaska state vehicle (State Troopers or DOT trucks) or even commercial truckers traveling remote main roads across the state. A sensor on that vehicle would be capable of scooping up vast amounts of data as it travels along. Transmitting devices attached to telephone poles, for example, would be capable of sending information across at least one kilometer.

Pass over a bridge, and the sensor on the bridge could report even a minute change in the bridge’s orientation – a deviation that might not be even noticeable to the traveler.

Move along a highway and gather data from every side road you pass. 

Further, if one node in the system is connected to a power grid, it can report the entire network’s data over a cellular network.  It would be possible to sit in a warm office in Fairbanks, and monitor infrastructure hundreds of miles away.

Imagine that this device costs no more than $10, and because it doesn’t have any batteries, lasts more than 50 years. Imagine that it gets installed at the point of construction – so no expensive retrofits are required.

Telephone poles can cost $4,000 a piece, a culvert can be $300.  A $10 monitoring device for expensive infrastructure security makes sense. Lund’s devices are aimed at long-term monitoring, capturing small changes that signal the need for more attention before something significant -- like a bridge failure -- occurs.

But what happens in winter, when light disappears and snow covers everything? If there is no snow cover, ambient light will be enough to power sensors. They’ll just report a little more slowly -- like every 90 seconds instead of every half-minute.  When covered by snow, they’ll go silent until light returns.

Their battery-free quality means temperature is no factor in their function. According to Lund, electronics only function to about minus 40 degrees F; batteries only to about minus 10. That eliminates a lot of Alaska’s geography, a flaw that his devices can overcome. 

Lund is using mostly off-the-shelf hardware to create the device. Programming its function is his added value.

“Until now, we haven’t put high tech and low tech together like this,” he said, “High tech was much too expensive. Now it’s possible.”

John Lund
John Lund grew up in Anchorage and graduated from East High School. He earned a B.A. in computer engineering from Washington State University in Pullman, WA, and his master’s and doctorate in electrical engineering from the University of Washington in Seattle.

He joined the UAA School of Engineering faculty in 2009. His research emphasis is micro/nano-scale fabrication, analog/digital filter design, control systems, automation, microscopy, computer vision, system integration, biosensors, surface/molecular engineering.

Wednesday, January 11, 2012

Alaska blueberries: Who knew they were THIS good for you?

Photo by Jeff Fay, UAF Cooperative Extension Service
There’s a certain delight in knowing that a UAA chemistry professor deciphering the exact properties of Alaska’s bog blueberries that make them so good for us is Fairbanks-born and raised. Surely his time spent gathering these gems on the tundra sparked curiosity about their antioxidant qualities?

Well, surprise, surprise, that wasn’t the case.

In  2005, as Colin McGill faced a choice between two research options for his doctoral work at UAF, he chose a new blueberry project because he hoped to discover and isolate the as-yet-unknown natural chemical compounds in the berry.  Today, he’s very glad he made that choice: Blueberries are turning out to be a new gold rush for health.

The berry’s beneficial qualities were already known when McGill started his research; but at every science conference where they were discussed, the first, second and third question was always: What is it – EXACTLY – that makes this berry so powerful?

People assumed it was the colored compounds that turned them blue, the anthocyanins. But McGill isolated two other anti-inflammatory compounds that give the berry its tartness: citric acid and malic acid. Domesticated berries have relatively little; Alaska’s bog blueberries are loaded.

In fact, the farther north and the harsher the climate, the higher the concentrations of these two acids in Alaska blueberries. If you dried interior berries, they would be 10 percent citric acid (that’s the same amount as a lemon!) and one percent malic acid, making those two compounds the berry’s dominant ingredients.

“It’s not just the species, but the location, that matters,” McGill says, noting that berries picked 400 miles north of Anchorage are more potent than those picked only 150 miles away. Again, the harsher the climate, the better the berry.

Now, the human body can make these compounds on its own. But McGill theorizes that when we are under “oxidative stress” (an imbalance that can create free radicals, which figure in lots of diseases), we may deplete our own supply. These two acids suppress inflammation, and their lack makes us more susceptible to it. Can we somehow inoculate ourselves against excess inflammation by fortifying ourselves with blueberries?

With the INNOVATE funds he just received, McGill will try and find out. He’ll apply these acids under different circumstances to document and understand their effects. He’s collaborating with Penn State researchers who’ve shown the compounds can slow tumor growth rate.

 “One way tumors grow is by inflaming surrounding tissue,” McGill explained. “While the compounds didn’t kill the cancer, they slowed it down.”

McGill has an additional collaborator from UAF, Kriya Dunlap, who is examining how the blueberry compounds – citric and malic acid -- affect insulin uptake in the body.

McGill’s own question is about neurodegeneration. In the case of Parkinson’s and Alzheimer’s diseases, cells – healthy cells – begin to commit suicide.  Why?

