Biology Commons^™

Lipid Dependence In Ras-Driven Tumors, Darin Salloum

Dissertations, Theses, and Capstone Projects

Over past decade, metabolic alterations in cancer cells have received a substantial amount of interest. It had been established that cancer cells undergo a significant amount of metabolic alterations, and some of these alterations are similar to those in normal highly proliferative cells. However, it is becoming more apparent that many of the metabolic alterations are specific to particular oncogenic signaling pathways. Although altered metabolic machinery makes cancer cells more efficient at promoting growth when nutrients are supplied at the sufficient amounts, the dependency of cancer cells on particular metabolic reprogramming deems cancer cells susceptible to disruptions within metabolic network. …

Metabolic Checkpoints In Cancer Cell Cycle, Mahesh Saqcena

Dissertations, Theses, and Capstone Projects

Growth factors (GFs) as well as nutrient sufficiency regulate cell division in metazoans. The vast majority of mutations that contribute to cancer are in genes that regulate progression through the G1 phase of the cell cycle. A key regulatory site in G1 is the growth factor-dependent Restriction Point (R), where cells get permissive signals to divide. In the absence of GF instructions, cells enter the quiescent G0 state. Despite fundamental differences between GF signaling and nutrient sensing, they both have been confusingly referred to as R and therefore by definition considered to be a singular event in G1. Autonomy from …

An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan

Dissertations, Theses, and Capstone Projects

This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation …

Identification And Characterization Of Protein Phopshatases Regulating The Sma/Mab Pathway In C. Elegans, Sheng Xiong

Dissertations, Theses, and Capstone Projects

TGF-beta signaling is a conserved signaling pathway among eukaryotes, which controls various normal cellular responses from cell proliferation to cell death. The mutations in its components are found in developmental disorders and cancer. Therefore, this signaling pathway is extensively investigated so that new therapeutic targets could be discovered and novel drugs could be developed. Previous studies suggested the involvement of phosphatases in regulation of TGF-beta signaling, but these studies were performed in cell culture rather than intact organisms. C. elegans is a tractable organism in which to study signaling in vivo. In C. elegans, growth is controled by a conserved …

Testing Assumptions Of Coevolution In An Egg-Rejecting Brood Parasite Host: Uncovering Sensory, Cognitive, And Evolutionary Drivers Of Responses To Parasitism In American Robins (Turdus Migratorius), Rebecca Croston

Dissertations, Theses, and Capstone Projects

Hosts of brood parasitic birds face fitness costs associated with rearing unrelated offspring. In response, the recognition and rejection of parasitic eggs is a common host defense. Brown-headed cowbirds (Molothrus ater) challenge coevolutionary theory, because although they exploit over 200 host species, they lay non-mimetic eggs, and most hosts do not combat cowbird parasitism with egg rejection. American robins (Turdus migratorius) are one of a handful of cowbird hosts known to recognize and remove cowbird eggs from the nest. I addressed the mechanistic and evolutionary drivers of egg rejection in this host species, by disentangling the roles of spectral tuning …

Polymerase Alpha Components Associate With Telomeres To Mediate Overhang Processing, Raffaella Diotti

Dissertations, Theses, and Capstone Projects

Telomeres consist of TTAGGG repeats, which end with a 3' G-overhang and are bound by a six-protein complex, known as Shelterin. In humans, telomeres shorten at each cell division, unless telomerase is expressed and able to add telomeric repeats to the 3' G-overhang. However, for effective telomere maintenance, the DNA strand complementary to that made by telomerase must be synthesized. In this study, I focused on the Polα/primase complex, in particular the subunits p68 (POLA2, the regulatory subunit) and p180 (Polα, the catalytic subunit), and their potential roles at telomeres. I was able to detect p180, p68 and OBFC1, a …

How Important Is Land-Based Foraging To Polar Bears (Ursus Maritimus) During The Ice-Free Season In Western Hudson Bay? An Examination Of Dietary Shifts, Compositional Patterns, Behavioral Observations And Energetic Contributions, Linda J. Gormezano

Dissertations, Theses, and Capstone Projects

Trophic mismatches between predators and their prey are increasing as climate change causes decoupling of phenological relationships. Predators linked to the life histories of a particular prey will have a more difficult time persisting through environmental change unless they can alter their behavior to maintain the historical match or possess the ability to pursue alternate prey. Arctic predators typically possess flexible foraging strategies to survive in the labile environment, however, quantifying the limits of those strategies can be difficult when life history information is incomplete. In such cases, piecing together different aspects of a predator's foraging behavior, particularly when environmental …

