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Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Bioinformatics Faculty Publications

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

Cosmic Dust, Maria Belina Manalang

Art

My thesis is a body of work collectively entitled Cosmic Dust. It consists of different series of paintings that I've produced as a Master of Fine Arts student here at University of Alaska Fairbanks. These series are the Drip Paintings, Celestial Objects, and Ellipsoids. Elements from different series sometimes combine to form hybrid paintings. Although I have categorized my paintings into these three series, they have many elements in common. They are all related to natural phenomena involving continuous cycles and the effects of gravitational force.

A Model Microfluidics-Based System For The Human And Mouse Retina., Shawn Mishra, Ankush Thakur, Stephen Redenti, Maribel Vazquez

Publications and Research

The application of microfluidics technologies to the study of retinal function and response holds great promise for development of new and improved treatments for patients with degenerative retinal diseases. Restoration of vision via retinal transplantation therapy has been severely limited by the low numbers of motile cells observed post transplantation. Using modern soft lithographic techniques, we have developed the μRetina, a novel and convenient biomimetic microfluidics device capable of examing the migratory behavior of retinal lineage cells within biomimetic geometries of the human and mouse retina. Coupled computer simulations and experimental validations were used to characterize and confirm the formation …

Hidden Voices: The Missing Narratives Of Voluntary Interdistrict Choice Participants From 2000 To 2004 And Student Transfer Participants From 2013 To 2014, Miranda Temecka Ming

Dissertations

This study explored the perspectives of students participating in the Voluntary Inter-district Choice program from 2000-2004 and the experiences of participants in the Student Transfer Program attending the same suburban district due to the lack of accreditation in their neighboring schools during 2013-2014. The study uncovered the voices of participants in the VICC and student transfer program and to provided their voices in hope that it may be used as an instrument of change. This subjective, phenomenological qualitative study explored the lived experiences of high school students transferring to suburban districts and provides an in-depth analysis of their social, emotional, …

Dean Of Engineering Receives Utah Governor’S Medal For Excellence | College Of Engineering, Usu College Of Engineering

College of Engineering News

Dec. 17, 2015 – Utah State University’s College of Engineering Dean Christine Hailey was among ten state leaders recognized this week by Utah Gov. Gary Herbert for outstanding service in academia, education and industry.

Hailey will receive the Governor’s Medal for Excellence at a special gala event on Jan. 13 at Rio Tinto Stadium along with fellow recipients including three other faculty members from USU.

Immunogenic Compositions Comprising Slcified Virus And Methods Of Use, Kenneth M. Stedman, James R. Laidler, Keith Bahjat

Technology Transfer - Patents

It is disclosed herein that viruses coated in silica retain infectivity and the capacity to induce an immune response in an infected host. In addition, silicified virus is remarkably resistant to desiccation. Provided herein are methods of inducing a virus-specific immune response in a subject by administering to the subject an effective amount of silicified virus or silicified virus particles. Methods of enhancing a virus-specific cell-mediated immune response (such as a T cell-mediated immune response) in a Subject by administering to the subject a silicified virus or silicified virus particles are also described herein. Further provided are immunogenic compositions comprising …

Immunogenic Compositions Comprising Slcified Virus And Methods Of Use, Kenneth M. Stedman, James R. Laidler, Keith Bahjat

Technology Transfer - Patents

No abstract provided.

The Weekly Challenger, December 17, 2015, The Weekly Challenger, Et Al

Weekly Challenger Newspaper Collection

The December 17, 2015, issue of The Weekly Challenger.

Knowledge, Attitudes, And Intentions Toward Fertility Awareness And Oocyte Cryopreservation Among Obstetrics And Gynecology Resident Physicians, L. Yu, Brennan Peterson, M. C. Inhorn, Julia K. Boehm, P. Patrizio

Marriage and Family Therapy Faculty Articles and Research

STUDY QUESTION What knowledge, attitudes and intentions do US obstetrics and gynecology (OB/GYN) residents have toward discussing age-related fertility decline and oocyte cryopreservation with their patients?

SUMMARY ANSWER Most OB/GYN residents believe that age-related fertility decline, but not oocyte cryopreservation, should be discussed during well-woman annual exams; furthermore, nearly half of residents overestimated the age at which female fertility markedly declines.

WHAT IS KNOWN ALREADY Oocyte cryopreservation can be utilized to preserve fertility potential. Currently, no studies of US OB/GYN residents exist that question their knowledge, attitudes, and intentions toward discussing age-related fertility decline and oocyte cryopreservation with patients.

