Life Sciences Commons^™

Animating And Exploring Phylogenies With Fibre Plots, William D. Pearse

Biology Faculty Publications

Despite the progress that has been made in many other aspects of data visualisation, phylogenies are still represented in much the same way as they first were by Darwin. In this brief essay, I give a short review of what I consider to be some recent major advances, and outline a new kind of phylogenetic visualisation. This new graphic, the fibre plot, uses the metaphor of sections through a tree to describe change in a phylogeny. I suggest it is a useful tool in gaining an rapid overview of the timing and scale of diversification in large phylogenies.

Importance Of Heat And Pressure For Solubilization Of Recombinant Spider Silk Proteins In Aqueous Solution, Justin A. Jones, Thomas I. Harris, Paula F. Oliveira, Brianne E. Bell, Abdulrahman Alhabib, Randolph V. Lewis

Biology Faculty Publications

The production of recombinant spider silk proteins continues to be a key area of interest for a number of research groups. Several key obstacles exist in their production as well as in their formulation into useable products. The original reported method to solubilize recombinant spider silk proteins (rSSp) in an aqueous solution involved using microwaves to quickly generate heat and pressure inside of a sealed vial containing rSSp and water. Fibers produced from this system are remarkable in their mechanical ability and demonstrate the ability to be stretched and recover 100 times. The microwave method dissolves the rSSPs with dissolution …

Better Late Than Never: Effective Air-Borne Hearing Of Toads Delayed By Late Maturation Of The Tympanic Middle Ear Structures, Molly C. Womack, Jakob Christensen-Dalsgaard, Kim L. Hoke

Biology Faculty Publications

Most vertebrates have evolved a tympanic middle ear that enables effective hearing of airborne sound on land. Although inner ears develop during the tadpole stages of toads, tympanic middle ear structures are not complete until months after metamorphosis, potentially limiting the sensitivity of post-metamorphic juveniles to sounds in their environment. We tested the hearing of five species of toads to determine how delayed ear development impairs airborne auditory sensitivity. We performed auditory brainstem recordings to test the hearing of the toads and used micro-computed tomography and histology to relate the development of ear structures to hearing ability. We found a …

A Novel Qtl Associated With Dwarf Bunt Resistance In Idaho 444 Winter Wheat, Jianli Chen, Mary J. Guttieri, Junli Zhang, David Hole, Edward Souza, Blair Goates

Green Canyon Environmental Research Area, Logan Utah

Dwarf bunt [Tilletia controversa J.G. Kühn [as ‘contraversa’], in Rabenhorst, Hedwigia 13: 188 (1874)] is a destructive disease of wheat (Triticum aestivum L.) that reduces grain yield and quality. A number of distinct genes conferring resistance to dwarf bunt have been used by breeding programs for nearly 100 years. However, few markers were identified that can be used in selection of dwarf bunt resistance. A recombinant inbred line (RIL) population derived from the bunt-resistant germplasm, Idaho 444 (IDO444), and the susceptible cultivar, Rio Blanco, was evaluated for phenotypic reaction to dwarf bunt inoculation in four trials in …

Convergence In Nitrogen Deposition And Cryptic Isotopic Variation Across Urban And Agricultural Valleys In Northern Utah, Steven J. Hall, E. M. Ogata, Samantha R. Weintraub, Michelle A. Baker, James R. Ehleringer, C I. Czimczik, David R. Bowling

Biology Faculty Publications

The extent to which atmospheric nitrogen (N) deposition reflects land use differences and biogenic versus fossil fuel reactive N sources remains unclear yet represents a critical uncertainty in ecosystem N budgets. We compared N concentrations and isotopes in precipitation-event bulk (wet + dry) deposition across nearby valleys in northern Utah with contrasting land use (highly urban versus intensive agriculture/low-density urban). We predicted greater nitrate (NO3−) versus ammonium (NH4+) and higher δ15N of NO3− and NH4+ in urban valley sites. Contrary to expectations, annual N deposition (3.5–5.1 kg N ha−1 yr−1) and inorganic N concentrations were similar within and between valleys. …

Secondary Structure Adopted By The Gly-Gly-X Repetitive Regions Of Dragline Spider Silk, Geoffrey M. Gray, Arjan Van Der Vaart, Chengchen Guo, Justin A. Jones, David Onofrei, Brian R. Cherry, Randolph V. Lewis, Jeffery L. Yarger, Gregory P. Holland

Biology Faculty Publications

Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X), which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X) segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X) regions of dragline silks, including β-turns, 310-helicies, and coil structures with a negligible population of α-helix observed.