Phylogeny, Taxonomy And Morphological Evolution In Conostegia (Melastomataceae: Miconieae), Ricardo Kriebel

Dissertations, Theses, and Capstone Projects

The genus Conostegia comprises 77 species of shrubs and trees ranging from Central America to northern South America and the Caribbean. They are ecologically important as they provide pollen for native bees and fruits for birds. One of the main questions of this study is if the genus Conostegia is actually monophyletic. I address this question for the first time by gathering genetic data from four chloroplast regions and two nuclear ribosomal regions of DNA. Phylogenetic analyses of these data revealed that Conostegia is not monophyletic and that a group of species in the genera Clidemia and Miconia fall within …

The Interplay Of Visual Attention And Saccade Planning In Active Vision, Afsheen Khan

Dissertations, Theses, and Capstone Projects

Vision is a highly active process. When we view the world, we do not hold our eyes still, but constantly move them around in order to view the object or area of interest with the fovea (the region of the retina with the highest acuity). Saccades are the step-like movements that we most often employ for this purpose. In addition, our attention is constantly being covertly attracted or directed to points of interest. Combining these different aspects of viewing: visual processing, the orienting of attention, and eye movements can be referred to as `active vision'.

Most work on active vision …

Physiological Effects Of Habitat Disturbance In The Wandering Gartersnake (Thamnophis Elegans), Austin Spence

Research on the Hill (Salt Lake City)

This study investigated the physiological effects of localized habitat disturbance around well-studied hibernacula of the wandering gartersnake, Thamnophis elegans. After three years of monitoring snake populations, construction occurred at two hibernacula. Individuals from the two populations with construction events were compared to a control population with no construction. At the time of emergence from the hibernacula the year following construction, blood samples were collected upon capture and again following a uniform stressor. The plasma was analyzed using a radioimmunoassay to measure corticosterone levels and a bacterial killing assay to measure innate immunocompetence. There were differences in baseline and post-stress …

Long-­‐Term Evaluation Of Leafy Spurge Biological Control At Richmond, Utah, Jacob Anderson

Research on the Hill (Salt Lake City)

Leafy spurge (LS) is an aggressive Eurasian weed that has been reduced in many areas in North America through biological control releases of flea beetles. Three flea beetle species were released in the mid-1990s at a site dominated by LS in Richmond, Utah. This study assessed the long term effects of LS biocontrol on the plant community at this site by addressing four questions:

(1) Is LS abundance significantly lower in 2013 than it was in the 1990s?

(2) What plant species are replacing LS and are they native or non-native?

(3) Have the flea beetle populations persisted since their …

Cytotoxicity Of Caffeine, Ephedrine, And Metabolites, Jennetta Watson, Dr. Gary Booth

Journal of Undergraduate Research

Caffeine and ephedrine are found together as constituents in a variety of dietary supplements promising to increase metabolism, raise energy levels, and promote weight loss. Much research has been done in this area; however, there is little to no information in the literature about studies focused on the toxicity and anti-proliferative properties of this same caffeine/ephedrine combination occurring at the cellular level. Caffeine’s toxicity against many cell types has been well documented for years.¹ In addition, a number of studies have shown that using caffeine or its metabolites in combination with other chemical or physical reagents increases the overall …

The Phylogeny And Evolution Of Color Patterning Among The Pleasing Fungus Beetles (Coleoptera: Erotylidae)., James A. Robertson, Dr. Michael F. Whiting

Journal of Undergraduate Research

The family Erotylidae (pleasing fungus beetles) currently includes 125 genera, and approximately 2,500 described species and has a worldwide distribution. There are five currently recognized subfamilies within Erotylidae: Dacninae, Megalodacninae, Eucaustinae, Tritominae, and Erotylinae. Erotylids are mycophagous, feeding on basidiomycete fungi, and exhibit a wide range of gregarious behavior. Most erotylids have a striking appearance, exhibiting bright colors including red, yellow, pink, and purple, frequently in combination with contrasting black. These colors are often arranged in zigzag, banding, or polka dot patterns. It has been suggested that the striking coloration found among erotylids is aposematic, and erotylids are consequently presumed …

Evolution Of Cytochrome B In Elapidae (Squamata: Serpentes), Dean H. Leavitt, Dr. David A. Mcclellan