When cells are under oxidative stress, they show a slight increase of a fat or lipid molecule, called a ceramide. These are known as “signaling” molecules and are known to trigger “programmed cell death.” The presence of a little ceramide launches a feedback loop, ratcheting up ceramide levels and avalanching cell death – hence the memory loss and disorientation of aging.

Could the malic and citric acid so common in Alaska bog blueberries be used to intervene here? To literally step in and stop this catastrophic chain reaction?

Stay tuned.  The world of blueberry-based pharmaceuticals is definitely heating up. McGill notes that research papers on the topic have tripled between 2005 and 2008.

“Americans, and people internationally, are much more concerned about what they eat, and where it comes from,” he said.

Meanwhile, McGill is enthusiastic about what he’s learned about blueberries, and a few other edibles that help prevent inflammation.

“If I were to make three dietary recommendations, they would be eat blueberries, drink green tea and take fish oil. All three are anti-oxidative and prevent inflammation,” he said.

He’s thrilled to be working with compounds that figure so prominently in important cancer, diabetes and neurodegenerative research.


Colin McGill is an assistant professor of Chemistry in UAA's College of Arts and Sciences.  Born and raised in Fairbanks, he completed his doctorate in Biochemistry/Molecular Biology at UAF in 2010 and subsequently trained as a Postdoc with the UAA WWAMI program. His research focus is on the identification of biologically relevant compounds in medicinal plants and determining the mechanism of their actions.

Wednesday, January 4, 2012

Does copper deficiency lead to liver disease?

The liver is the second largest organ in the body, located under the right rib. It weights three pounds and is shaped like a football, but flat on one side.

The liver processes what we eat and drink into energy and nutrients the body can use. It also removes harmful substances from the body.

Nonalcoholic fatty liver disease occurs when the liver has trouble breaking down lipids or fats, causing them to build up in the organ. Doctors are not sure what causes this to happen, but if more than 5-10 percent of the liver’s weight is fat, that person has the disease. It tends to develop in those who are overweight or obese, or have diabetes, high cholesterol or high triglycerides.

Non-alcoholic fatty liver disease, Wikipedia Commons
This image illustrates nonalcoholic fatty liver disease. The white/clear/oval spaces represent fat accumulation that is so large it distorts the cell’s nucleus.

This is a common disease (about 30 percent of the U.S. population has it) and for most people, it causes no signs and symptoms and no complications. But at its most severe, it can progress to liver failure.

The liver is also the central organ for maintaining proper levels of copper, an essential metal nutrient we get through diet. Too much copper is lethal. Too little copper has been linked to the development of non-alcoholic fatty liver disease.

Jason Burkhead was recently awarded INNOVATE seed money to develop a mouse model to investigate the role of copper in non-alcoholic liver disease.

“We know that copper deficiency causes changes in liver lipid metabolism, but we do not know why deficiency induces these changes, or the changes in gene expression and cell machinery that lead to pathology, “ Burkhead said.

His main questions are:
  • What is the copper handling machinery in cells and how is it regulated?
  • What are the molecular-level changes due to copper excess or deficiency?
  • How do these changes lead to disease?
Looking forward, he says he’s excited about moving from basic to translational research, and developing collaborations with clinicians who specialize in liver disease, including the Alaska Native Tribal Health Consortium.


Jason Burkhead is an assistant professor of Biology and researcher at UAA affiliated with INBRE (IDeA Network of Biomedial Research Excellence) and ENRI (Environment and Natural Resources Institute). He came to UAA after earning a Ph.D. in biology from Colorado State University in Fort Collins, CO and doing postdoctoral work at the Oregon Health & Science University in Portland, OR. His research focuses on understanding the molecular machinery that regulates cellular copper levels and what goes wrong when those levels aren’t maintained.

The fast-fattening arctic ground squirrel may hold clues to why and how humans become obese

U.S. obesity rate, 1960-2004, CDC
Obesity is a concern in most industrial nations, and especially in the United States where 74.1 percent of the population is either overweight or obese.  This condition can be a prelude to some serious illnesses, including type 2 diabetes, hypertension and cardiovascular disease.

The medical costs are astounding, estimated at $117 billion in direct and indirect costs, half of that borne by Medicare and Medicaid. Did someone mention out-of-control health care costs?

So how can the humble little arctic ground squirrel help with such a serious health issue?

Khrys Duddleston, an associate professor in the Department of Biological Sciences at UAA, is finding that out in her lab, examining the microbial community in the intestinal tract of Urocitellus parryii. These squirrels are good for this study because they fatten up fast for hibernation  -- in only about three weeks time.

Duddleston, along with her collaborators Dr. Loren Buck and Dr. Fred Rainey, and her graduate and undergraduate students Tim Stevenson and Brian Quinlan, are curious whether the squirrel’s gut microbial community assists the host animal in putting on weight.  Using “next generation” genetic sequencing and other methods, they are mapping changes in the gut-microbial community during pre-hibernation fattening.