Human Observers Differ In Ability To Perceive Insect Diversity, Joseph S. Wilson, Joshua P. Jahner, Matthew L. Forister

Biology Faculty Publications

Human perception of biological variation is an important and understudied issue in the conservation and management of natural resources. Here, we took a novel approach by asking 1152 participants, primarily college biology students, to score examples of insect mimicry by the number of distinct kinds of animals they saw. Latent class analysis successfully separated participants based on their accuracy of perception as well as demographic information and opinions about biodiversity. Contrary to expectations, factors such as childhood experience (growing up in urban, suburban or rural areas) did not affect the ability to see biodiversity as much as political views (location …

System-Aware Smart Network Management For Nano-Enriched Water Quality Monitoring, Bassem Mokhtar, Mohamed Azab, Nader Shehata, Mohamed Rizk

Biology Faculty Publications

This paper presents a comprehensive water quality monitoring system that employs a smart network management, nano-enriched sensing framework, and intelligent and efficient data analysis and forwarding protocols for smart and system-aware decision making. The presented system comprises two main subsystems, a data sensing and forwarding subsystem (DSFS), and Operation Management Subsystem (OMS). The OMS operates based on real-time learned patterns and rules of system operations projected from the DSFS to manage the entire network of sensors. The main tasks of OMS are to enable real-time data visualization, managed system control, and secure system operation. The DSFS employs a Hybrid Intelligence …

Pheromone Lure And Trap Color Affects Bycatch In Agricultural Landscapes Of Utah, Lori R. Spears, Chris Looney, Harold Ikerd, Jonathan B. Koch, Terry L. Griswold, James P. Strange, Ricardo A. Ramirez

Biology Faculty Publications

Aerial traps, using combinations of color and attractive lures, are a critical tool for detecting and managing insect pest populations. Yet, despite improvements in trap efficacy, collection of nontarget species (“bycatch”) plagues many insect pest surveys. Bycatch can influence survey effectiveness by reducing the available space for target species and increasing trap screening time, especially in areas where thousands of insects are captured as bycatch in a given season. Additionally, bycatch may negatively impact local nontarget insect populations, including beneficial predators and pollinators. Here, we tested the effect of pheromone lures on bycatch rates of Coccinellidae (Coleoptera), Apoidea (Hymenoptera), and …

Influence Of Free Water Availability On A Desert Carnivore And Herbivore, Bryan M. Kluever, Eric M. Gese, Stephen Dempsey

Wildland Resources Faculty Publications

Anthropogenic manipulation of finite resources on the landscape to benefit individual species or communities is commonly employed by conservation and management agencies. One such action in arid regions is the construction and maintenance of water developments (i.e., wildlife guzzlers) adding free water on the landscape to buttress local populations, influence animal movements, or affect distributions of certain species of interest. Despite their prevalence, the utility of wildlife guzzlers remains largely untested. We employed a before–after control-impact (BACI) design over a 4-year period on the US Army Dugway Proving Ground, Utah, USA, to determine whether water availability at wildlife guzzlers influenced …

Collybolide Is A Novel Biased Agonist Of Κ-Opioid Receptors With Potent Antipruritic Activity, Achla Gupta, Ivone Gomes, Erin N. Bobeck, Amanda K. Fakira, Nicholas P. Massaro, Indrajeet Sharma, Adrien Cavé, Heidi E. Hamm, Joseph Parello, Lakshmi A. Devi

Biology Faculty Publications

Among the opioid receptors, the κ-opioid receptor (κOR) has been gaining considerable attention as a potential therapeutic target for the treatment of complex CNS disorders including depression, visceral pain, and cocaine addiction. With an interest in discovering novel ligands targeting κOR, we searched natural products for unusual scaffolds and identified collybolide (Colly), a nonnitrogenous sesquiterpene from the mushroom Collybia maculata. This compound has a furyl-δ-lactone core similar to that of Salvinorin A (Sal A), another natural product from the plant Salvia divinorum. Characterization of the molecular pharmacological properties reveals that Colly, like Sal A, is a highly potent and selective …

Stoichiometry Of Microbial Carbon Useefficiency In Soils, R. L. Sinsabaugh, B. L. Turner, J. M. Talbot, Bonnie G. Waring, J. S. Powers, C. R. Kuske, D. L. Moorhead, Shah J. Follstad

