January 2019 Newsletter

Alaska INBRE

NEWSLETTER {January 2019}

Happy New Year!

The Alaska INBRE office looks forward to serving you again in 2019!

Upcoming funding opportunities and events can be found on the Alaska INBRE event calendar

Photo courtesy of Jynene Black

Chanta Spain , Alaska INBRE summer undergraduate research assistant, sharing her research with Gloria Eldridge, INBRE Steering Committee member, at the 2018 INBRE Retreat. You can read about the retreat on page 4.

In this issue:

Talkeetna Lodge Photo Courtesy of Tom Moran

FROM THE DIRECTOR

RESEARCH RETREAT

A message from Alaska INBRE Director Brian Barnes…………………………………………………

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Alaska INBRE Retreat—celebrating our statewide network………………………………...

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TAILS FROM THE TRAIL Sara Wilbur shares her DNA adventures in

FROM THE BENCH

ANNOUNCEMENTS

Vienna…………………………………………………….

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Kat Miligan-yhre, A lab of her own……………

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Student Spotlight: Amy Klink …………………...

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Alaska INBRE announces new leadership..

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ALASKA INBRE 108 Irving I Building (UAF) Fairbanks, AK 99775-7040 Phone: 907-474-1104 Email: ua-akinbre@alaska.edu

January 2019

Cover Photo: Mountain view from Talkeetna, Alaska, courtesy of Tom Moran

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From the Director A MESSAGE FROM THE DESK OF THE ALASKA INBRE DIRECTOR BRIAN BARNES

Alaska INBRE Community: 2018 has been an exciting year for the Alaska INBRE program. Here’s a quick look at the accomplishments in our network: Pilot Research Awards – in our current funding period, Alaska INBRE awarded ~$700K in pilot research awards. For additional details about the exciting research happening this year, visit our website.

Research Retreat – In October, the network gathered together in Talkeetna, Alaska to celebrate the research accomplishments from the prior year. Please read more about this exciting event on page 4 of this newsletter.

Grant Writing Workshop – In November, Alaska INBRE hosted a grant writing workshop. This event included participants from across the network.

Looking ahead to 2019, there are many ways for you to be involved in the Alaska INBRE program. Please visit our website and subscribe to the weekly e-digest for the many opportunities. At this time, our Developmental Pilot Research opportunity just closed and the Graduate Research opportunity is open for applications along with ongoing solicitations for travel, exceptional requests, and bioinformatics awards.

As always, we welcome your questions and input. If you have an idea or a suggestion about ways we can work to better meet your needs and address your challenges, please let us know.

I look forward to seeing you in 2019!

Brian Barnes January 2019

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2018 Research Retreat Alaska INBRE celebrates our statewide network at the annual Alaska INBRE Research Retreat.

Photo courtesy of Tom Moran

By Tom Moran

wanting to make a difference in biomedical research “ Barnes said.

For two days in October, Alaska INBRE had the run of For the first time, in addition to faculty, undergrads the place. and graduate students from across the project, and The 2018 Alaska INBRE Research Retreat took place at two members of INBRE’s External Advisory Comthe Talkeetna Alaskan Lodge, a four-hundred-plus mittee were also able to attend. Glen Gaulton, of the person resort that had closed for the season. The 80 University of Pennsylvania , offered “An Inspirational attendees from Anchorage, Fairbanks and Juneau had Message on the Importance of Biomedical Research” the expansive grounds to themselves as they listened as his keynote speech, describing recent successes in to presentations, shared posters and savored the opthe fields of retinal gene therapy and treatments for portunity to get better acquainted with the diverse leukemia. He concluded with a slide entitled “Words researchers on the statewide project. of Encouragement” and a message that students “This is our annual opportunity for faculty and other should seize the sort of opportunities for mentorship scientists and graduate and undergraduate students, that INBRE provides. “Let people who care about you all Alaskan biomedical investigators or trainees, to get and who know something about you give you some together to exchange ideas and updates on their re- advice about where your talents lie.” search” said Brian Barnes, Principal Investigator of INBRE. “It’s great to see first-time students talking with senior faculty, all about science“.

The event is now in its fourth year and the location has varied between the Talkeetna lodge and the Grande Denali Hotel outside Denali National Park.

Barnes said getting out of town is part of the point of the retreat.

