Biology Commons^™

A Systematic Classification Of Fungus Gnats (Diptera: Mycetophilidae) Of The Grand Staircase Escalante National Monument (Gsenm), Utah, Mark Robert Nelson, Dr. C. Riley Nelson

Journal of Undergraduate Research

Mycetophilidae (fungus gnat) is a species-rich family of flies, existing on every continent but Antarctica, which has received little documentation on a global basis and no documentation in Utah (Vockeroth, 1981). In the most recent and comprehensive catalog of flies in North America only about sixty of the thousands of fungus gnats known are predicted to be found in Utah (Laffoon, 1965). My mentor, Riley Nelson, and I believe that this figure is likely a gross underestimate that will be rectified, in part, with the conclusion of my study. Not only will my research document the known fungus gnats in …

Pioneer Lizards: Speciation In South America, Cameron R. Turner, Dr. Jack W. Sites

Journal of Undergraduate Research

Understanding the processes by which new species are formed is a primary objective of evolutionary biology. My project aimed to contribute to this understanding by measuring the genetic and geographic structure of a population of South American lizards, Liolaemus koslowskyi. Previous research (1) had provided evidence for a trend of more complex genetic structure in northern versus southern ends of distribution ranges in several lizard complexes of the genera Liolaemus and Cnemidophorus in temperate South America. L. koslowskyi is limited to the extreme northern end of the genus’ distribution and by sampling its entire range I would be able to …

An Objective Means Of Diagnosing Anorexia Nervosa And Bulimia Nervosa Using 15n/14n And 13c/12c Ratios In Hair, Kent A. Hatch, Morgan A. Crawford, Amanda W. Kunz, Steven R. Thomsen, Dennis L. Eggett, Stephen T. Nelson, Beverly L. Roeder

Journal of Undergraduate Research

An objective means based on the carbon and nitrogen stable isotope analysis of five hairs per individual is presented for distinguishing between individuals with anorexia nervosa and/or bulimia nervosa from non-clinical individuals (i.e. clinically normal controls).

Development Of Software Program For Organizing Dna Sequence Data From Genbank, Heather Vernon, Dr. David Mcclellan

Journal of Undergraduate Research

Nucleotide sequence data on GenBank (a government sponsored repository located on http://www.ncbi.nlm.nih.gov/entrez/) is organized in a flat file format that can be accessed by searches. Obtaining a large volume of sequences from GenBank is a tedious process because the sequence data must be extracted from the flat files for every sequence. The goal of this project was develop a java program to upload many sequences from GenBank in one file, extract the gene names to allow the user to group synonyms, and save the data into either tab-delimited or FASTA format for easy importation into other sequence manipulating programs. This …

A Molecular Phylogenetic Analysis Of The Genus Habromys (Rodentia: Muridae), Christopher Funk, Dr. Duke Roger

Journal of Undergraduate Research

Habromys (crested-tailed mice) is a rodent genus that historically has not been analyzed well enough to be accurately classified. Before 1980, Habromys had been relegated as a subgenus of Peromyscus (deer mice), a closely related genus. As a subgenus, Habromys consisted of only three arboreal species living in the cloud forests of Southern Mexico and Central America (P. simulatus, P. lophurus, and P. lepturus – Hooper and Musser, 1964; Hall, 1981; Musser, 1969). Despite the distinct morphological features of Habromys, it remained as a subgenus due to small sample size and limited morphological analysis. Upon more closely examining its morphology, …

Functional Comparisons Of Lta And Tnf-A Gene Protein, Raymond Gram Ii, Dr. David Mcclellan

Journal of Undergraduate Research

TNF-a is a cytokine released by activated macrophages and lymphotoxin alpha (LTA) is a cytokine released by activated lymphocytes. Both proteins act as modulators of the immune response and competitively bind to the same protein receptors TNFR-1 and TNFR-2. The protein sequences themselves are 35% identical and 50% homologous to one another.

The Effects Of Stage Of Reproduction On Survival Of The Livebearing, Western Mosquitofish (Gambusia Affinis), Jacob Michael Condon, Dr. Mark C. Belk

Journal of Undergraduate Research

Reproduction is costly not only in terms of energy allocated to form embryos (allocation costs), but also because of a potential decrease in the probability of survival of the female as a result of reproduction (viability costs).

The Cftr Protein: Evolution And Disease, Adam Allred, Dr. David Mcclellan

Journal of Undergraduate Research

The principal aim of my research has been to aid in the understanding of complex molecular pathologies by identifying evolutionary patterns that maintain the structural and functional integrity of a particular protein product. A disease phenotype often results when such delicate patterns are disturbed. The Cystic Fibrosis Transmembrane conductance Regulator (CFTR), an epithelial chloride channel, has proven to be an especially worthy vehicle for understanding the link between molecular evolution and human disease. Aberrant functioning of this physiologically important channel results in cystic fibrosis, the most common lethal genetic disorder among European-derived populations.

