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Analysis Of Nucleosome Isolation And Recovery: From In Silico Invitrosomes To In Vivo Nucleosomes, Collin Brendan Skousen

Theses and Dissertations

There are a vast number of factors that influence nucleosome formation, and consequently gene regulation. These factors include histone modifications, nucleotide composition, transcriptional region elements, and specific nucleotide motifs, among others. Although the amount we know now is limited, we are creating new techniques and discoveries to assist us in continued understanding of chromatin. To make a significant contribution to the field of chromatin, I conducted two hypothesis driven sets of experiments that address the topic of chromatin structure. First, I created a technique for tissue specific nucleosome isolation with the goal of observing the effect of single nucleotide polymorphisms …

Recent Desiccation-Related Ecosystem Changes At Lake Abert, Oregon: A Terminal Alkaline Salt Lake, Ron Larson, Joseph Eilers, Keith Kreuz, Wolf T. Pecher, Shiladitya Dassarma, Steve Dougill

Western North American Naturalist

Lake Abert, a terminal alkaline salt lake in south central Oregon, has been a key staging area for migratory waterbirds along the Pacific Flyway. In 2014, the lake shrank to about 5% of its maximum size, and its salinity increased from 75 g · L^–1 to 250 g · L^–1. This resulted in a major ecosystem shift from one dominated at higher trophic levels by invertebrates and waterbirds to one composed primarily of hypersaline-adapted microbes. A large variety of halophilic bacteria and archaea were also detected using 16S rRNA metagenomic sequence analysis. The loss of prey and …

Fine-Scale Genetic Structure In Female Mule Deer (Odocoileus Hemionus), Cortney W. Noble, Jeremy M. Bono, Helen K. Pigage, David W. Hale, Jon C. Pigage

Western North American Naturalist

Fine-scale genetic structure in animal populations can have important consequences for evolutionary processes and can influence conservation and management decisions. Cervids often live in matrilineal social groups, and this spatial grouping can create fine-scale genetic structure among females. We used DNA and radio-location data at Fort Carson Military Reservation in south central Colorado, USA, to determine whether female mule deer (Odocoileus hemionus) living in close proximity were more likely to be related. Spatial data were obtained over an 18-month period using data transmitted from GPS collars. Average positions for each animal were correlated with relatedness estimates calculated using …

Ancient Maya Agricultural Resources In The Rio Amarillo Valley Near Copán, Honduras, Bryce Matthew Brown

Theses and Dissertations

The purpose of this study was to use soil physical and chemical analyses to better understand the ancient agricultural landscape around the ancient Maya cities of Rio Amarillo and Piedras Negras, two tributary sites to Copan, Honduras. Our primary objective was to determine whether a mass erosion event around 800 A.D. occurred which could have caused crop failure and famine or if stable soil conditions persisted during the collapse of these city-states. Stable carbon isotope analysis of the humin fraction of the soils showed that much of this valley was used anciently for agriculture, including hillslopes and hilltops; however, there …

Control Of Matrix Metalloproteinases In A Periodontitis Model: Molecules That Trigger Or Inhibit Mmp Production, Catalina Matias Orozco

Theses and Dissertations

In periodontitis, there is a disruption in the homeostasis of the oral microbiome by peridontopathogenic bacteria. However, while bacteria is essential for periodontitis to occur, the severity, pattern and progression of the disease is not solely determined by the microbial burden, and in fact has a lot to do with the overwhelming host inflammatory response. The response can vary even in two individuals with similar periodontopathogenic profiles. The host response leads to extracellular matrix (ECM) destruction, loss of attachment, alveolar bone resorption and eventually, edentulism. The host's reaction is orchestrated by proinflammatory cytokines and chemokines and matrix metalloproteinases (MMPs). MMPs …

An Investigation Of Ssglux, A Glucosidase Co-Expressed With Cslf6 In Oat (Avena Sativa) And Barley (Hordeum Vulgare), Michael Christopher Gines