“No offices to hide in while surrounded by mountains and fall colors; everyone here are part of AK INBRE, January 2019

Photo courtesy of Tom Moran

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EAC member Jim Berner, Senior Director for Science at the Alaska Native Tribal Health Consortium also delivered a keynote that focused on community-based environmental monitoring by Alaska Native groups using a One Health Approach. One Health, which examines human, animal and environmental health as interrelated phenomena, is the overarching theme of Alaska INBRE’s current project and was the organizing principle of the retreat, which divided poster sessions into themes of Human Health, Environmental Health and Animal Health. It also featured a talk by Arleigh Reynolds, who heads the One Health program at UAF. A final presentation was given by Jason Burkhead, Eric Bortz and Devin Drown of the INBRE Bioinformatics Core, who gave an involving blow-by-blow account of their quest to quickly sequence a strain of swine flu. Barnes called it one of the more revelatory elements of the retreat.

for the winter, one night featured a special showing of “The Shining.”

Congratulations to the following students for winning awards at our 2018 Research Retreat! Winners received a $2,000 travel award and runners-up a phone battery bank.

URA winner: Chanta Spain (UAF) – Rabies glycoprotein interact with neuronal nicotinic acetylcholine receptors in a subtype-selective manner URA runner-up: Heidi McKee (UAF) — Role of co-receptor CXCR4 in gp120mediated HIV-associated neurodegeneration GRA winner: Sara Wilbur (UAF) – Enhancing Tumor Antigen Presentation with Complement Targeted Liposomes

“It’s great to see UAF and UAA faculty collaborating in cutting-edge science, in this case within an international network and on a real One Health GRA runner-up: Alex Francian (UAA) – topic.”

Intratumoral delivery of antigen with comThe event was replete with ample unstructured plement C3-bound liposomes reduces tutime for participants to socialize, network, and ex- mor growth in mice plore the grounds and nearby Talkeetna. And as befits a retreat held in a mammoth lodge closed

Photo courtesy of Tom Moran

January 2019

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Tales from

the trail

Sara Wilbur shares her DNA adventures in Vienna. Her trip was funded through an Alaska INBRE travel award.

Adventures In Telomere Measurements

By Sara Wilbur

rad Lorenz Institute, part of the University of Veterinary Medicine, Vienna. I arrived a week later. My intention to come to Vienna was to train in quantitative polymerase chain reaction (qPCR) techniques at the Institute for two weeks.

To run qPCR, one requires only tiny amounts of DNA. Each of my sample tubes contained 50 microliters of liquid. After diluting the DNA samples to five nanograms per microliter, I had enough DNA to run several qPCR reactions over a two-week period. Side note: a microliter is a millionth of a liter and a nanogram is a billionth of a gram. Imagine, five-billionths of a gram of DNA in one-millionth of a liter of liquid. Imagine further: DNA weighing anything at all!

There is something completely magical about coming to understand DNA. Although this work is accompanied by frustrating troubleshooting, perplexing results, and expensive reagents, when everything aligns and your various calculations and graphs tell you something meaningful about the invisible nucleotide chains floating in tiny amounts of In theory, qPCR is beautifully simple. It revolves around three components: time, temperature, and clear liquid… fluorescence. First, DNA (or copy DNA, if you’re workIt’s difficult to conceptualize that something so miing with RNA) is heated to break the double strand nuscule, yet so essential to life, can be measured, can into two single strands. Then the temperature is lowbe quantified, in ways that my brain can understand ered to the best annealing temperature of the primer and put patterns to. That I can tell a story about an pair you are working with (primers are short DNA seindividual’s particular genome. quences that bind to genes of interest on your sample My arctic ground squirrel DNA samples have been on DNA). Finally, once the primers have annealed to the an international journey. I have been carefully exsample DNA sequence, the temperature is raised to tracting and storing DNA from several animals over an intermediate level. This temperature shift actithe past few months. Two weeks before I left I obvates the DNA polymerase enzyme to add freetained the right permits, found the right packaging, floating nucleotides (also included in the qPCR reachad the right people inspect my shipment, and got tion) to the primers as extension templates, thereby the box to the right place at the right time. The sam- creating new double-stranded DNA. ples (and their twenty-some pages of documentation) After this cycle is repeated ~25 times you are left with traveled for two days on dry ice to arrive at the Konmany copies of your sequence of interest. This is all January 2019

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INBRE travel awards are the ticket to academic adventure.

tracked with a fluorescent dye. As the cycles proceed, fluorescent dyes attach to the new double-stranded DNA. The qPCR machine tracks the amount of fluorescence emitted, giving you a real-time understanding of how much DNA template you originally started with.

or neither of the genes are non-VCN. One must keep searching!

