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A Weak Structural Approach To Decentralized Control, David Ward, Dr. Sean Warnick Aug 2013

A Weak Structural Approach To Decentralized Control, David Ward, Dr. Sean Warnick

Journal of Undergraduate Research

The research discussed here explores the interplay between dynamical structure functions, the communication structure of a controller and the zero pattern of a controller. Precisely understanding this interplay is a necessary result to utilize dynamical structure functions to help broaden the known tractable class of decentralized control problems. The long term goal of this research is to broaden the set of tractable convex decentralized control problems by utilizing the structure encapsulated in dynamical structure functions. The research highlighted here was presented during the 2010 BYU Spring research conference and published in detail as my undergraduate honors thesis “Decentralized Control Problems: …

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Identification Of Important Pathways In Cancerogenesis, Michelle Withers, Dr. W. Evan Johnson Aug 2013

Identification Of Important Pathways In Cancerogenesis, Michelle Withers, Dr. W. Evan Johnson

Journal of Undergraduate Research

The human body interacts at a cellular level through a series of events known as biological pathways. These pathways consist of communications at the molecular, cellular, and genetic levels to maintain a healthy, functional body. When the pathways are disrupted, new pathways are formed that can lead to disease. Currently, researchers are trying to understand the role of disrupted and normal pathways in cancer cells. It is necessary to understand the cancerous pathway in order to return the cell to its normal, healthy function.

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An Adaptive Bayesian Approach To Threat-Detection Modeling, Bradley Ferguson, Dr. C. Shane Reese Aug 2013

An Adaptive Bayesian Approach To Threat-Detection Modeling, Bradley Ferguson, Dr. C. Shane Reese

Journal of Undergraduate Research

Detection of biological and chemical threats is an important consideration in the modern national defense policy. Much of the testing and evaluation of threat detection technologies is performed without appropriate uncertainty quantification. Under the guidance of Dr. Shane Reese, my ORCA project dealt with developing a more effective and cost-efficient way of testing threat detection technologies. I utilized a Bayesian Gaussian Process model that allows for a more flexible and robust model t. I also developed an adaptive experimental design scheme that provides more information than a typical experimental design by learning the concentration levels that we are more interested …

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Veterinary Medicine, Jeffrey Tucker, Dr. Michael Mackay Aug 2013

Veterinary Medicine, Jeffrey Tucker, Dr. Michael Mackay

Journal of Undergraduate Research

It is not an overstatement to claim that the work Dr. Michael MacKay and I were able to conduct through the benevolence of the ORCA programme represents the cutting of history of medicine research. We have engaged a field that is strikingly underdeveloped, yet extremely relevant to early modern history. Within the last five years the World Association for the History of Veterinary Medicine has fostered new interests in veterinary history throughout this world. Our scholarship questions current interpretations of the emergence of veterinary science and demonstrates that through the creation of organized horse hospitals systematized veterinary medicine developed almost …

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Third World Water Filtration System Implementation, Christopher Welton, Perry Carter Aug 2013

Third World Water Filtration System Implementation, Christopher Welton, Perry Carter

Journal of Undergraduate Research

Approximately 70 million people in rural India do not have access to clean water. Chemicals such as cesium, arsenic, and others contaminate India’s drinking water, rendering it unsafe. Biological contaminates pose increased health risks to those drinking the water. If a water source is bad, large populations need to relocate to find a better source of water. Creating an economic water filtration system capable of being obtained through a micro-loan is beginning alleviate this problem. By creating an affordable and quality system, clean water is becoming a reality for the world’s poor, especially in Third World countries. Through my efforts …

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Increasing Bilayer Membrance Fusion Rates By Increasing Cholesterol Content, David Lee, Dr. Dixon Woodbury Aug 2013

Increasing Bilayer Membrance Fusion Rates By Increasing Cholesterol Content, David Lee, Dr. Dixon Woodbury

Journal of Undergraduate Research

A bilayer is a two-layered membrane made of lipids that form around cells. These membranes are formed by hydrophobic tails (water fearing) and hydrophilic heads (water loving) that align such that the tails are isolated from water, while the heads are exposed to water to form micelles, liposomes, or sheets (Fig. 1). They are used to regulate what can enter and exit a cell. A fusion event occurs when a liposome fuses with a sheet. In our experiments, we are able to see the effects on fusion rate by altering the cholesterol content of the sheets.