Journal of Undergraduate Research

DNA sequences provide a wealth of information that allows systematists to better understand the phylogenetic history of the earth’s current biota. Some genes are better suited for phylogenetic studies than others, and one that has been commonly used is the mitochondrial gene cytochrome b. Cytochrome b (cyt-b) is a membrane-bound protein that is the central catalytic subunit of the Q-cycle in the electron transport chain (Zhang et al., 1998). The structure and function of cyt-b has been studied extensively and is well understood (Degli Esposti et al., 1993). Changes within cyt-b have been studied at the nucleotide, amino acid and …

Bacteria As Bioindicators: Bioassessment In The Bonneville Basin Of Utah, Mark Merkley, Russell Rader

Journal of Undergraduate Research

Bioassessment is the practice of using organisms to detect environmental health and integrity. Ecosystem health and integrity depend on the interaction between living organism and ecosystem function. All organisms or groups of organisms do not respond the same to environmental stress. Depending on various disturbance characteristics, each group may respond at different rates and provide different information (Rader, 2001). Besides the usual macrophytes, macroinvertebrates, or algae, bacteria have the capability of being strong bioindicators. Because of their extremely small size, bacteria have the highest surface-to volume ratios of any living organisms. Thus, bacteria should be the most environmentally aware organisms, …

Survey Of Calyx Gland Morphology In Navarrettia (Polemoniaceae) Using Scanning Electron Microscopy, Taina Matheson, Dr. Leigh Johnson

Journal of Undergraduate Research

Many flowering plants possess small epidermal hairs and glands. The variation in these features has been used to infer relationships among plant groups. The Phlox family (Polemoniaceae) is one such group. Many species in this family are described as having “woolly or arachnose hairs.” These hairs are present in many taxa that are considered to be unrelated, however, and may not be structurally identical. Thus, it may be unrealistic to score these features the same in phylogenetic analyses. First, we need to accurately describe the variation that is present. The genus Gilia has historically been used as a sort of …

Population Genetic Analysis Of Astacopsis Gouldi., Aaron Madsen, Dr. Keith Crandall

Journal of Undergraduate Research

Astacopsis gouldi has been known to weigh up to 6 kg, and live for as long as 60 years (Horwitz and Hamr, 1988). However, fishing pressure, as well as habitat destruction and pollution have had detrimental effects on A. gouldi populations. The populations of the species in accessible rivers have declined, as have the number of males reaching sexual maturity. These factors led to the placement of A. gouldi on the endangered species list in 1996 (IUCN, 1996). Conservationists are considering the relocation of crayfish from populations in more remote rivers and streams where the decline in numbers has been …

Multiple Paternity In Podocnemis Expansa Of The Orinoco Basin, R Brigham Dastrup, Devon Pearse, Dr. Jack W. Sites

Journal of Undergraduate Research

On June 2, 1970, the turtle Podocnemis expansa was designated as endangered throughout its entire range by the US Fish and Wildlife Service. The turtle is known to exist in the Orinoco and Amazon river basins in South America.ⁱ Conservation efforts continue to try and preserve the species. Additionally, several studies have been conducted to increase the knowledge base about P. expansa, including many aimed at better understanding their behavior. This knowledge could be critical in conservation efforts.

Conflicting Selection In The Course Of Adaptive Diversification: The Interplay Between Mutualism And Intraspecific Competition, Rafael L.G. Raimundo, Jean P. Gibert, David H. Hembry, Paulo R. Guimaraes Jr.

School of Biological Sciences: Faculty Publications

Adaptive speciation can occur when a population undergoes assortative mating and disruptive selection caused by frequency-dependent intraspecific competition. However, other interactions, such as mutualisms based on trait matching, may generate conflicting selective pressures that constrain species diversification. We used individual-based simulations to explore how different types of mutualism affect adaptive diversification. A magic trait was assumed to simultaneously mediate mate choice, intraspecific competition, and mutualisms. In scenarios of intimate, specialized mu- tualisms, individuals interact with one or few individual mutualistic partners, and diversification is constrained only if the mutualism is obligate. In other scenarios, increasing numbers of different partners per …

Perennial Grasslands Enhance Biodiversity And Multiple Ecosystem Services In Bioenergy Landscapes, Ben P. Werling, Timothy L. Dickson, Rufus Isaacs, Hannah Gaines, Claudio Gratton, Katherine L. Gross, Heidi Liere, Carolyn M. Malmstrom, Timothy D. Meehan, Leilei Ruan, Bruce A. Robertson, G. Philip Robertson, Thomas M. Schmidt, Abbie C. Schrotenboer, Tracy K. Teal, Julianna K. Wilson, Douglas A. Landis