STUDY …

Maternal Predictors Of School Readiness Among At-Risk Head Start Preschool Children, Rachel Chase

Master's Theses and Doctoral Dissertations

Preschool has been identified as a critical period during which children who are at-risk for school difficulties are most responsive to intervention (National Institute of Mental Health, 2002; National Research Council & Institute of Medicine, 2001). Because of this, school readiness has recently become a prioritized area of interest for the educational system, the health care industry, and the federal government. However, many efforts to comprehensively prepare a child to begin school have not been successful because factors beyond the educational system (e.g., parenting/parent attributes, environmental stressors, and other demographic characteristics) have not been closely considered nor adequately researched. Therefore, …

How Can Participatory Social Network Analysis Contribute To Community-Led Natural Resources Management?: A Case Study From Bua Province, Fiji Islands, Brook. M. Mcdavid

Natural Resources

Adaptive co-management of natural resources requires a variety of stakeholders across different scales and sectors to communicate and collaborate effectively. Social network theory recognizes that stakeholders interact with each other through networks and that various network characteristics affect the way in which they function. Social relationships can be visualized through network mapping and their patterns systematically analyzed in a process known as social network analysis (SNA). Participatory SNA allows members of the network to be involved in the mapping or analysis process. Participants can then apply their knowledge of these relationships to build, improve, or better utilize their connections to …

Handheld Stand-Alone Microfluidics Compatible Field Use Fluorimeter For Analyzing The Concentration Of Analytes In A Sample, Matthew B. Anctil

Engineering

This thesis presents the work performed to produce a handheld fluorometric tool for the analysis of microfluidics lab chips. The first section of this thesis describes the methods used for the design and development of this fluorometric tool. Each of the major components was tested individually to determine how effectively it would perform under different circumstances and configurations. Compensations were made for the weaknesses identified in each of the major components. The second section describes the laboratory testing of the developed photofluorimeter. Initial testing was carried out using a photo fluorescent tracer dye known as fluorescein sodium salt. Additional testing …

Assisting School Personnel With Youth Transitioning From Residential Treatment To A School Environment, Kristi Smith

Counseling

The following research project examines the data and literature regarding youth who reside in residential treatment centers for behavior and mental health purposes. The paper introduces common risk factors that youth are experiencing which contribute to their placement in the facilities, as well as the difficulties they face upon exiting the treatment program. This project explores how schools can assist students in the transition from residential treatment to a school setting using a bio-ecological model that supports the students on an individual level up to a systemic level. School counselors serve as a key point of contact for transitioning students …

Space Use And Movements Of Moose Hunters And Wolves In The Yukon Flats, Alaska, Ian Johnson

Biological Sciences

Within the Yukon Flats, Alaska, subsistence communities utilize moose (Alces alces) as a primary resource (78% of households) and wolves (Canis lupus) hunt them as an obligatory prey item. Hence, understanding the potential of direct or indirect competition between wolves and humans is useful for managers. In Chapter 1, I used a novel approach utilizing spatially-linked interviews to quantify the distance subsistence users were traveling from communities and rivers to harvest moose in the Yukon Flats. My study was the first to quantify hunter access in the Arctic and may provide managers with a harvest estimation approach that may supplement …

Identifying Industry Defined Best Practices Within Educational Youtube Content, An Exploratory Study, Martin Van Der Kroon

Communication

No abstract provided.

Stopover Ecology Of Semipalmated Sandpipers (Calidris Pusilla) At Coastal Deltas Of The Beaufort Sea, Alaska, Roy Thomas Churchwell

Biological Sciences

Avian migration is one of the wonders of the natural world. Stored fats are the main source of nutrients and fuel for avian migration and it is assumed the fat deposition at stopover sites is a critical component of a successful migration. Stopover sites are crucial in the successful migration of many birds, but particularly for arctic-breeding shorebirds that migrate long distances from breeding to wintering grounds. Despite the importance of stopover sites, it is often difficult to determine the importance of these sites to migrating shorebirds. I investigated three aspects of stopover ecology of Semipalmated Sandpipers (Calidris pusilla) foraging …

Linkages Between Protein Ubiquitination, Proteasome Activity And The Expression Of Oxygen-Binding Proteins In Antarctic Notothenioid Fishes, Corey A. Oldham

Biological Sciences

Antarctic icefishes lack hemoglobin (Hb), and some species lack cardiac myoglobin (Mb). As iron-centered proteins, Hb and Mb can promote the formation of reactive oxygen species that may damage biological macromolecules. Consistent with this, we find higher levels of oxidized proteins in some tissues of red-blooded notothenioids than in icefishes. Oxidized proteins are marked for degradation by the conjugation of the protein ubiquitin. I hypothesized that levels of ubiquitinated proteins and 20S proteasome activity (which degrades oxidized proteins) would be higher in +Hb and +Mb notothenioids than icefishes lacking the proteins. Levels of ubiquitinated proteins and rates of proteasome activity …