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Bridging The Gap Between Simulation And Experiment With Multi-State Protein Folding, Jacob Lewis, Dr. Thomas Knotts Aug 2013

Bridging The Gap Between Simulation And Experiment With Multi-State Protein Folding, Jacob Lewis, Dr. Thomas Knotts

Journal of Undergraduate Research

Proteins are made up of extremely long chains of amino acids. Depending on it constituent amino acids, proteins fold in many 3-dimensional patterns to facilitate various biochemical processes such as catalyzing chemical reactions which allow us to live. How proteins fold is thought to be the “holy grail” of biochemistry research and, as of yet, no one has been able to predict exactly how a given sequence of amino acids will fold a priori. Protein folding has been probed in experiment and simulated on computers, but there are discrepancies between the two methods. Naturally, the experimental results are what computer …

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Transformative Processes In Marriage: Effects On Father-Adolescent Relationships, Brandon Mcdaniel, Dr. Erin Holmes Aug 2013

Transformative Processes In Marriage: Effects On Father-Adolescent Relationships, Brandon Mcdaniel, Dr. Erin Holmes

Journal of Undergraduate Research

Researchers suggest that marital processes and the father-child relationship are linked (Holmes, Duncan, Bair, & White, 2007). Unfortunately, much of this work focuses on negative marital processes. For example, low marital satisfaction, emotional distance between spouses, and high marital conflict undermine father involvement by increasing risk for divorce (Clements, Stanley, & Markman, 2004), lowering parenting quality (Erel & Burman, 1995), and decreasing child adjustment (Grych & Fincham, 2001).

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Phytoestrogens: Effects On Male Sexual Health Parameters, Trevor Hansen, Dr. Edwin Lephart Aug 2013

Phytoestrogens: Effects On Male Sexual Health Parameters, Trevor Hansen, Dr. Edwin Lephart

Journal of Undergraduate Research

Phytoestrogens are estrogen-like molecules derived from soy-based foodstuffs such as soybeans, tofu and even certain cereals. In particular, our study focused on a subclass of phytoestrogens called isoflavones. Of the many isoflavones, daidzene and genistein are thought to exert the most potent estrogenic hormone activity, and thus have been the subject of much recent research.

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“A Rose By Any Other Name…” A Study Of Flowering Plant Classification And Species Recognition, Angela Jensen, Dr. Leigh Johnson Aug 2013

“A Rose By Any Other Name…” A Study Of Flowering Plant Classification And Species Recognition, Angela Jensen, Dr. Leigh Johnson

Journal of Undergraduate Research

Speciation is a scientific “gray area.” Conservation biologists are familiar with the many different proposed definitions for a species, encased in the 10 or so existing species concepts. Individual organisms of the same species are inherently different, possessing a wide variety of characteristics and behaviors. When is an individual a new species? Why does it matter?

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Moving Nucleosomes To Regulate And Maintain Gene Function, Benjamin Jorgensen, Dr. Steven Johnson Aug 2013

Moving Nucleosomes To Regulate And Maintain Gene Function, Benjamin Jorgensen, Dr. Steven Johnson

Journal of Undergraduate Research

Gene therapy is a technique that uses gene insertions or transgenes to alter and correct genetic mutations that cause hereditary diseases. Gene therapy holds hope in curing diseases such as Cystic Fibrosis and Duchenne Muscular Dystrophy or any disease caused by a recessive mutation in a single gene target. Transgenes may be incorporated into the nuclei of the patient’s cells, however, problems occur with the genes being turned off after time, negating the positive effects of the therapy. The goal of my research is to elucidate the contribution of underlying DNA sequences in the formation of nucleosomes (the basic unit …

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Family-Level Phylogeny Of Orthoptera (Arthropoda: Insecta) Based On Complete Mitochondrial Genome Data, Kevin Hiatt, Dr. Michael Whiting Aug 2013

Family-Level Phylogeny Of Orthoptera (Arthropoda: Insecta) Based On Complete Mitochondrial Genome Data, Kevin Hiatt, Dr. Michael Whiting

Journal of Undergraduate Research

The insect order Orthoptera (grasshoppers, katydids, and crickets) is the most diverse member of the group of polyneopteran insect orders, with more than 23,000 described species (Kevan 1982). Previous studies have recovered the monophyly of the two orthopteran suborders Caelifera (grasshoppers) and Ensifera (crickets and katydids); however, the family-level phylogeny of the order remains largely unresolved. Flook et al. (1995) sequenced the first entire orthopteran mitochondrial genome (mtgenome), and 25 complete mtgenomes are currently available on GenBank. These available mtgenomes only represent two caeliferan and four ensiferan families. Flook et al. (1995) also discovered a tRNA rearrangement (a reversal of …