Biology Faculty Publications

Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global population. Producing bioenergy crops on marginal lands—farmland suboptimal for food crops—could help meet energy goals while minimizing competition with food production. However, the ecological costs and benefits of growing bioenergy feedstocks—primarily annual grain crops—on marginal lands have been questioned. Here we show that perennial bioenergy crops provide an alternative to annual grains that increases biodiversity of multiple taxa and sustain a variety of ecosystem functions, promoting the creation of multifunctional agricultural landscapes. We found that switchgrass and prairie plantings harbored significantly greater plant, methanotrophic bacteria, arthropod, …

A Phylogenetic Examination Of The Primary Anthocyanin Production Pathway Of The Plantae, James Campanella, John V. Smalley, Maureen E. Dempsey

Department of Biology Faculty Scholarship and Creative Works

Background: Anthocyanin pigments aid in reproduction and provide ultraviolet protection to land plants. We have examined the phylogenetic relationships among the five primary enzymes responsible for producing anthocyanin pigment in its three major forms. Dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), Flavonoid 3'glucosyltransferase (F3GT), flavonoid 3'hydroxylase (F3'H), and flavonoid 3'5' hydroxylase (F3'5'H) are responsible for the final steps in anthocyanin pigment production. Results: We were interested in how conserved the anthocyanin pathway genes may be among land plants, and evolutionarily how far back into the plant lineage anthocyanin production may be traced. The DFR, ANS, F3GT, and F3'H genes date back …

Atrial Fibrillation Associated Chromosome 4q25 Variants Are Not Associated With Pitx2c Expression In Human Adult Left Atrial Appendages, Shamone R. Gore-Panter, Jeffery Hsu, Peter Hanna, A. Marc Gillinov, Gosta Pettersson, David W. Newton, Christine S. Moravec, David R. Van Wagoner, Mina K. Chung

Biological, Geological, and Environmental Faculty Publications

Atrial Fibrillation (AF), the most common sustained arrhythmia, has a strong genetic component, but the mechanism by which common genetic variants lead to increased AF susceptibility is unknown. Genome-wide association studies (GWAS) have identified that the single nucleotide polymorphisms (SNPs) most strongly associated with AF are located on chromosome 4q25 in an intergenic region distal to the PITX2 gene. Our objective was to determine whether the AF-associated SNPs on chromosome 4q25 were associated with PITX2c expression in adult human left atrial appendages. Analysis of a lone AF GWAS identified four independent AF risk SNPs at chromosome 4q25. Human adult left …

Morphologic And Molecular Description Of Metopus Fuscus Kahl From North America And New Rdna Sequences From Seven Metopids (Armophorea, Metopidae), William A. Bourland, Laura Wendell, Greg Hampikian

Biology Faculty Publications and Presentations

Most species in the large ciliate genus Metopus Claparède & Lachmann, 1858 lack detailed descriptions based on modern morphologic and molecular methods. This lack of data for the vast majority of species hampers application of a morphospecies approach to the taxonomy of Metopus and other armophorids. In this report we redescribe the large species, Metopus fuscus Kahl, 1927 based on in vivo observation, silver impregnation, scanning electron microscopy, and single-cell 18S rDNA sequencing of a freshwater North American (Idaho) population. Metopus fuscus invariably has a perinuclear envelope of endosymbiotic bacteria not found in other species. Unlike the original description of …

Phylogeny And Conservation Of The Utah Land Snail Oreohelix Peripherica (Gastropoda: Pulmonata: Camaenidae), Ashley Nelson, Dr. Keith A. Crandall

Journal of Undergraduate Research

The land snail Oreohelix consists of 35 species that are distributed throughout the western United States, southwest Canada and northern Mexico. The majority of these species are endemic to the Great Basin and the Rocky Mountains (Bequaert et al., 1973). Pilsbry (1939) made the last taxonomic revision of the Oreohelix snail in Utah. He described seven species: Oreohelix eurekensis, O. haydeni, O. parawanensis, O. peripherica, O. strigosa, O. subrudis, and O. Yavapai. Traditionally, three subspecies have been ascribed to O. peripherica: O. p. wasatchensis, O. p. newcombi and O. p. weberina, which are distributed in Logan and Ogden Ranger Districts …

Studies On Theraputic Potential Of Dichloroacetic Acid And Hene Laser In Cancer Treatment: Understanding The Mechanism Of Action, Zeiyad Nassaif Al-Karakooly