The Effect Of Celecoxib On 17-Estradiol (E2) Treated Mcf-7 Cells Using The Enzyme Linked Immunoabsorbent Assay (Elisa), Jason Kinyon

Journal of Undergraduate Research

There has been evidence that shows inhibiting Cyclo-oxygense 2 (COX-2) enzymes may decrease angiogenic factors such as Vascular Endothelial Growth Factor (VEGF), which may prove beneficial in halting angiogenesis and metastasis, stopping cancer progression. It has been shown that there is a significant positive correlation between COX-2 and VEGF mRNA expression in breast cancer specimens. 17b-Estradiol (E2) has shown to increase VEGF production by binding to estrogen receptor positive breast cancer cell lines such as MCF-7. The COX-2 inhibitor celecoxib can be added to E2 treated MCF-7 cells to determine its effect on VEGF production using the Enzyme Linked Immunoabsorbent …

The Effects Of A Restoration Project On The Feeding Habits Of Local Trout Populations In The Provo River System, Lance Bastian, Dr. Dennis Shiozawa

Journal of Undergraduate Research

In the fall of 1999, the state of Utah began to implement a plan involving several diversions of the Provo River. Over the course of the next several years, there arose a heated debate between the state, local ecologists and local fisherman with regard to the trout populations that inhabit the river. The fishermen claimed to be pulling out overly skinny fish, and the restoration project was blamed. Many claimed that debris from the project had washed down the river and settled on the feeding areas of the local species of insects and gastropods. As a result, these primary prey …

Genomic Pathway Analysis Reveals That Ezh2 And Hdac4 Represent Mutually Exclusive Epigenetic Pathways Across Human Cancers, Adam L. Cohn, Stephen R. Piccolo, Luis Cheng, Rafaella Soldi, Bing Han, W. Evan Johnson, Andrea H. Bild

Faculty Publications

Background: Alterations in epigenetic marks, including methylation or acetylation, are common in human cancers. For many epigenetic pathways, however, direct measures of activity are unknown, making their role in various cancers difficult to assess. Gene expression signatures facilitate the examination of patterns of epigenetic pathway activation across and within human cancer types allowing better understanding of the relationships between these pathways.

Methods: We used Bayesian regression to generate gene expression signatures from normal epithelial cells before and after epigenetic pathway activation. Signatures were applied to datasets from TCGA, GEO, CaArray, ArrayExpress, and the cancer cell line encyclopedia. For TCGA data, …

Cytotoxicity Of Traditional Medicinal Plants Of Ghana, Stephanie Henderson, Dr. Gary M. Booth

Journal of Undergraduate Research

Medicinal plants are the oldest known health-care products in the world (WHO, 1996), and according to the World Health Organization, 80% of the population in Africa still use traditional medicines for primary health care (WHO, 2003). The situation in Ghana is particularly significant. In the Upper Region of Ghana, a population of over 1.2 million, there is one traditional healer to approximately 490 people, as opposed to one biomedical physician to every 66,667 people (Boye and Ampofo, 1987).

Blood Protein Isotopic Investigation, Michael J. Gravett, Kent Hatch

Journal of Undergraduate Research

Stable isotope ratios have been used for a variety of purposes in the biological sciences. These ratios have been used by plant ecologists to asses the photosynthetic mode, to measure water balance, and to trace nitrogen sources (Gannes, 1997). They have been used by animal ecologists to determine trophic relationships in food webs, to discriminate between animals that live in different biomes, to trace migratory animals, to follow nutrients through the body, and to undertake dietary reconstruction of both current and extinct species (Bearhop, 2002).

Cruisin’ In The Bat-Mobile: Coevolution Of S-Symbiont Arsenophonus Spp. In Batflies (Diptera: Streblidae), Richard E. Trowbridge, Dr. Michael F. Whiting

Journal of Undergraduate Research

Symbiotic relationships between bacteria and insect hosts are common, with more than ten percent of insect species relying upon intracellular bacteria for their development and survival (Braendle 2003). These symbionts can stem from an obligatory association [primary (P-) endosymbionts], involving a number of properties (e.g. localization within special host cells; close concordance of the evolutionary trees of endosymbiont and host species). Besides P-endosymbionts, most bacteria contain a heterogeneous assemblage of bacteria called secondary (S-) endosymbionts. Usually, evolutionary trees of S-endosymbionts show little congruence to host trees, which is often interpreted as the result of independent horizontal transmissions. However, some evidence …

Do Inquiry, Constructivist Based Biology Laboratories Affect The Confidence And Attitude Of Preservice Elementary Education Teachers Toward Teaching Science In Their Classrooms?, Heddie L. Richard, Dr. Larry St. Clair

Journal of Undergraduate Research

Integrative Biology 101 is an optional course for preservice elementary education students to improve their science teaching skills. The format of the course allows each student the option to teach a science lesson and participate in a lab directed by the teacher’s assistant (T.A). Each lab follows a ‘cookbook’ style method. The T.A. gives the directions and explains the findings. The purpose of my research was to determine what science teaching methods improved the pre-service elementary school teachers’ attitude and confidence level.