Although we’ve hit some dead ends, made some mistakes, and quit the qPCR run early because it was time to get coffee and treats (which made for rather inconclusive results), I’ve felt little-to-no discouragement while working here in Vienna. I can so clearly qPCR can be used for many applications, including see that this is a learning process. My mentors here gene expression analysis, microRNA analysis, gene consistently encouraged me to try, understand, troucopy number variation, and relative telomere meas- bleshoot, and learn. I left Thursday morning with a urement. I was in Vienna to learn the arts of the last more thorough appreciation of the task before me and have full confidence I will see it through to the two applications. end. Above all, I feel so lucky to be supported finanOne way to measure telomeres is by quantifying rela- cially through Alaska INBRE and with hours of donattive telomere length (RTL). RTL is a ratio of calculated ed personal time from researchers here in Vienna. I’m qPCR values. The values from telomere measurelooking forward to other challenges and discoveries ments are divided by values from non-variable copy that crop up along the way. number (non-VCN) gene measurements. (non-VNC genes are repeated in equal numbers in every individual within a species.) This ratio is then divided by a standard telomere/non-VCN ratio. Basically, this big happy family of normalizing ratios eventually provides you with an RTL. These calculated values can then be used within a study to compare telomere lengths over time, between species, between sexes, or between any other meaningful comparison.

Applications are due the

INBRE STUDENT TRAVEL AWARDS

Much of my time in Vienna was spent trying to discover a non-VCN gene for arctic ground squirrels. One way this is done is to calculate several (~12) telomere/non-VCN ratios for two potential non-VCN genes and plot them. If the points from the ratio values make a straight line, they are both non-variable in copy number and can be used in subsequent qPCR runs for telomere measurements. If the points are quite scattered and don’t follow a linear pattern, one January 2019

15th of every month.

For more information, click here

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A lab of her own September 4, 2018

Written by Catalina Myers, UAA Office of University Advancement

Kathryn Milligan-Myhre, assistant professor of biological sciences, leads a micro and genetics lab for students in the Della Keats Health Sciences Summer Program earlier this summer. (Photo by James Evans / University of Alaska Anchorage)

“When I graduated from high school in Kotzebue I didn’t really know what was out there for job opportunities, so I went with what I knew,” said Kathryn (Kat) Milligan-Myhre, UAA assistant professor of biological sciences. “What I knew was tourism — because Kotzebue has a booming tourism industry — so I went to Cornell for hotel administration.”

landed with one foot in academia and the other in research.

Zeroing in

The daughter of a high school teacher mother and a subsistence and commercial fisherman father, Milligan-Myhre spent her childhood growing up in Kotzebue experiencing a blend of both her Inupiaq A year into the program, Milligan-Myhre decided hoand Western heritages. In the summers, she spent tel management was not for her, returned home and her time fishing with her father and attending Camp came up with life plan B. While living at home, one of Sivunnigvik, a weeklong camp for Alaska Native her four jobs was working as a nursing assistant and youths to immerse themselves in their language, culthat’s when brilliance struck — medicine. Not only ture and traditions. She would also head to the Lower did she enjoy her nursing assistant job, she was good 48 to visit her grandparents in Wisconsin and experiat it and could see herself in the medical field long ence the Midwest heat. term.

“I was lucky enough to have this life, but as a high She applied for nursing school, but life threw her an- school student, I never realized that,” recalled Milliother curveball and she was diverted to Wisconsin to gan-Myhre. “I got to go up to camp and help bring help care for her grandmother. So on to plan C. Milli- home subsistence meat to have year-round and was gan-Myhre scratched nursing school and opted for a extremely lucky — I really didn’t know how lucky I pre-med program at the University of Wisconsin, was.”

Madison. It was life plan C where Milligan-Myhre found her niche and discovered her passion for medi- For Milligan-Myhre, once she graduated high school and left Alaska, hindsight would become 20/20. She cal research. She would live in a few more states, have a few more life experiences, but eventually, all quickly realized how much she missed her home state roads pointed home — back to Alaska — where she’s and community in Kotzebue, and how unprepared she was as a college freshman. It would be more than January 2019

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the time,” Milligan-Myhre said. “I thought I could help more people as a researcher than I could as a doctor — I could make strides in research and help generations of people.”

Merging two cultures As indigenous and Western cultures continually intersect with each other, and more students of Alaska Milligan-Myhre shows Moses Wiseman from Chaputnguak Native heritage find their way to scientific areas of School in Chefornak and Alice Samuelson from Z.J. Williams Mestudy, Milligan-Myhre said more needs to be done in morial School in Napaskiak basic lab skills as part of the micro and genetics lab of the Della Keats Health Sciences Summer Pro- opening the gates to the field of medicine. Which is why, when the opportunity arose to return to Alaska gram. (Photo by James Evans / University of Alaska Anchorage) and work at UAA, she jumped at the chance. two decades before Milligan-Myhre would have the opportunity to return home.

