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Full Issue, Comparative Civilizations Review

Comparative Civilizations Review

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A Quadruplex Real-Time Pcr Assay For The Rapid Detection And Differentiation Of The Burkholderia Pseudomallei Complex: B. Mallei, B. Pseudomallei, And B. Thailandensis, Chinn-Woan Lowe

Theses and Dissertations

Methods for the rapid detection and differentiation of the Burkholderia pseudomallei complex comprising B. pseudomallei, B. mallei, and B. thailandensis, have been the topic of recent research due to the high degree of phenotypic and genotypic similarities of these species. B. pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively. B. pseudomallei and B. mallei are recognized by the CDC as tier 1 select agents. Although B. thailandensis is generally avirulent in mammals, this species displays very similar phenotypic characteristics to that of B. pseudomallei. Optimal identification of these species remains problematic, …

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, …

Catalytic Reactions For The Production Of Biomarkers From The Biological Warfare Agent Anthrax (Dr.), Jason E. Hawkes, Dr. Milton L. Lee

Journal of Undergraduate Research

Bacillus anthracis, more commonly known as anthrax, poses a serious threat to the national security of the United States of America. In its weaponized form, anthrax spores are easily aerosolized, demonstrate long residence times in the atmosphere (typically variable for several days), and can be fatal if ingested or inhaled into the lungs. Following ingestion or inhalation, rapid growth and reproductive activity is triggered, releasing large amounts of deadly toxin. The lethal dose of anthrax spores is very small, approximately 10 nanograms of spores.1 As a result of its easy dispersal, long residence times, and high toxicity, anthrax is becoming …

Synthesizing Racemic And Optical Active 6-Methylsulfinylhexyl Isothiocyanate, Bo Duan, Dr. Merritt Andrus

Journal of Undergraduate Research

6–methylsulfinylhexyl isothiocyanate (MS-ITC) is the active component of wasabi, Japanese horseradish. Wasabi plant (Wasabia Japonica), a member of the Cruciferae family, is native to Japan and is traditionally found growing in or by cold mountain streams. The root and stem of this plant has a fiery hot flavor that quickly dissipates in the mouth, leaving a lingering sweet taste.

Chemical Isolation From Plant Endophytes, David Dahl, Dr. Steven Wood

Journal of Undergraduate Research

The major research that I have worked with is on the extraction of biologically active compounds from plant endophytes native to the west desert of Utah and high altitude Paramo of Ecuador. For a year I have been working the Department of Chemistry and Biochemistry’s Natural Product Research Group under Dr. Noel Owen and Dr. Steven Wood. I planned and am executing a project that combines several different disciplines; anthropology, botany, and chemistry.

Relative Binding Affinity Of Non-Occupied And Single-Ion-Occupied Acetylcholinesterase With Acetylcholine, Scott Hollingshaus, Dr. James P. Lewis

Journal of Undergraduate Research

Trans-membrane channels are the highway mechanisms of biological cells. Through these channels, cells transfer information in the form of ions and other molecules. These transferred materials are called permeating ions. It is well known that most channels work on the principles of size, shape, and charge. Charged channels allow permeating ions of the opposite charge and appropriate shape to pass, while similarly charged ions cannot pass. However, the fluid inside and outside a cell contains many atomic ions, such as sodium (Na+) ions. Because these atomic ions are both small and charged they are able to fit through many different …

Engineering Small Molecule-Dependent Tools For The Study Of Protein Function In Vivo, Jonathan Dewey, Dr. Allen R. Buskirk

Journal of Undergraduate Research

Analyzing the function of newly discovered genes and the proteins that they encode is crucial to the advancement of genetics, cell and molecular biology, and medicine. Scientists have implemented various methods to study individual proteins within a cell, including genetic and small-molecule dependent approaches. Our goal is to combine the generality of genetic manipulation with the time-sensitivity of small-molecule dependence to create tools to study the function of Hedgehog pathway proteins and validate them as drug targets.

Three-Dimensional Modeling Of Poliovirus Structure And Activity, Roane Noel, Dr. David Belnap

Journal of Undergraduate Research

The Poliovirus image to the left is from a collection of three-dimensionally reconstructed images of virus particles found at the website: http://www.cgl.ucsf.edu/Research/virus/capsids/viruses.html October 10, 2005. This image is identical to the type of Poliovirus image I reconstructed with the help of mentor Dr. David Belnap.

Size-Based Separation Of Bioparticles Using Planar Nanofluidic Devices, Jie Xuan

Theses and Dissertations

Nanofluidic devices are structures having at least one dimension in the submicron range, which is of the same order of magnitude as the sizes of biomolecules and bioparticles such as proteins and viruses. As a result, size-selective separations are important applications for nanofluidics. Well-defined micro or nano device structures fabricated via micromachining have greatly reduced sample consumption and enabled separations in a parallel fashion, promising significant speed and resolution advantages over conventional size separation techniques, such as gel electrophoresis and size exclusion chromatography. In collaboration with others, I have developed a size separation method using nanofluidic devices consisting of an …

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).

Rates Of Carbon And Nitrogen Stable Isotope Turnover In Fin Tissues Of Gambusia Affinis, Michael Bingham, Dr. Jeff Bullock

Journal of Undergraduate Research

The principle objectives of this research analysis were to determine the uptake and turnover rates of carbon and nitrogen stable isotopes in fish and to establish if this isotope verification procedure is possible by testing tissue samples of their fins. This investigation is separated into two main experiments: first, the stable isotope incorporation in the new growth of fin tissue, and second, the rate of stable isotope turnover in the old growth of fin tissue. Both experiments of this study were done with Gambusia affinis, a species of fish better know as mosquito fish.