Non-Invasive Methods For Obtaining Occupancy Probabilities And Density Estimates Of Interior Alaska's Mesocarnivore Populations, Casey Pozzanghera

Biological Sciences

Mesocarnivore species worldwide have been shown to be significant drivers of ecological communities. Changes in their abundance and distributions are known to cause cascading effects throughout ecosystems, and changes to the landscape and climate will likely lead to shifts in mesocarnivore population sizes and distributions. However, the current status of these species in some of the world's most susceptible landscapes is not known. I assessed the impacts of abiotic factors on the distributional patterns and abundance of boreal mesocarnivores and evaluated methods commonly used to estimate density and occupancy. I conducted non-invasive winter surveys of coyotes (Canis latrans), red foxes …

Trophic Pathways Supporting Juvenile Chinook And Coho Salmon In The Glacial Susitna River, Alaska: Patterns Of Freshwater, Terrestrial, And Marine Resource Use Across A Seasonally Dynamic Habitat Mosaic, Kristin M. Rine

Biological Sciences

In large, seasonally dynamic and spatially complex watersheds, the availability and relative importance of various food resources for stream fishes can be expected to vary substantially. While numerous studies have attempted to uncover the trophic linkages that support stream salmonids, much of these efforts have occurred at small scales that disregard variability of food resources inherent in lotic systems. This study aimed to determine large-scale patterns in the contributions of freshwater, terrestrial, and marine-derived food resources to juvenile Chinook and Coho salmon (Oncorhynchus tshawytscha and O. kisutch) in the large, glacially influenced Susitna River, Alaska. I quantified diet patterns both …

Direct And Indirect Effects Of Wolves On Interior Alaska's Mesopredator Community, Kelly J. Sivy

Biological Sciences

Large carnivores may indirectly benefit small predators by suppressing competitively dominant mesopredators. However, our current understanding of interactions within the carnivore guild does not account for carrion subsidies provided by large carnivores, which could facilitate mesopredators during times of prey scarcity. This could be particularly relevant in northern ecosystems characterized by long harsh winters and decadal prey cycling. In Alaska, state-sponsored wolf (Canis lupus) control programs reduce wolf populations by as much as 50-80% across 8 game management units that collectively total over 165,000 km2, yet the impact of this practice on the Alaska's diverse mesopredator community remains unknown. We …

Comparison Of Lower Body Segment Alignment Of Elite Level Hockey Players To Age-Matched Non-Hockey Players, Jim R. Kimbal

Biological Sciences

Lower body overuse and insidious onset injuries are thought to have an underlying biomechanical component which may be predisposing to injury. The purpose of this study was to compare lower body biomechanical characteristics for elite hockey players to matched controls. I hypothesize that elite hockey players have a greater degree of anterior pelvic tilt, greater varus knee angle, a higher foot arch and feet held in parallel more during gait than a matched non-skating population. Measures were taken of elite level, college aged, male hockey players and compared to cross country runners (ten subjects in each group) who served as …

Winter Commencement: December 17-18, 2015, University Of North Dakota

UND Commencement Programs

UND Winter Commencement program from December 17-18, 2015.

A Statement, Cein Watson

Theses and Dissertations

The thesis paper is a map of my studio practice. It is meant to be a resource to help the viewer read my artwork. By laying out the tools of my practice the paper gives the reader a context on how I digest and synthesis works of art. These tools range from references to art history, architecture, and a grounding in traditional craftsmanship. The result is a culmination of influences that situate the work and give the reader an intimate understanding of the final art exhibition. With this map, the viewer can navigate the processes and contexts of the artwork.