How does this work relate to humans and obesity?

In humans, microbes live within the human digestive system and contribute to immunity, synthesize vitamins and help digest fiber. Studies have shown that the gut microbial community in lean individuals is different from that of obese individuals, and that gut microbes may send signals to the host that predispose them to deposit fat. Duddleston and her colleagues contend that the arctic ground squirrel, due to its rapid fattening, is the ideal organism in which to further study the potential role the gut microbial community plays in obesity.

“We are doing basic science, using genetic sequencing to identify members of the gut-microbial community and how the community makeup changes as the squirrels deposit fat in preparation for hibernation,” Duddleston said.

Duddleston’s project received INNOVATE seed funds, which she is linking to start-up funding she received from INBRE (IDeA Networks for Biomedical Research Excellence, sponsored by NIH). This work has been supported by funds from the U.S. Department of Defense, and her undergraduate and graduate students have successfully applied for grants and fellowships from NIH-INBRE, the UAF Center for Global Change and the Alaska Hearth Institute that they used in this early work.

“INNOVATE funding will allow us to use next generation sequencing to get a deeper look at the gut microbial community,” she said. The results will enable her graduate student to publish his master's thesis with better, more specific information in a top-flight science journal. This, in turn, will strengthen Duddleston's application over the next one to two years for larger grants from the National Institutes for Health and the National Science Foundation.

Duddleston says a logical next step is to consider the use of antibiotics to manipulate the community of gut microbes to see how this affects pre-hibernation fattening in the squirrels. Could the growing propensity of humans to become obese be shut down by adjustments to our own digestive microbes?


Khrys Duddleston teaches microbiology in the Department of Biological Sciences at UAA. She graduated from Virginia Tech with a bachelor's and master's in Biology, and earned her doctorate in Microbiology from Oregon State University.  She is an INBRE (IDeA Networks for Biomedical Research Excellence) faculty affiliate. She joined UAA in 1998 as a post-doctoral research associate. (That Kenai king, by the way, weighed 42 pounds.)

Beetle-killed spruce: finally good for something?

Make that a definite maybe.

Alaska is an abundant source of fish, wildlife, mountains, minerals and wide-open spaces. Something we don’t necessarily toss into that “abundant” category is beetle-and fire-wasted spruce. But we’ve got acres by the millions of it.

If civil engineering professor Scott Hamel has anything to do with it, these damaged trees might someday become the source for manufacturing wood-plastic composite building materials right here in Alaska. Think jobs, and lower construction costs.

Alaska-made planks for your dream deck?
If you’ve added a deck in the last 10 years, you likely used planks formed from wood-plastic composite (WPCs). It’s been a hot commodity for about a decade. WPCs are considered sustainable because they use recycled plastic and wood by-products. They also don’t require the same chemical treatments that wooden planks do. However, because of their plastic component, they are sensitive to temperature, and little or no testing in cold has been performed. That’s Hamel’s aim.

Hamel, who arrived in August of 2011 at UAA, will set up his first lab here with the newly-awarded  INNOVATE dollars. He’ll test the properties of WPCs at cold temperatures in three different conditions, including one called “relaxation response,” but it’s not the “relaxation response” we usually think of.

Those testing situations are: 
  • Ramp, “applying an increasing extension to a specimen at a constant strain rate until failure.” This will provide findings on stress-strain, strength and rupture.
  • Creep, “applying and maintaining a constant load on the specimen and measuring time-dependent strain response.”  Or, how much does the plank sag over time.
  • Relaxation, “applying and maintaining a constant displacement to the specimen and measuring the time-dependent stress response.”  Or, how much softer or more flexible does the plank become?
Off-the-shelf equipment will be used for most of the testing, except for relaxation. In that case, Hamel will be designing and creating it.

He hopes to add one or two undergraduate research assistants. His timetable for results is a year, and includes publication in peer-review journals. His results may influence an ASTM building standard for structural grade plastics currently under discussion. (ASTM stands for the American Society for Testing and Materials). Hamel is a member of the subcommittee that governs this standard.

Originally from New Hampshire, Scott Hamel completed a B.S. in Civil Engineering at Worcester Polytechnic Institute in Massachusetts.  After inspecting and designing bridges in Boston for three years, he moved to Boulder, CO to complete a master’s in Civil Engineering with an emphasis in structures. He worked for a structural engineering firm in Denver for three years, designing commercial buildings and earning his license as a Professional Engineer. He completed his Ph.D. at the University of Wisconsin-Madison in structural engineering with a dissertation on computer modeling the behavior of Wood-plastic Composites. He joined the engineering faculty at UAA in 2011 where he teaches courses in structural engineering, such as steel and concrete design.