Theses and Dissertations

Mixed Linkage Glucan (MLG, or (1,3;1,4)-ß-D glucan) is a component of cell walls for major cereal crops and is significant to food and beverage industries. To better understand genetic factors affecting MLG content in oats, this study investigates the presence of glucosidases likely to participate in MLG production. A glucosidase showing co-expression with CslF6—the primary gene responsible for MLG synthesis—could indicate a hand in MLG production by association. Reference genes for expression analysis as well as glucosidase candidates were first selected using in silico methods. In both cases, barley was used as model species because it has abundant public bioinformatic …

Reproduction By Black-Tailed Prairie Dogs And Black-Footed Ferrets: Effects Of Weather And Food Availability, Shaun M. Grassel, Janet L. Rachlow, Christopher J. Williams

Western North American Naturalist

Food availability is one of the most important factors influencing reproduction in mammals. Reproductive success of some species can be negatively affected when body reserves are depleted during long periods of adverse weather conditions. We investigated the relationship of forage availability and weather variables on reproduction by black-tailed prairie dogs (Cynomys ludovicianus) and the effects of black-tailed prairie dog reproduction on reproduction by black-footed ferrets (Mustela nigripes), a prairie dog specialist predator. Prairie dogs draw on stored energy reserves to support reproduction (i.e., capital breeding), while ferrets likely rely on availability of prey during the reproductive …

Investigation Of Dynamic Biological Systems Using Direct Injection And Liquid Chromatography Mass Spectrometry, Adam Clayton Swensen

Theses and Dissertations

In biological systems, small changes can have significant impacts. It is, therefore, very important to be able to identify these changes in order to understand what is occurring in the organism. In many cases, this is not an easy task. Mass spectrometry has proven to be a very useful tool in elucidating biological changes even at a very small scale. Several different mass spectrometry based techniques have been developed to discover and investigate complex biological changes. Some of these techniques, such as proteomics, have been through years of development and have advanced to the point that anyone can complete complex …

The Effects Of L-Cysteine On Alzheimer's Disease Pathology In Apoe2, Apoe3, And Apoe4 Homozygous Mice, Stephen Gerard Cieslak

Theses and Dissertations

The APOE gene is of profound importance regarding the onset of Alzheimer's disease (AD). From the small physical differences among the protein products of the isoforms of this gene arises a profound difference in their physiologies. For example, the APOE2 isoform confers resistance to AD, the APOE3 isoform confers neutral susceptibility to AD, and the APOE4 isoform confers proneness to AD. L-cysteine is an amino acid that has several anti-AD properties, among which are its ability to sequester iron and form glutathione – a powerful antioxidant – and therefore may be a promising potential dietary supplement for ameliorating AD …

Effects Of Tethering Placement And Linker Variations On Antibody Stability On Surfaces, Rebecca Ellen Grawe

Theses and Dissertations

An antibody microarray consists of antibody bound to a surface. Antibody microarrays have great potential in many fields, particularly as a tool to detect antigens. Unfortunately, antibodies suffer from poor performance. A greater understanding of how antibodies interact with surfaces would improve microarray design and performance, but experimental methods fall short of being able to observe these interactions. Therefore molecular simulation has emerged as the primary method to study protein/surface interactions.The simulations here were coarse grain simulations performed using the model of Karanicolas and Brooks. Additionally, an advanced surface model was used that allows for different surface chemistries. PyMBAR analysis …

Endocannabinoid-Mediated Synaptic Plasticity In The Ventral Tegmental Area And Hippocampus, Lindsey Nicole Friend

Theses and Dissertations

Synaptic plasticity is the process whereby connections between neurons can be altered in an experience dependent manner. For example, drugs of abuse alter plasticity in the ventral tegmental area (VTA) of the midbrain. A large amount of research has been applied to uncovering the mechanism whereby synapses on the reward signaling dopamine cells is altered, however, less is known regarding the VTA inhibitory GABA neurons. Our objective was to examine the ability of GABA neurons to exhibit plasticity, and determine how drugs of abuse could influence it. Here we report a novel type of plasticity of excitatory neurotransmission onto VTA …

From Warning To Wallpaper: Why The Brain Habituates To Security Warnings, Bonnie Anderson, Anthony Vance, C. Brock Kirwan, Jeffrey L. Jenkins, David Eargle