Biology Faculty Publications

The carbon use efficiency (CUE) of microbial communities partitions the flow of C from primary producers to the atmosphere, decomposer food webs, and soil C stores. CUE, usually defined as the ratio of growth to assimilation, is a critical parameter in ecosystem models, but is seldom measured directly in soils because of the methodological difficulty of measuring in situ rates of microbial growth and respiration. Alternatively, CUE can be estimated indirectly from the elemental stoichiometry of organic matter and microbial biomass, and the ratios of C to nutrient-acquiring ecoenzymatic activities. We used this approach to estimate and compare microbial CUE …

Beyond The Urban Stream Syndrome: Organic Matter Budget For Diagnostics And Restoration Of An Impaired Urban River, Dave M. Epstein, Julia E. Kelso, Michelle A. Baker

Biology Faculty Publications

In response to water quality standard violations linked to excessive organic matter (OM) and a lack of sampling data informing the Total Maximum Daily Load (TMDL), an organic matter budget was created to quantify and identify sources of OM in the lower Jordan River (Salt Lake City, UT). By sampling dissolved, fine and coarse particulate OM, as well as measuring ecosystem metabolism at seven different sites, the researchers aimed to identify the origin of excess OM, and understand pathways by which different size classes of the OM pool are generated. The dissolved fraction (DOM; 94 %) was found to be …

Prenataland Newborn Immunoglobulin Levels From Mother-Child Pairs And Risk Of Autismspectrum Disorders, Judith K. Grether, Paul Ashwood, Judy Van De Water, Robert H. Yolken, Meredith C. Anderson, Anthony T. Torres, Jonna B. Westover, Aimee G. Tallian, Robin L. Hansen, Martin Kharrazi, Lisa A. Croen

Biology Faculty Publications

Background: An etiological role for immune factors operating during early brain development in children with autism spectrum disorders (ASD) has not yet been established. A major obstacle has been the lack of early biologic specimens that can be linked to later diagnosis. In a prior study, we found lower risk of ASD associated with higher levels of maternally-derived total IgG and Toxoplasmosis gondii (Toxo) IgG in newborn blood spot specimens from children later diagnosed with ASD compared to population controls. Methods: We obtained maternal mid-gestational serum specimens and newborn screening blood spots from the California Genetics Disease Screening Program (GDSP) …

Greater Sage-Grouse Vital Rate And Habitat Use Response To Landscape Scale Habitat Manipulations And Vegetation Micro-Sites In Northwestern Utah, Charles P. Sandford

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The greater sage-grouse (Centrocercus urophasianus; sage-grouse) has been a species of conservation concern since the early 20^th century. The decline of populations has largely been attributed to loss and degradation of sagebrush (Artemisia spp.) habitats. To contribute to the knowledge of sage-grouse ecology and quantify the effectiveness of landscape scale habitat manipulations intended to benefit sage-grouse, I monitored habitat use and vital-rates (i.e., nest and brood success) of 45 sage-grouse females in the Box Ender Sage-Grouse Management Area (SGMA) in northwestern Utah. Using telemetry locations of sage-grouse females with known nest and brood fates, I generated …

Anthropogenic And Natural Stressors And Their Effect On Immunity, Reproduction, And The Stress Response, Lorin A. Neuman-Lee

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Animals must be able to cope with many natural and human-made stressors in order to successfully survive and reproduce. These stressors can come in many forms and are increasing as human activities become more and more prevalent across the globe. In order to cope with these stressors, organisms must allocate limited energy away from processes such as reproduction to mount a stress response. This stress response involves the activation of the hypothalamic-pituitary-adrenal axis and results in a cascade of hormones and down-stream effects, such as changes in reproduction and immune function. In order to understand how reptiles and amphibians cope …

Biodiversity, Community Dynamics, And Novel Foraging Behaviors Of A Rich Native Bee Fauna Across Habitats At Pinnacles National Park, California, Joan M. Meiners

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Global concern about honeybee declines has spurred feverish research about the status and protection of this single species, yet our understanding of the ecology and issues impacting thousands of species of native bees lags behind. Pinnacles National Park, America's newest, near Salinas, California, is currently the most densely biodiverse area for native bees known on the planet. Recent work by researchers at Utah State University and the USDA-ARS has documented 479 species of native bees in only 42 square miles of this park. During two years of field studies and 308 collector days, we assembled data on 52,853 bee specimens …