Developing A New Fluctuating-Charge Force Field For Charmm, Soren Harward, David Busath

Journal of Undergraduate Research

Molecular Dynamics (hereafter abbreviated MD) is a method of simulating on a computer the behavior of molecules. For over twenty years, it had been a valuable tool that has allowed chemists and physicists to observe chemical interactions that would are difficult or impossible to measure with standard laboratory equipment. The rapid growth of computing power has made feasible simulations of larger and larger systems, so that now biologists can use MD to study the complex chemistry of living organisms.

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.

Erythrocyte Shape Change And Vesicle Release With Methyl-Beta-Cyclodextrin, Jeremy Fairbourn, Dr. John Bell

Journal of Undergraduate Research

The study of membrane properties has direct applications in many branches of science. These properties influence the shape and behavior of the cell. With respect to erythrocytes, the membrane becomes susceptible to the action of secretory Phospholipase A2 (sPLA2) following treatment with ionophores such as ionomycin. The changes produced by ionomycin are experimental analogs to occurrences in the body. The normal actions of the immune system and metabolism cause changes to the cells such that apoptosis is eventually the endpoint of the cell.

Influenza A Virus M2 Protein Selectivity And Permeability Of Ammonium Ions At Varying Ph, Jared Kevin Pearson, David D. Busath

Journal of Undergraduate Research

The M2 protein inside the Influenza A virus capsid is vital to the virus’ replication. When the virus enters a cell, the M2 protein forms ion channels that allow the viral RNA to dissociate from stabilizing proteins, enter the host cell nucleus, and replicate. Blocking the formation of these ion channels, or disabling M2 protein ion transport therefore is an important area of research; inactivating the channel will prevent Influenza A replication.

The Effects Of Interleukin-1, Interleukin-6, And Tumor Necrosis Factor On Aldosterone Release From The Bovine Adrenal Cortex, Todd A. Richards, Dr. Allan M. Judd

Journal of Undergraduate Research

The adrenal is an endocrine gland that is important for the release of steroid hormones and cathecholamines. The adrenal gland is closely associated with the immune system. This association is closely linked by the release of cytokines. Cytokines are a diverse group of proteins first isolated within the immune system but have now been identified in numerous tissues, including those of the endocrine system. The principle cytokines affecting the adrenal gland are interleukin-1 (IL-alpha and IL-beta), interleukin-6 (IL-6) and tumor necrosis factor (TNF). These cytokines can regulate adrenal function, particularly during increased stress and disease, and because they are produced …

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.

Medical Options For Treating Parasitic Diseases In Ashanti-Mampong, Ghana, West Africa, Whitney Elizabeth Wheeler, Dr. James B. Jensen

Journal of Undergraduate Research

I conducted my research in Ashanti-Mampong, Ghana, West Africa over the course of 3 months. My project was to study the medical options available to patients that had malaria and/or worms.

Development Of A Novel Human Vestibular Schwannoma Xenograft Model In Scid Mice, John Welling, Dr. Kim O'Neil

Journal of Undergraduate Research

Vestibular Schwannoma (VS) is a benign, slow growing tumor that arises from the myelin sheath of the vestibular nerve (cranial nerve VIII). The myelin sheath is composed of flat, layered cells known as Schwann cells, which serve to insulate nerve fibers. It is increased proliferation of these Schwann cells which leads to VS tumor growth. As VS tumors grow, they place increasing pressure on cranial nerve VIII, causing hearing loss, tinnitus (ringing in the ear), and balance dysfunction. Eventually VS tumors may lead to brainstem compression and even death.1

Stromal-Cell Derived Factor-1Α And Macrophages Increased Invasive Potential Of Breast Cancer Cells, Devin Twitchell, Dr. Kim L. O'Neill

Journal of Undergraduate Research

Research has demonstrated that in some tumors, up to fifty percent of a breast tumor’s mass is composed of macrophages (1). It is well recognized that macrophages can inhibit tumor growth and, paradoxically, stimulate tumor growth and metastasis depending on the proteins produced (2). Macrophages located within the tumor environment are classified as tumor-associated macrophages. The migration of cancer cells from the primary tumor to a secondary site is a multipart process. How tumors are able to proliferate and invade into foreign areas is still unclear. However, it is becoming increasingly clear that the presence of macrophages in primary tumors …

Multidisciplinary Database For Byu Fag El Gamous Excavations, Ryan Pail Peters, Richard Paul Evans

Journal of Undergraduate Research

In 1990, under the direction of Wilfred Griggs, he and six other Brigham Young University (BYU) professors, R. Paul Evans, James Farmer, Marek Kaliszewski, Donald Robertson, Mark Rowe, and Scott Woodward, and at the request of the Egyptian Government Supreme Council of Antiquities, united to begin tissue sampling and DNA analysis of the estimated 150,000 burials at the ancient Fag el Gamous cemetery in Fayum, Egypt, which was utilized approximately between 350 B.C.E. to 500 C.E.

Improved Culture Technique For Mycobacterium Ulcerans, Neal S. Thomson, Dr. Richard Robison

Journal of Undergraduate Research

Mycobacterium ulcerans is a pathogenic bacterium and is the causative agent of Buruli Ulcer, a common mycobacterial disease similar to tuberculosis and leprosy. Buruli Ulcer is endemic to Western Africa and produces a deforming and sometimes lethal skin disease. One major obstacle for research is the slow growth of the bacterium in batch culture. M. ulcerans currently grows in vitro with a doubling time of about 4.8 days, resulting in an average culture time of 8-10 weeks before the appearance of colonies. This evidence makes it difficult to study M. ulcerans in the laboratory. The goal of my research was …

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 …