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) …

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 …

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 …

Contrasting Soil Nitrogen Dynamics Across A Montane Meadow And Urban Lawn In A Semi-Arid Watershed, Steven J. Hall, Michelle A. Baker, Scott B. Jones, John M. Stark, David R. Bowling

Biology Faculty Publications

Urbanization substantially increases nitrogen (N) inputs and hydrologic losses relative to wildland ecosystems, although the fate of N additions to lawns and remnant grasslands remains contested. In montane semi-arid ecosystems, N cycling is often closely coupled to snowmelt (the dominant period of infiltration) and snow cover, which impact soil temperature and moisture. Here, we compared soil N dynamics between a fertilized and irrigated urban lawn and nearby riparian meadow in Salt Lake City, Utah during a snow manipulation experiment. Snow removal increased freeze/thaw events but did not affect N pools, microbial biomass, denitrification potential, or soil oxygen (O2). Mineral N …

Herbivore Density Mediates The Indirect Effect Of Herbivores On Plants Via Induced Resistance And Apparent Competition, Ricardo A. Ramirez, Micky D. Eubanks

Biology Faculty Publications

Herbivore-induced plant resistance and apparent competition are two indirect ways herbivores interact. If a less damaging herbivore indirectly suppresses the abundance of a more damaging herbivore via these mechanisms, then plants may ultimately benefit. Changes in herbivore density, however, can dictate the intensity of species interactions and may play a critical role in determining the outcome of plant- and predator-mediated herbivore interactions. We tested the effects of herbivore density on the strength of indirect interactions among phloem-feeding aphids and herbivorous caterpillars and the outcome of these interactions for their shared host plant, cotton (Gossypium hirsutum). We quantified the …

Plant Diseases And Pests In Utah Raspberries, Sean Christensen

Research on Capitol Hill

Very little information exists on pathogens and pests that affect Utah raspberry production. In fact a survey of Utah raspberry growers at the 2015 USU Urban and Small Farms conference showed that 72% said the largest problem they had was with diseases and pests, and 71% of those did not know what the diseases actually were.

Several viruses, bacteria, pests, and nutrient deficiencies can have a large influence on raspberry yield. This survey was designed to raise awareness among Utah raspberry growers, help them to better prepare for, and manage these possible disease problems. This will be increasingly more important …

Beyond The Fiber: Novel Spider Silk Coatings And Adhesives, Danielle A. Gaztambide, Breton A. Day

Research on Capitol Hill

Natural spider silks have long been recognized for their combination of incredible strength and elasticity. Spider silk is more elastic than nylon, tougher than Kevlar, and stronger than steel by weight. Due to an inability to farm spiders, much work has been done to produce spider silks in transgenic hosts for large -scale production. Our work was done using recombinant spider silk proteins produced in transgenic goats and the bacteria E. coli.

More recently spider silks have also been recognized for their biocompatibility and lack of immunogenicity. Spider silks' incredible strength and ability to be implanted safely within the body …

Insecticides Are Not Always The Answer For Combatting Pests In Onion Fields, Harlie Hutchinson

Research on Capitol Hill

Onion thrips are the insect vector of a severe virus in onion, Iris yellow spot virus. The thrips and virus are primary threats to the economic stability of onion production worldwide. Overuse of insecticides to suppress onion thrips has resulted in the development of resistance, reduced performance of insecticides, and reduced onion yields.

There is a compelling desire to find alternatives to better manage these pests. In this study, we assessed onion thrips populations on onions with low and high nitrogen rates, and near and far from corn and wheat, two common neighboring crops in the onion farm-scape.