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A Study Of Biological Photonic Crystals In The Internal Opal Scale Structures Of Iridescent Beetle Species In The Cerambycidae Family, Lauren Richey, Dr. John Gardner Aug 2013

A Study Of Biological Photonic Crystals In The Internal Opal Scale Structures Of Iridescent Beetle Species In The Cerambycidae Family, Lauren Richey, Dr. John Gardner

Journal of Undergraduate Research

A photonic crystal is a periodic structure that confines, manipulates, and guides photons. Such structures affect the propagation of electromagnetic waves by defining allowed and forbidden frequency bands known as photonic band gaps. Therefore, a photonic crystal can be thought of as the optical counterpart of a semiconductor, allowing only certain frequencies, or wavelengths, to propagate through the crystal. It is difficult to create photonic crystals operating in the visible frequencies due to the requirement of small periodicities to interact with visible light frequencies.

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An Evalutaion Of Robber Fly (Diptera: Asilidae) Diversity In Mongolia, Tristan Mcknight, Dr. C. Riley Nelson Aug 2013

An Evalutaion Of Robber Fly (Diptera: Asilidae) Diversity In Mongolia, Tristan Mcknight, Dr. C. Riley Nelson

Journal of Undergraduate Research

The last few decades have seen an explosion of agricultural expansion and mining in Mongolia. These developments—loosely regulated at best—strain the ecological health of the steppe environment with pollution and overgrazing. Robber flies (Fig. 1) are small predators common in most terrestrial ecosystems that may play an important, yet frequently overlooked role in maintaining balanced insect populations. Unfortunately, very little baseline data exist for evaluating robber fly diversity in Mongolia. Our study set out to provide a comprehensive catalogue of Mongolian robber flies which we hope will assist future efforts to manage and conserve Mongolia’s ecosystems.

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The Misapplication Of Dna Barcodes To Taxonomic Classification, Taylor Southwick, Dr. Keith Crandall Aug 2013

The Misapplication Of Dna Barcodes To Taxonomic Classification, Taylor Southwick, Dr. Keith Crandall

Journal of Undergraduate Research

The classification of organisms into different taxa is a central issue in biology. If similar organisms are grouped together, then comparative analyses can be used from the genome to the systems level to understand how they work, both biologically and behaviorally. There are two ways to perform this classification: morphologically and phylogenetically. Morphological demarcations are based on visual differences in anatomical structure and physiological function. Phylogenetic classification is based upon the evolutionary relationship among the individuals in the population quantified by the similarity or dissimilarity of their DNA strands.

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Evolution Of Nuclear Mitochondrial Pseudogenes Of Three Genes Within Orthoptera (Arthropoda:Insecta), Matthew Moulton, Dr. Michael Whiting Aug 2013

Evolution Of Nuclear Mitochondrial Pseudogenes Of Three Genes Within Orthoptera (Arthropoda:Insecta), Matthew Moulton, Dr. Michael Whiting

Journal of Undergraduate Research

Mitochondria are unique organelles that contain their own genomes. Metazoan mitochondrial genomes typically encode 37 genes (13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes) that are used for cellular respiration.

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Phylogeography And Population Structure Of Scottnema Lindsayae, Mac Martin, Dr. Byron Adams Aug 2013

Phylogeography And Population Structure Of Scottnema Lindsayae, Mac Martin, Dr. Byron Adams

Journal of Undergraduate Research

Glaciologists have suggested that because of the extent of the ice sheets during the last glacial maximum (LGM) in Antarctica no terrestrial species could have survived these harsh conditions. However, substantial evidence suggests that some invertebrate species did indeed survive the LGM. We hypothesize that S. lindsayae survived the LGM in Antarctica through hypothetical refugia, areas that remained ice-free during the LGM. These are coastal areas characterized by high elevation, which would have remained ice-free during the LGM and would not have been inundated under episodes of elevated sea levels.