The Role Of Gpr84 In Medium-Chain Saturated Fatty Acid Taste Transduction, Yan Liu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The prevalence of overweight or obese in adults has nearly doubled during the past two decades, and obesity increases the risk of heart disease, diabetes, and even some types of cancer. One of the factors closely linked with the obesity epidemic is overconsumption of dietary fat. Accumulating evidence has supported the existence of the "taste of fat", and more and more studies have focused on identifying the mechanisms of fatty acid detection by gustatory system. In this study, I showed for the first time that medium-chain saturated fatty acids (MCFAs) were able to activate taste cells isolated from mice, and …

Stable Isotopes And The Ecology And Physiology Of Reptiles, Andrew M. Durso

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

When animals don’t have enough food, they have to “choose” between “spending” their limited energy on themselves or on their offspring. Biologists think that reptiles can make this choice quickly in response to different environments. But, it can be hard to study these choices because it is hard to convert between, for example, the number of eggs laid and the speed of healing a wound. By using stable isotope chemistry, we can collect more detailed and comparable information about how lizards and other animals spend their limited resources than with any other method. For example, lizards in the wild have …

An Allometric Approach To Evaluate Physiological And Production Efficiencies In Tree Size For Tart Cherry And Apple Orchard Systems, Zachary T. Brym

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In orchard systems, the size of a tree and the physical structure of its canopy influences how the tree gathers resources and uses them to produce fruit. Smaller orchard trees produce a higher proportion of fruit relative to their size. Small trees also produce higher quality fruit than larger trees. These relationships were demonstrated for apples and tart cherries grown in Utah. In physiological ecology, models called allometries have been developed that explain how the size of wild plants is related to growth, architecture, and reproduction. These models were applied to apple and tart cherry orchard systems and revealed consistent …

Spider Aggregate Glue Sequence Characterization And Expression, Kyle Berg

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Orb-weaving spiders create a glue which is secreted onto the web to capture and retain insects. This glue is made from aggregate protein. Aggregate glue is sticky when wet and can stretch far when pulled at slow speeds, and pull back with a greater force if pulled at high speeds which helps it achieve its purpose as the adhesive that keeps insects in the web. These features also make it an attractive target for applications such as a surgical glue or underwater adhesive. Unfortunately, very little is known about the aggregate glue gene, and knowledge of the genetic sequence is …

Hybridization, Population Genetic Structure And Gene Expression In The Genus Boechera, Martin Peter Schilling

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

When we look at life on earth, we can see a lot of different life forms, but we still do not fully understand how these different life forms came to be and at which points in time these life forms began to be different enough from each other so we could call them by different names, or species. Some groups of species on earth, especially plants, seem to reproduce with each other, even though they are already very different from each other so that we call them different species. This process is called hybridization, and it can stir up the …

The Role Of Orexin Receptors In Diurnal Variations In Learning And Memory, Jacob Christian Blotter

Undergraduate Honors Capstone Projects

The brain's ability to learn and remember is a topic of extensive debate and research. Mammals share many similarities, including the way in which information from the outside world is processed and stored. Mammalian circadian rhythms have long been thought to be essentially involved with these processes. Orexin, a neurotransmitter in the brain, plays a crucial role in arousal and circadian rhythm. This study is designed to explore the brain's ability to process and store information at different times of the circadian period, and to explore the role of orexin by comparing the performance of normal (wild-type) mice and abnormal …

Beyond The Urban Stream Syndrome: Organic Matter Budgets For Diagnostics And Restoration Of An Impaired Urban River, Dave M. Epstein, Julia E. Kelso, Michelle A. Baker

Biology Faculty Publications

In response to water quality standard violations linked to excessive organic matter (OM) and a lack of sampling data informing the Total Maximum Daily Load (TMDL), an organic matter budget was created to quantify and identify sources of OM in the lower Jordan River (Salt Lake City, UT). By sampling dissolved, fine, and coarse particulate OM, as well as measuring ecosystem metabolism at seven different sites, the researchers aimed to identify the origin of excess OM, and understand pathways by which different size classes of the OM pool are generated. The dissolved fraction (DOM; 94 %) was found to be …

Presence Of Wolbachia In Sandfly Populations And Correlation With Pesticide Resistance, Cody Bills, Carol Von Dohlen, Katie Weglarz