Theses and Dissertations

Cancer cells are often characterized by anaerobic glycolysis due to dysfunctional mitochondria that limits pyruvate uptake for aerobic respiration. Dichloroacetic acid (DCA), used in this study as a potential cancer treatment agent, targets mitochondria in cancer cells and is likely to correct mitochondrial dysfunction by resuming pyruvate uptake and therefore normal aerobic respiration. Our results suggest that DCA causes a significantly higher cytotoxicity in aggressive MCF-7 breast cancer cells than in non-aggressive MC3T3 osteoblastic cells. Apparently lower doses of DCA induce apoptosis whereas higher doses lead to non-specific cytotoxicity or necrosis. Increased cytotoxicity might be related to oxidative stress due …

Mutation Of A Dna Repair Enzyme Causes Lupus In Mice, Ali Senejani, Yanfeng Liu, Dawit Kidane, Stephen E. Maher, Caroline J. Zeiss, Hong-Jae Park, Michael Kashgarian, Jennifer Madison Mcniff, Daniel Zelterman, Alfred L.M. Bothwell, Joann B. Sweasy

Biology and Environmental Science Faculty Publications

A replication study of a previous genome-wide association study (GWAS) suggested that a SNP linked to the POLβ gene is associated with systemic lupus erythematosus (SLE). This SNP is correlated with decreased expression of Pol β, a key enzyme in the base excision repair (BER) pathway. To determine whether decreased Pol β activity results in SLE, we constructed a mouse model of POLβ that encodes an enzyme with slow DNA polymerase activity. We show that mice expressing this hypomorphic POLβ allele develop an autoimmune pathology that strongly resembles SLE. Of note, the mutant mice have shorter immunoglobulin heavy-chain junctions and …

Developmental Link Between Sex And Nutrition; Doublesex Regulates Sex-Specific Mandible Growth Via Juvenile Hormone Signaling In Stag Beetles, Hiroki Gotoh, Hitoshi Miyakawa, Asano Ishikawa, Yuki Ishikawa, Yasuhiro Sugime, Douglas J. Emlen, Laura C. Lavine, Toru Miura

Biological Sciences Faculty Publications

Sexual dimorphisms in trait expression are widespread among animals and are especially pronounced in ornaments and weapons of sexual selection, which can attain exaggerated sizes. Expression of exaggerated traits is usually male-specific and nutrition sensitive. Consequently, the developmental mechanisms generating sexually dimorphic growth and nutritiondependent phenotypic plasticity are each likely to regulate the expression of extreme structures. Yet we know little about how either of these mechanisms work, much less how they might interact with each other. We investigated the developmental mechanisms of sex-specific mandible growth in the stag beetle Cyclommatus metallifer, focusing on doublesex gene function and its …

Homing Behavior Of The Limpet Species Collisella Scabra Living On The Limpet Species Lottia Gigantea, Lee F. Braithwaite

Journal of Undergraduate Research

Limpets are one-shelled marine mollusks that live on rocky beaches in the intertidal zone. The limpet species Collisella scabra is also found living on the shell of the limpet species L. gigantea. C. scabra exhibits an interesting phenomenon known as homing. This means that while not feeding, C. scabra are always found on the same spot on the rock or shell where they live. The C. scabra leave this spot, known as a home scar, to feed, but always return to it after they are done feeding. In this research, Chris Miller, Bryant Low, Christian Armstrong, and I examined the …

Our Impressive Immune System: More Than A Defense, Alan L. Gillen, Jason Conrad

Faculty Publications and Presentations

Most likely the immune system was put into place in the original human body design. We know from Exodus 20:11 and other verses that God completed His work of creation in six days. Therefore, the human body and its functional parts, including the components of the immune system, must have been part of the original creation. God said that all He had made was very good (Genesis 1:31). Since there were no pathogens (germs), parasites, or diseases prior the Edenic Fall and subsequent Curse, the immune system may have functioned differently in that world unmarred by sin and death.

The …

The Role Of Piua, An Outer Membrane Iron Receptor, In The Pathogenesis Of Pseudomonas Aeruginosa, Brandon J. Beddingfield

Biology Theses

Pseudomonas aeruginosa is a common pathogen in those with compromised immunity. It has been attributed to deaths in the majority of cases of Cystic Fibrosis. Using a strain of P. aeruginosa containing no functional piuA gene, coding for an outer membrane siderophore/iron complex receptor, we show that several virulence determinants are upregulated. These include pyocyanin production, adherence to lung epithelia, and cytotoxicity of lung epithelia. Growth was diminished in iron depleted media, suggesting that even though individual cells may be more virulent in the knockout strains, the overall resulting infection may be less severe. This may have important implications for …