‘We Are The Monitors Now’: Experiential Knowledge, Transcorporeality And Environmental Justice, Dayna Scott

Articles & Book Chapters

Residents of pollution hotspots often take on projects in ‘citizen science’, or popularepidemiology, in an effort to marshal the data that can prove their experience of the pollution to the relevant authorities. Sometimes these tactics, such as pollution logs or bucket brigades, take advantage of residents’ spatially ordered and finely honed experiential and sensory knowledge of the places they inhabit. But putting that knowledge into conversation with law requires them to mobilize a new, ‘foreign’ set of tools, primarily oriented to the observation, measurement and sampling of pollution according to conventional scientific standards. Here, I employ qualitative empirical methods in …

Visual Artists Experiencing Nature: Examining Human-Environment Relationships, Amy Lynn Wiita

Anthropology

Anthropology has a long history collaborating with artists to understand their artwork. However, little research exists in the discipline that focuses on artists as a group, their creative process, and what may influence that process. In particular, how artists use nature and place has not been studied; instead, anthropology has generally considered nature and place as merely a backdrop for culture rather than for its impact on cultural expression. Identification of diverse aspects of the interdependence of ecological and social systems can inform our understanding of how people address issues of environmental concern. Managers, scientists, creative people, and others working …

Alternative Project Delivery In Rural Alaska: Experiences, Quality And Claims, Katrina L. Monta, Gerald S. Pehrson, Matthew N. Cryer

Engineering

The popularity of alternative project delivery systems has expanded beyond the private sector and into the public sector. Alaska embodies unique challenges that may present obstacles while using alternative project delivery systems. This analysis will provide an understanding of alternative project delivery systems in Alaska and how local experiences, quality and claims are affected. Alaska's unique characteristics present both challenges and opportunities for implementing alternative project delivery systems. This report begins with a discussion of experiences from several rural Alaska projects, and how alternative project delivery systems can be utilized. Some impacts that alternative project delivery systems have on quality …

Seasonal Movements And Habitat Use Of Rainbow Trout In The Susitna River Basin, Southcentral Alaska, Kevin Marshall Fraley

Fisheries

Potamodromous Rainbow Trout are an important ecological and recreational resource in freshwater systems of Alaska, and increased human development, hydroelectric projects, declining Pacific salmon stocks, and climate change may threaten their populations. We used aerial and on-the-ground telemetry tracking, field-measured and remotely-sensed aquatic habitat characteristics, snorkel surveys, and resource selection and occupancy models to characterize seasonal movements and habitat use of adult Rainbow Trout (>400 mm FL) at multiple spatial and temporal scales across the large (31,221 km²) and complex Susitna River basin of southcentral Alaska during 2003-2004 and 2013-2014. We found that trout overwintered in mainstem habitats near …

Resource Competition, Space Use And Forage Ecology Of Sea Otters, Enhydra Lutris, In Southern Southeast Alaska, Zachary N. Hoyt

Fisheries

The growing sea otter population in southern Southeast Alaska is impacting commercial shellfish, through foraging and expanding in range and abundance except where hunted for subsistence. Sea otters and their prey have coexisted in the North Pacific Ocean for approximately 750,000 years, but due to exploitation of sea otters from the 1770s until 1911, the species became extinct over much of its range, including southern Southeast Alaska. Subsequently, invertebrate species flourished and were commercially targeted in the late 1900s. Sea otters were relocated (n = 106) to southern Southeast Alaska in 1968. In this dissertation, I evaluated this marine mammal-fisheries …

The Effects Of Dietary Essential Fatty Acid Enrichment On The Nutrition And Condition Of Red King Crab (Paralithodes Camtschaticus) Larvae, Asia Beder

Fisheries

Alaska red king crab (Paralithodes camtschaticus) is a commercially valuable crab species in Alaska; however, six of the nine red king crab stocks in Alaska are depleted and have failed to recover even after closures of the fisheries. Hatchery rearing is being explored as a possibility for rehabilitating these stocks. In Chapter 1, I review the importance of diet, particularly fatty acids (FAs), when raising crustacean larvae in hatcheries. Long-chain polyunsaturated FAs (PUFAs) are important in molting success, growth, ability to handle stress, and overall survival of crustaceans. Specifically, when the FAs docosahexaenoic acid (DHA, 22:6n-3), eicosapentaenoic acid (EPA, 20:5n-3), …

Physiological Effects Of The Parasite Ichthyophonus On Spawning Chinook Salmon And Their Offspring In A Yukon River Tributary, Theresa Floyd-Rump

Fisheries

In recent years, Chinook salmon Oncorhynchus tshawytscha returns to the Yukon River, Alaska, have been substantially reduced. In summer 2010-2012, spawning Chinook salmon (n=51, 32, and 23, respectively) were collected from the Salcha River, a tributary of the Yukon River, to determine the effects of Ichthyophonus, a protozoan parasite, on salmon reproductive success. Eggs and milt from Ichthyophonus-infected and non-infected parents were collected in 2010 and cross-fertilized to investigate offspring survival and potential second-generation effects induced by the parasite. Proximate composition analysis of adult muscle, eggs, and alevins, and blood chemistry analysis of adult blood plasma and alevin whole body …