Faculty Publications

Warning messages are fundamental to users' security interactions. Unfortunately, research has shown that they are largely ineffective. A key contributor to this failure is habituation: decreased response to a repeated warning. Previous research has inferred the occurrence of habituation to warnings or measured it indirectly, such as through the proxy of a related behavior. Therefore, there is a gap in our understanding of how habituation to security warnings develops in the brain. Without direct measures of habituation, we are limited in designing warnings that can mitigate its effects. In this study, we use neurophysiological measures to directly observe habituation as …

Running Decreases Knee Intra-Articular Cytokine And Cartilage Oligomeric Matrix Concentrations: A Pilot Study, Robert D. Hyldahl, Alyssa Evans, Sunku Kwon, Sarah T. Ridge, Eric Robinson, J. Ty Hopkins, Matthew K. Seeley

Faculty Publications

Introduction Regular exercise protects against degenerative joint disorders, yet the mechanisms that underlie these benefits are poorly understood. Chronic, low-grade inflammation is widely implicated in the onset and progression of degenerative joint disease.

Purpose To examine the effect of running on knee intra-articular and circulating markers of inflammation and cartilage turnover in healthy men and women.

Methods Six recreational runners completed a running (30 min) and control (unloaded for 30 min) session in a counterbalanced order. Synovial fluid (SF) and serum samples were taken before and after each session. Cytokine concentration was measured in SF and serum using a multiplexed …

Small Mammal Abundance In Mountain Big Sagebrush Communities After Fire And Vegetation Recovery, Aaron L. Holmes, W. Douglas Robinson

Western North American Naturalist

Managing fire for the conservation of biodiversity is a widespread challenge. An important disturbance mechanism in big sagebrush (Artemisia tridentata) communities, fire has well-known effects on vegetation structure but poorly described consequences for sagebrush wildlife communities. We estimated the abundance of small mammals in relation to fire history in mountain big sagebrush (A. t. ssp. vaseyana) communities by way of a chronosequence approach that included 3 wildfires and adjacent unburned areas. We compared patterns of mammal community succession with expectations of the habitat accommodation model by associating responses of mammals to change over time in vegetation …

Front Matter, Vol. 76 No. 3

Western North American Naturalist

No abstract provided.

End Matter, Vol. 76 No. 3

Western North American Naturalist

No abstract provided.

A Field Inventory And Collections Summary Of Herpetofauna From The Sutter Buttes, An "Inland Island" Within California's Great Central Valley, Eric O. Olson, Jackson D. Shedd, Tag N. Engstrom

Western North American Naturalist

The Sutter Buttes (Buttes) are a small, isolated mountain range in the Great Central Valley of California. Systematic study of the fauna and flora of this unique habitat has been limited by the private ownership of the entire mountain range. As a result, much of our knowledge about the herpetofauna of the Buttes is based on isolated observations and scattered museum records, most over 4 decades old. In this study, we present an updated inventory of the herpetofauna of the Buttes, based on a 2-year field survey within the boundaries of the first publicly protected property within the Buttes (Sutter …

Physiological Response Of Tamarix Ramosissima (Tamaricaceae) To A Biological Control Agent, Evan B. Craine, Ann Evankow, Katherine Bibee Wolfson, Kathryn Dalton, Holly Swedlund, Casey Bowen, M. Shane Heschel

Western North American Naturalist

Within the last century, the floristic composition of riparian communities in the Southwest has drastically changed following introduction of the exotic tree Tamarix ramosissima. In an attempt to control Tamarix populations, the tamarisk leaf beetle (Diorhabda carinulata) has been utilized as a biological control agent. Three years of data collection at our study sites along Fountain Creek (Fountain, CO) allowed us to characterize the response of Tamarix to invasion by the biological control agent. In analyzing data collected before, during, and after the beetle invasion, we observed a significant effect of foliar herbivory on Tamarix physiology and life …

Grazing Effects On Precipitation-Driven Associations Between Sagebrush And Perennial Grasses, Maike F. Holthuijzen, Kari E. Veblen