Taxonomy Of Animal Hair Using A Scanning Electron Microscope, Britten D. Sessions, Dr. Wilford M. Hess

Journal of Undergraduate Research

Using a scanning electron microscope (SEM), selected mammalian species were studied to determine hair cuticular patterns. Although other studies have been conducted on mammalian hair, there exists no classification or taxonomy of Western U.S. mammals using an SEM.

Preservation Of Mexican Harvest Mice, Daniel Hardy, Dr. Duke Rogers

Journal of Undergraduate Research

The preservation of wildlife has been a growing concern in Mexico. Specifically, the natural habitat of many Mexican mice has been rapidly diminishing over the past few decades. A more extensive understanding of these types of animals will help contribute to increasing the awareness of the rich diversity of Mexican biota and augment the conservation efforts in this area of the world.

Phylogenetic Analyses Of The Burrowing Members In The Freshwater Crayfish Genera Fallicambarus And Procambarus In Arkansas, Timothy D. O'Connor, Dr. Keith A. Crandall

Journal of Undergraduate Research

There are an estimated 338 taxa of freshwater crayfish in the United States, with approximately 48% considered to be endangered, threatened, or of special concern (Taylor et al. 1996). Life history information for the majority of the primary burrowing species is lacking because they dig deep burrows and venture out only during breeding periods. Burrowing members of the genera Procambarus and Fallicambarus are found in seasonally moist habitats across Arkansas, such as roadside ditches and open pastures. To date, no phylogenetic study has been conducted that establishes a phylogenetic framework for the classification of these elusive species.

Lichen Flora Of Boulder Mountain, Aquarius Plateau, Wayne County, Utah Usa: An Altitudinal Comparison Of Lichen Communities, Steven Leavitt, Dr. Larry St. Clair

Journal of Undergraduate Research

Lichen ecology is a facet of biology that remains relatively unexplored in many parts of the United States. Lichens can play an important role as indicators of local environmental conditions, as lichen species density and community structure are significantly affected by airborne contaminants and other anthropogenic influences. Obtaining baseline ecological data for local lichen communities will make it possible to continually monitor local communities and evaluate future changes in community structure.

The Effects Of Point Mutation Saturation On The Loss Of Information In Mutated Dna Sequences, Kimberly Baer, Dr. David Mcclellan

Journal of Undergraduate Research

The research I am conducting fills a niche in molecular adaptation. My experiment uses accepted methods of reconstruction to evaluate the accumulation of multiple hits at single sites. It is accepted that over time point mutation saturation in specific sequences occurs in a clock-like manner following Poisson-like pattern leading to loss of information in empirical data being very unrecoverable. This area of study shows a gap in scientific knowledge as to how molecules change and develop over time. I want to understand how saturation accumulates and what it means for the loss of information.

Reconstructing The Phylogeographic History Of The Chilea Catfish (Trichomycterus Areolatus), Andre Bennin, Dr. Jerald B. Johnson

Journal of Undergraduate Research

The current geographic distribution of Chilean freshwater fishes has likely been shaped by several abiotic factors, including fragmentation caused by the Pacific Ocean, glaciers that covered the entire southern part of Chile during the Pleistocene Epoch, and orogenic and volcanic activity. Exactly how these factors have impacted population histories of Chilean freshwater fishes remains unknown. In this project, we examined the phylogeographic history of the freshwater catfish Trichomycterus areolatus, a species native to Chile that occurs across most of the latitudinal range of this country (Fig. 1). Given the distribution and ubiquity of this species, we anticipate that the results …

Establishing Isotopic Patterns Among Rock Pools, Heather Semon, Kent Hatch

Journal of Undergraduate Research

Isotopic analysis with natural markers has been applied to tracking the migration of birds and butterflies as well as many other species over large geographic scales.1-4 We wanted to zoom in on a much smaller scale and determine whether stable isotopes could be used to track the small-scale dispersal of insects among rock pools and tenajas (a series of rock pools in a drainage).5 Stable isotopes have been used to study aquatic invertebrate dispersal and metapopulation dynamics by artificially spiking water sources with 15N-enriched NH4Cl. 6,7 However, it is not known how this chemical may have altered the ecology of …

Evolution Of Thrips (Thysanoptera) Phylogenetic Patterns And Mitochondrial Genome Evolution, Mark Terry, Dr. Michael Whiting

Journal of Undergraduate Research

Thysanoptera (thrips) is an order of insects currently comprised of 7400 species, 1200 genus-groups, and nine living families with three fossil families (Mound, 2005). Two major suborders are recognized in Thysanoptera: Tubulifera (thrips with abdominal segment 10 tubular in shape) and Terebrantia (thrips with abdominal segment 10 subdivided ventrally).