“I want Native students to stay here in Alaska and get a quality education,” she said. “We have a really diverse population here in Alaska and I just feel like “We had a lot of really dedicated teachers at the time, who were working really hard for us,” she said. there is so much potential from the students that we “But they didn’t offer calculus, or anything other than have here.” general chemistry — I know I was not prepared that Part of the reason for her returning to her home was first year. Growing up in Kotzebue, we didn’t really to help mentor Alaska Native students, which she has get an education that prepared us for college, or sup- done as an ANSEP instructor for the past couple of ported our traditional lifestyle.” years, and this past summer she participated in Milligan-Myhre said that in the subsequent years fol- the Della Keats Health Sciences Summer Program. lowing her freshman year at college in Madison were The other reason goes back to her academic roots — hard. Although there were Native American students research. on campus, in addition to clubs and organizations, she often felt disconnected from the rest of her Native American classmates, because she was the only Inupiaq. There was no one else like her on campus who could relate to her. She was 12 years into her studies in Madison before another Alaska Inupiaq attended the school.

“There’s so much research potential here and I feel like we’re missing out as a research community because we’re not taking advantage of the fact that we have diverse climates, animals and microbes — we have all of these different things,” said MilliganMyhre. “Right now they’re being explored by a handful of folks from the Lower 48, but this is something our students, that know the best.”

But she persisted, and despite feeling detached from her life in Alaska, she was forging her own path in the Stickleback — a researcher’s goldmine lab. It surprised her to learn that her love of research Currently, Milligan-Myhre is juggling four major grant could be turned into a career. projects, a National Institute of Health (NIH) Academ“It was heartbreaking working in nursing homes or ic Research Enhancement Awards (AREA), also known hospitals where you just saw people at their worst all as an NIH R15, a National Science Foundation (NSF), January 2019

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to curing diseases plaguing the human population.

“The whole reason we’re studying all this is that we’re

interested in this big overall question of how genes and environment contribute to inflammatory diseases,” Milligan-Myhre said. Inflammation is the body’s immune response to fight infections, heal wounds or damaged tissue and without it, the body cannot protect itself from disorders like asthma or inflammatory Milligan-Myhre believes there needs to be more opportunities bowel disease to more painful disorders like arthritis. for Alaska Native youth in the areas of medicine and medical research, which is why she instructed the micro and genetics Milligan-Myhre loves her lab work and the comprecourse this summer for the Della Keats Health Sciences Summer hensive approach stickleback research has and how it Program. (Photo by James Evans / University of Alaska Anchorgives her and fellow scientists a bird’s eye view of the age) problem. an NIH RO1 and an Alaska IDeA Network of Biomedi“This is really systems biology,” she said. “We’re lookcal Research Excellence (INBRE), all of which have ing at the microbial community, the host, several one common denominator — stickleback. different aspects of the host, including development This mainly ocean (but also found in freshwater) fish, and immune response — it’s an overall view of how evolved with unique characteristics after the last Ice all these things interact with each other.”

Age, which sets them apart from other fish species and lends themselves perfectly to scientific study — Milligan-Myhre’s research with stickleback — solving medical issues from an overall viewpoint — is a metaparticularly when it comes to genetics. phor of how she feels about academia and the medi“They’re found all over the Northern Hemisphere and cal and research communities. She believes there there are many different populations of these fish, needs to be more inclusiveness of all cultures and found in different areas, that have the same genetic backgrounds, and in our state, of traditional Alaska diversity between populations that humans have,” Native practices. said Milligan-Myhre. “We can use them as a model to “That’s something that I haven’t really been able to study human diseases.” do yet — weave indigenous knowledge into science,” Because of the stickleback’s enormous diversity with- Milligan-Myhre said. “We have this idea that Western in its own populations — similar to humans — rescience is the only way to do science, and I think that searchers can ask big questions like, how does the has turned off a lot of indigenous people. But, what I host’s genetics contribute to host-microbe relationwould love to see are two things: One, that indigeships? In other words, how might a person’s predenous people have been scientists for thousands of termined genetics affect the relationship of the milyears. And two, I would like to see more indigenous lions of microbes living in our bodies? Or, does our scientists.” environment contribute to our relationship with our "A lab of her own" is licensed under a Creative Commicrobes? Stickleback can help researchers answer mons Attribution-NonCommercial 4.0 International some of these big biological questions to help solve some of medicine’s puzzling answers when it comes License.