Western North American Naturalist

While many studies have addressed the effect of individual stresses on plant–plant associations, few have addressed the effects of co-occurring stresses. We therefore investigated how associations between Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) and 2 native grasses (Poa secunda and Elymus elymoides) responded to different combinations of grazing and moisture stresses in the Great Basin, USA. Positive (i.e., facilitative) interactions between nurse plants and their beneficiaries are predicted to increase with increasing moisture limitation and grazing stress, but these interactions may break down at extreme levels of stress. We hypothesized that (1) competitive interactions and …

The Science Of Life: Animal Classification, Laura Trumbo

Children's Book and Media Review

The Science of Life: Animal Classification is a reference book that introduces young readers to how scientists classify and organize animals. Without going into depth, Jenny VanVoorst defines important terms like taxonomy, and takes the reader on a brief sampling of the animal kingdom. She begins with taxonomy's founding father, describes all the divisions of animal classification, and ends with explaining where the human reader fits within taxonomy's classification system.

Social Supers: A Content Analysis Of Non-Physical Aggressions In Popular Superhero Movies, Ian Trent Gillespie

Theses and Dissertations

In recent years superhero movies have skyrocketed in popularity, bringing with them plots and characters that tend to exhibit high levels of aggression. As social learners, humans often learn from what they observe, and especially emulate characters they admire – including fictional superheroes and villains. Consequently, this study content analyzed non-physical aggressions (verbal aggression, relational aggression, and violent ideation) in the top 25 highest grossing superhero movies between 2005 and 2015. Results found an average of 171.8 acts of non-physical aggression per movie. Females in these movies were also significantly more likely to engage in verbal and relational aggressions, which …

Childhood Abuse Types And Adult Relational Violence Mediated By Adult Attachment Behaviors And Romantic Relational Aggression In Couples, Tabitha Nicole Webster

Theses and Dissertations

The current study investigated how three distinct types of childhood abuse—witnessing of parental domestic violence, experiencing physical abuse and total in-home violence, and experiencing sexual abuse—predicted partner reports of relational violence through the mediating factors self-perceptions of attachment and partner reports of relational aggression. The study used paired dyadic data from 1,658 couples who had completed the RELATionship Evaluation (RELATE). The Family Violence, the Brief Accessibility and Responsiveness, Couples Relational Aggression and Victimization, and the Conflict Tactics scales were the measures used. Data was analyzed by using structural equation modeling to estimate an actor-partner interdependence model exploring these relationships. Results …

Overexpression Of Hdac1 Induces Functional Β-Cell Mass, Carrie Draney

Theses and Dissertations

Type 2 diabetes is a metabolic disorder that results in β-cell dysfunction and ultimate destruction, and leads to impaired glucose homeostasis. High rates of proliferation and differentiation of pancreatic β-cells occurs mostly during neonatal development. However, research shows these mechanisms remain intact as β-cell proliferation has been observed during pregnancy and obesity. We have shown that overexpression of the β-cell transcription factor Nkx6.1 is sufficient to induce β-cell proliferation. Exploration of the transcriptional targets of Nkx6.1 has identified histone deacetylase 1 (HDAC1) as a down-stream target of Nkx6.1. Here we demonstrate that HDAC1 overexpression is sufficient to induce β-cell proliferation, …

A Cryab Interactome Reveals Clientele Specificity And Dysfunction Of Mutants Associated With Human Disease, Whitney Katherine Hoopes

Theses and Dissertations

Small Heat Shock Proteins (sHSP) are critical molecular chaperones that function to maintain protein homeostasis (proteostasis) and prevent the aggregation of other proteins during cellular stress. Any disruption in the process of proteostasis can lead to prevalent diseases ranging from cancer and cataract to cardiovascular and Alzheimer's disease. CryAB (αB-crystallin, HspB5) is one of ten known human sHSP that is abundant in the lens, skeletal, and cardiac muscle. This protein is required for cardiac function and muscle cell integrity. When the cell experiences physiological stress, including heat shock, CryAB moves to the cytoskeleton to act as a chaperone and prevent …

Assessing Diversity Among Corporations In Brazil: An Exploratory Study, Helga Sheyla Pereira