Stream Water Nitrogen Inputs Reflects Groundwater Across A Snowmelt-Dominated Montane-To-Urban Watershed, Steven J. Hall, Samantha R. Weintraub, David Eiriksson, Paul D. Brooks, Michelle A. Baker, Gabriel J. Bowen, David R. Bowling

Biology Faculty Publications

Snowmelt dominates the hydrograph of many temperate montane streams, yet little work has characterized how streamwater sources and nitrogen (N) dynamics vary across wildland to urban land use gradients in these watersheds. Across a third-order catchment in Salt Lake City, Utah, we asked where and when groundwater vs shallow surface water inputs controlled stream discharge and N dynamics. Stream water isotopes (δ2H and δ18O) reflected a consistent snowmelt water source during baseflow. Near-chemostatic relationships between conservative ions and discharge implied that groundwater dominated discharge year-round across the montane and urban sites, challenging the conceptual emphasis on direct stormwater inputs to …

Thermoregulatory Responses In Lamprophis Fuliginosis, Michael Ryan

Biology Posters

No abstract provided.

Purification Of Recombinant Spider Silk Protein From Escherichia Coli., Randolph V. Lewis, Justin Jones, Todd Brown

Biology Posters

Spider silk has many applications including human health (sutures, vaccine encapsulations, i.e.) and military usage (underwater Velcro-type fasteners). In order to test these applications, we need large quantities of spider silk protein to use in our experiments. One way to make spider silk is by using Escherichia coli (E. Coli) to produce the protein. E. Coli has many advantages: it can be produced in larger amounts, it is inexpensive to grow, and it can be easily transported. We usually start with a culture mass weighing 4 kg but we are scaling up to produce even greater amounts of product. The …

Conductive Ink Meets Spider Silk, Jay Merrill, Amir Ghazi, Thomas I. Harris, Ibrahim Hassounah, Randolph V. Lewis

Biology Posters

Spider silk proteins can be created synthetically and are highly valued for their strength, durability, and flexibility. By altering the genome of goats, silk worms, and the bacteria E. coli we are able to manufacture spider silk products in lab. The production and manipulation of these ‘recombinant spider silk proteins’ along with the process of aqueous solubilization can yield many useful spider silk materials such as films, fibers, gels, coatings, and more. Conductive ink is a recent and popular scientific discovery that let’s you create flexible working circuits. This product has many applications including RFID tags, circuit boards, and printers. …

Development Of Archaeal And Algalytic Bacteria Detection Systems, Andrew Walters, Anna Doloman, Charles Miller

Biology Posters

Natural gas (methane) is emerging as a viable power source for many industrial, commercial, and domestic applications. Bio-methane provides a promising replacement for mined natural gas. Methanogenic bacteria produce this bio-methane. These anaerobic bacteria pertain to the Domain Archaea, and are found in extreme environments where few other bacteria survive. They are employed by Up-Flow Anaerobic Sludge Blanket (UASB) reactors in the digestion of wastes to a marketable product (methane). The genome of methanogenic bacteria can be amplified using polymerase chain reaction (PCR), a synthetic DNA replication system. This system employs specific sequences of DNA called primers. The primers employed …

From Spider To Silk: Constructions Of Synthetic Genes Of The Acinoform Spider Silk Protein (Acsp1), P. Tate Weller, Samuel T. Briggs, Paula F. Oliveira, Fernando A. Agarraberes, Randy V. Lewis

Biology Posters

Spider silks have remarkable physical properties due to a combination of strength and elasticity. In addition, spider silks are biocompatible and biodegradable. Our laboratory has shown that the strength products, such as fibers, produced with other silk proteins correlates with the size of the silk protein. The aciniform silk (AcSp1), has been shown to produce the thinnest and strongest fibers of all the natural spider silks. Aciniform silk is composed of a nonrepetitive amino-terminal region, 14 repeats of approximately 200 amino acids each, and a nonrepetitive carboxy-terminal region. We have been able to produce different versions of these genes encoding …

Observation Of Fertilized Bovine Oocytes, Tyce Addley, Kenneth Campbell

Biology Posters

Oocytes were extracted from bovine ovaries by perforation of the follicle wall. Oocytes extracted were chosen for culture based on the cumulus-oocyte complex (COC), graded by the density of cumulus cells on a scale of A-D, in vitro fertilization (IVF) was performed on COC’s rated A or B. Healthy COC were placed into a maturation media for incubation at 29 degree C with a 5 percent CO2 air mixture for twenty four hours. After the maturation period the chosen oocytes were fertilized by IVF using frozen/thawed semen from one bull.