January 2019

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Student Spotlight Amy Klink, INBRE Graduate Research Assistant adapts the MinION sequencer to detect full viral genomes in Alaska marine mammals.

Amy Klink is a 2018-2019 Alaska INBRE Graduate Research Assistantship awardee who works in the lab of Eric Bortz at the University of Alaska Anchorage. Prior to starting graduate school at UAA, her research interests focused on using ecological methods to understand population demographics. As an undergrad at Clemson University, she worked as part of a research team focused on detecting Eastern spotted skunks in upstate South Carolina.

Photo credit: William George

Klink’s current research, funded by Alaska INBRE, is focused on detecting viruses in Alaskan marine mammals. Viruses such as influenza are readily passed between species. Marine mammals tend to coexist with several other species (e.g. seabirds) so they are at a higher risk of infection. Understanding viral evolution can help us predict the epidemiological risks it brings to populations in the marine ecosystem. To do this, she is adapting the MinION, Nanopore’s next generation sequencer, to obtain full viral genomes and evaluating the geographical spread of disease.

“INBRE has been an integral part of my research, providing support to use cutting-edge technology to understand viral evolution,” Amy said.

Amy actively participates in presenting her research with the MinION handheld sequencing device. She presented a poster at the Alaska INBRE research retreat in Talkeetna. In November, Amy gave a talk on her research at the UAA sponsored Nanopore Day Practicing necropsy techniques on a small that only featured current Nanopore research efforts stranded black bear from Kodiak, Alaska in Alaska. Recently, she received an INBRE travel Photo Credit: Sonia Kumar award to attend the Nanopore Community Meeting in San Francisco at the end of November to present her After her junior year, she received a fellowship with research. This meeting will further her opportunity to the Alaska Sealife Center to assist in monitoring Stellearn novel sequencing methods from experts in the ler sea lions in the Chiswell Islands. While working field and to use MinION to its highest potential. This with these species, she found herself wanting to learn experience will also help her build collaborations with more about the impact diseases have on these popuresearchers from around the world, which will be imlations and the effects of climate change on the prevportant as she continue her education beyond a masalence and spread of pathogens. ter’s degree.

January 2019

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Announcements Alaska INBRE would like to welcome Cindy Knall, Jonathan Stecyk, and Diane O’Brien to the Alaska INBRE Leadership team.

Cindy Knall, Associate Professor, University of Alaska Anchorage

to understand how the cardiovascular system of anoxia-tolerant vertebrates functions during Knall earned her Ph.D. from the times of oxygen deprivation. Dr. Stecyk brings University of Colorado HSC, in to the program his dedication to teaching and 1994. She joined UAA from his excitement for biology. He has supervised the Lovelace Respiratory Rethree M.Sc. students to completion, mentored search Institute and University four post-doctoral fellows, one research profesof New Mexico in 2005. Dr. Knall’s research fosional, two undergraduate honors students, cuses on aspects of innate immunity and inand 39 undergraduate researchers. flammation relevant to tobacco exposures, such as a study to determine the biochemical and molecular changes detectable in the blood Diane O’Brien, Professor, University of Alaska Native mothers and their neonates of Alaska Fairbanks associated with tobacco use. As well as leading Diane received her Ph.D. at a successful research program, Knall has held Princeton University in 1998. multiple leadership positions within the univerHer research interests include sity and professional community. Her experihow naturally-occurring variaence makes her well suited to successfully tions in stable isotope ratios can serve as AK INBRE PC. be used as markers for nutritional and physiological processes. Diane serves as deputy director of UAF Institute of Biology, deputy director Jonathan Stecyk, Associate Pro- of the COBRE funded Center of Alaska Native fessor, Department of Biological Health Research (CANHR), chaired multiple Sciences, University of Alaska committees, serves as a faculty mentor, and Anchorage was a CANHR core lead. She will bring adminisDNA sequencer.

Stecyksized earned his Ph.D. in trative and scientific expertise to the Alaska IN2007 from the University of BRE Management Advisory Committee.

British Columbia. He is a comparative physiologist and his research aims January 2019

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Join our list serve here and stay up to date on all INBRE-related opportunities!

Upcoming Funding Opportunities  

Graduate Research Assistantship

Undergraduate Research Assistantship 

Curriculum Development Award

Funding Opportunities can be found on our website.

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