Theses and Dissertations

The purpose of this thesis is to explore what corporations in Brazil, whether with Brazilian headquarters or not, are doing in regards to communicating their diversity practices and initiatives to the public. Understanding these companies' positions on diversity can paint a better picture of how much Brazil has advanced on diversity in the workplace matters, since the topic started coming about in discussions in the 1990s (Fleury, 2000). A sample of 15 companies was selected from Exame magazine "Melhores e Maiores Ranking 2014" (2015), and a content analysis of each company's website was performed during the summer of 2016, based …

Genetic And Biochemical Analysis Of The Micrococcin Biosynthetic Pathway, Philip Ross Bennallack

Theses and Dissertations

Declining antibiotic discovery and flourishing antibiotic resistance have led to a modern antibiotic crisis which threatens to compromise our ability to treat infectious disease. Consequently, there is significant interest in developing new antibiotics with novel modes of action and chemical properties. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural compounds with the appealing attributes of being derived directly from a genetic template while possessing numerous exotic chemical features that contribute to stability and antimicrobial activity. Abundant in nature, their diverse range of biological activities makes them excellent prospects for antibiotic development. Thiopeptides, a RiPP family rich in chemical complexity, …

The Intestinal Parasites Of An Assemblage Of Stream Fishes In Central Utah, Matthew Rambo, Ashlee N. Smith, Mehmet Cemal Oguz, Mark C. Belk

Western North American Naturalist

Parasite communities of stream fish assemblages in the western United States are poorly known. We investigated the intestinal parasites of an assemblage of stream fishes in Spanish Fork River in central Utah, USA. Two species, mottled sculpin (Cottus bairdii) and redside shiner (Richardsonius balteatus), had no observable parasites. In the other 3 species, southern leatherside chub (Lepidomeda aliciae), mountain sucker (Catostomus platyrhynchus), and longnose dace (Rhinichthys cataractae), we identified metacercia of an unidentified trematode. We found adult cestodes in southern leatherside chub only. Prevalence and intensity of parasites was highest …

Directional Floral Orientation In Joshua Trees (Yucca Brevifolia), Steven D. Warren, L. Scott Baggett, Heather Warren

Western North American Naturalist

Joshua tree (Yucca brevifolia Engelm.) is a large, arborescent member of the yucca genus. It is an endemic and visually dominant plant in portions of the Mojave Desert, USA. We document the unique and heretofore unreported directional orientation of its flower panicles. The flower panicles grow primarily at the tips of branches that are oriented to the south. When branches with flower panicles are not oriented in a southerly direction, the flower panicles themselves tend to bend or tilt toward the south. This strategy maximizes exposure of the panicles to direct solar radiation, which, within the latitudes where the …

Sagebrush, Greater Sage-Grouse, And The Occurrence And Importance Of Forbs, Victoria E. Pennington, Daniel R. Schlaepfer, Jeffrey L. Beck, John B. Bradford, Kyle A. Palmquist, William K. Lauenroth

Western North American Naturalist

Big sagebrush (Artemisia tridentata Nutt.) ecosystems provide habitat for sagebrush-obligate wildlife species such as the Greater Sage-Grouse (Centrocercus urophasianus). The understory of big sagebrush plant communities is composed of grasses and forbs that are important sources of cover and food for wildlife. The grass component is well described in the literature, but the composition, abundance, and habitat role of forbs in these communities is largely unknown. Our objective was to synthesize information about forbs and their importance to Greater Sage-Grouse diets and habitats, how rangeland management practices affect forbs, and how forbs respond to changes in temperature …

Snakes, Alligators, And Broken Hearts: Journeys Of A Biologist's Son, Tessa Mcmillan

Children's Book and Media Review

Sneed B. Collard III was born to biologist, Sneed B. Jr. and Patricia Collard. Naturally, Sneed was raised to love animals and be curious about his world. Unfortunately, his parents divorced when Sneed was in third grade. Sneed had a difficult time coping, especially when both parents married new spouses and moved to opposite coasts. For most of his childhood and into adolescence, Sneed’s life was split between living with his mother during the school year and visiting his father during the summer. Sneed treasured the summers with his dad as he helped with his father’s research or vacationed at …