Student Research Symposium

Leishmaniasis is a serious skin disease, affecting 12 million people worldwide, caused by a protozoan vectored by sand flies. These flies can harbor the bacterium Wolbachia, a microorganism which blurs the line between symbiont and parasite. On one hand, it skews sex ratios in sand fly populations but, on the other hand, it confers certain benefits, specifically increased insecticide resistance. In closely related flies, specifically the mosquito, pesticide resistance is developed when Wolbachia infection rates increase. The range of impacts of Wolbachia on their hosts may offer a secondary control pathway for sand fly populations where pesticide resistance has developed, …

Development Of Archaeal And Algalytic Bacteria Detection Systems, Andrew Walters

Student Research Symposium

Many methods for the production of methane are being developed in response to the growing energy crisis. One such method is the digestion of wastewater algae in a UASB (Up-Flow Anaerobic Sludge Blanket) reactor. In this reactor, algae grown in wastewater treatment facilities can be digested by alga-lytic bacteria into its carbon rich substituents and later used by methanogenic archaebacteria to produce methane.

The objective of this project is to design detection systems that employ specific DNA primers that will precisely target two bacterial groups: alga-lytic and archaeal bacteria. If successful, these systems will allow us to identify the bacteria …

Tag-Team Takeover: Usurpation Of Woodpecker Nests By Western Bluebirds, Sammy Cowell, Hannah Domgaard, Phil Fischer, Teresa Lorenz, Sara Lorscheider, Mariah Panoussi, Lindsey Parrish, Taryn Rodman, Kim Sullivan

Student Research Symposium

Woodpeckers provide important ecological services by excavating nesting cavities that are used by many forest birds and animals. Black-backed woodpeckers (Picoides arcticus) have been declining throughout their range and are now a threatened species. The failure of black-backed woodpeckers to reproduce can lead to a decline of nesting cavities, which in turn can lead to a decline in secondary cavity nesters. One of the challenges black-backed woodpeckers face is displacement from their nesting cavities by aggressive secondary cavity nesters.The western bluebird (Sialia Mexicana) is known to usurp nests, even from its own kind. However, the process by which bluebirds take …

Biology And Management Of Billbugs (Coleoptera: Curculionidae) In Turfgrass, Madeleine Dupuy, Ricardo A. Ramirez

Biology Faculty Publications

Billbugs (Coleoptera: Curculionidae: Sphenophorus spp.) are a complex of weevil pests affecting turfgrass throughout the United States. Billbug larvae cause damage by feeding in stems, on roots, and on the crowns of turf, causing severe discoloration and eventual plant death. Monitoring efforts have focused on nondestructive pitfall sampling of ground-active billbug adults and on destructive sampling using soil cores for larval stages in the soil. Given the cryptic nature of the susceptible larval stages, billbugs are typically managed by preventive applications of long-residual, systemic insecticides, including neonicotinoids and anthranilic diamides. Despite knowledge of effective management practices including pest-resistant turf varieties, …

A Continuous Correlated Beta Process Model For Genetic Ancestry In Admixed Populations, Zachariah Gompert

Biology Faculty Publications

Admixture and recombination create populations and genomes with genetic ancestry from multiple source populations. Analyses of genetic ancestry in admixed populations are relevant for trait and disease mapping, studies of speciation, and conservation efforts. Consequently, many methods have been developed to infer genome-average ancestry and to deconvolute ancestry into continuous local ancestry blocks or tracts within individuals. Current methods for local ancestry inference perform well when admixture occurred recently or hybridization is ongoing, or when admixture occurred in the distant past such that local ancestry blocks have fixed in the admixed population. However, methods to infer local ancestry frequencies in …

What, If Anything, Are Hybrids: Enduring Truths And Challenges Associated With Population Structure And Gene Flow, Zachariah Gompert, C. Alex Buerkle

Biology Faculty Publications

Hybridization is a potent evolutionary process that can affect the origin, maintenance, and loss of biodiversity. Because of its ecological and evolutionary consequences, an understanding of hybridization is important for basic and applied sciences, including conservation biology and agriculture. Herein, we review and discuss ideas that are relevant to the recognition of hybrids and hybridization. We supplement this discussion with simulations. The ideas we present have a long history, particularly in botany, and clarifying them should have practical consequences for managing hybridization and gene flow in plants. One of our primary goals is to illustrate what we can and cannot …