Geneworkshop: A Dynamic, Developing Environment For Biologists, Computer Scientists, And Bioinformaticians, Joshua Sailsbery, Dr. David Mcclellan

Journal of Undergraduate Research

The GeneWorkshop project had one goal, to enable biologists to better utilize bioinformatic tools. Generally, bioinformatic tools have a large learning curve and are not very robust as to the data they accept. In order to meet these criteria, GeneWorkshop was separated into two main objectives. The first objective was the obtaining and maintaining of genetic data. The second objective was interpreting and implementing various bioinformatic software packages.

Conservation Genetics Of Mexican Deer Mice, Melina C. Walden, Dr. Duke S. Rogers

Journal of Undergraduate Research

In the field of biology, the job of documenting, describing, and defining the species of the world is a critical, yet overwhelming task. By focusing research in a specific area of interest, however, scientists work to contribute one small piece at a time to the much larger puzzle. In researching the biological relationships between the Mexican deer mice Peromyscus megalops and P. melanurus, my project contributes to one of the primary goals of biology.

In Quest Of Scientific Literacy And Civic Engagement: Innovations In Biology 100, Timothy Larsen, Dr. Gary M. Booth

Journal of Undergraduate Research

Scientific literacy is increasingly becoming a concern for citizens and consumers in a scientifically and medically advancing world. Service-Learning, Inquiry-Based Learning, and Concept Mapping have been implemented as a means of helping students to adopt deeper approaches to learning. It is the goal of my mentor, Dr. Gary Booth, to use these instructional methods to better prepare BYU students to participate as informed citizens and consumers in society.

Cheatgrass, Scott A. Davis, Dr. Bruce Roundy

Journal of Undergraduate Research

The invasion of non-native species, mainly cheatgrass (Bromus tectorum), into our rangelands, especially following the destruction caused by wildfires, has made it necessary to find viable options for the restoration of native plant species to these areas. The aim of this project was to determine whether or not it was possible to create models for the germination and seminal root growth of a suite of species using heat accumulation. By creating these models, we hoped to be able to discover other native species that not only compete with cheatgrass by establishing early, but provide a good food source for native …

Population Structure Of The Cuttlefish Sepia Officinalis From The North Atlantic-Mediterranean Region, Mark Joseph Nolte, Dr. Keith Crandall, Marcos Pérez-Losada

Journal of Undergraduate Research

An understanding of the relatedness of a population of organisms, or their phylogeny, combined with knowledge of that population’s geographical distribution, can illuminate which geographic forces and events may have played a role in forming the “family tree” of that organism. Therefore past speciation events and the incipient stages of speciation can be discerned when phylogenetic and geographic information is merged. This process, broadly known as the practice of phylogeography or biogeography, is important because it permits researchers to visualize the evolutionary interplay between environment and organism. Additionally, an understanding of an organism’s population structure, or family tree, enables scientists …

Correctly Assigning Dna Barcodes To Organisms, James B. Finlay, Dr. Keith A. Crandall

Journal of Undergraduate Research

Harvard biologist Edward O. Wilson suggested that what makes humans unique is our innate need for closeness to other forms of life. This “biophilia” has been evident since recorded history and was brought to the forefront of science with Darwin’s famous writings about the origin of species. Since that time there has been a major thrust to categorize all life into groups and subgroups in a field known as taxonomy. There are an estimated 10-15 million extant species (Hammond, 1992) on the earth. Taxonomists have classified roughly 1.6 million of these organisms (Wilson, 1992), indicating that much work needs to …

The Significance Of Isotopic Ratios In Migratory Pathways, Rachel Hart, Kent Hatch

Journal of Undergraduate Research

Stable isotope research is an important asset in securing the migratory paths of birds. By matching elemental isotopic ratios in different parts of a bird’s body to the water it drinks, important stopover sites may be conserved and the biological phenomenon of migration may be preserved. Thus far, such research among migratory birds has suggested a positive correlation between certain elemental isotopic ratios found in water sources and those in the composition of bird feathers. Hydrogen (δD) and oxygen (18O and 16O) isotopes have been examined in scientific literature but have not been tested thoroughly, as there are still many …