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What Can Phylogeographic Breaks In The Livebearer Poeciliopsis Turrubarensis Tell Us About Fish Community Boundaries In Western Costa Rica?, April Larson, Dr. Jerald B. Johnson Aug 2013

What Can Phylogeographic Breaks In The Livebearer Poeciliopsis Turrubarensis Tell Us About Fish Community Boundaries In Western Costa Rica?, April Larson, Dr. Jerald B. Johnson

Journal of Undergraduate Research

One active area of study in ecology, termed biogeography, is the determination of how communities are formed. A basic knowledge of what factors have shaped the formation of ecological communities leads to greater understanding of a system as a whole and specific species interactions. One possible factor that is rarely taken into account when studying biogeography is the effect that early earth history events could have playing in the shaping of community boundaries. Molecular phylogeographic data is a useful tool in helping to determine the contribution of vicariant events in community formation. If single species genetic breaks coincide with community …

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Function Of Novel Nuclear-Variant Bone Morphogenic Protein (Nbmp2) In Muscle Fiber Type Differentiation, Nicholas Wallace, Dr. Laura Bridgewater Aug 2013

Function Of Novel Nuclear-Variant Bone Morphogenic Protein (Nbmp2) In Muscle Fiber Type Differentiation, Nicholas Wallace, Dr. Laura Bridgewater

Journal of Undergraduate Research

Bone morphogenetic proteins (BMPs) are in the transforming growth factor B (TGF-) super family of proteins, which were originally identified by their ability to induce bone formation in animals.A novel nuclear variant of BMP2 (nBMP2) was recently discovered by Dr. Bridgewater and her graduate researchers. In order to discern the exact function of this nuclear form of BMP2, nBMP2 chimeric mice were created.

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Identification Of Yersiniapseudotuberculosisgenes That Affect Congo-Red Binding, Ryan Stewart, Dr. David Erickson Aug 2013

Identification Of Yersiniapseudotuberculosisgenes That Affect Congo-Red Binding, Ryan Stewart, Dr. David Erickson

Journal of Undergraduate Research

The plague bacterium Yersiniapestis recently evolved from the enteric pathogen Yersinia pseudotuberculosis, during which time it has adopted a flea-borne lifestyle.

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Chemokine-Mediated Migration Of B-1 B Cells, Lauren Zagieboylo, Dr. Eric Wilson Aug 2013

Chemokine-Mediated Migration Of B-1 B Cells, Lauren Zagieboylo, Dr. Eric Wilson

Journal of Undergraduate Research

B-1 B cells are an understudied type of white blood cell that provide T cell-independent antibody production, allowing them to play an important role in the early immune response to many bacterial and viral pathogens. They are especially important for defense in mucosal sites, such as the intestinal tract, where many infections occur.

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Pas Kinase Interactions, Steven Sowa, Dr. Julianne Grose Aug 2013

Pas Kinase Interactions, Steven Sowa, Dr. Julianne Grose

Journal of Undergraduate Research

Signal transduction pathways are critical to the function of a cell. Correct signals help the cell to manage its resources effectively while improper or inactive signals contribute to cancer and many other human diseases. One protein involved in signal transduction is PAS kinase.

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Quantification Of Kaposi’S Sarcoma Herpesvirus Gene Expression In Infected Humanized Mice, Mark Rowan, Dr. Bradford K. Berges Aug 2013

Quantification Of Kaposi’S Sarcoma Herpesvirus Gene Expression In Infected Humanized Mice, Mark Rowan, Dr. Bradford K. Berges

Journal of Undergraduate Research

Kaposi’s Sarcoma Herpesvirus (KSHV) is a prevalent disease around the world. Some Sub- Saharan African countries have infection levels as high as 40 percent. Usually the effects of this disease are not fatal unless the infected person has already been infected with HIV or has some other immunodeficiency. If both of these problems exist, deadly cancers can form within the infected person1. Studies have shown that people with HIV are 200,000 times more likely to have Kaposi’s sarcoma (a cancer caused by KSHV) than those not infected. Until now, no competent animal model existed to study KSHV pathogenesis.

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The Effect Of Kalanchoe-Pinnata Extract On Epstein-Barr Virus, Miles Murri, Dr. Brian D. Poole Aug 2013

The Effect Of Kalanchoe-Pinnata Extract On Epstein-Barr Virus, Miles Murri, Dr. Brian D. Poole

Journal of Undergraduate Research

For the last year I have been working on a project that would test the efficacy of a potential drug on a common human virus called Epstein-Barr Virus (EBV). Though the virus often resides in a latent or dormant state, it is commonly found in nearly all adults worldwide (1). When it is active, its upregulated gene expression leads to conditions ranging from ear infections and tonsillitis to highly serious conditions like lymphomas (1). It has also been linked substantially with multiple autoimmune diseases such as Lupus (2). A certain immunosuppressive plant extract called Kalanchoe has been used traditionally as …

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Real-Time, In Vivo, Nad Biosensor, Jonathan Neubert, Dr. Julianne Grose Aug 2013

Real-Time, In Vivo, Nad Biosensor, Jonathan Neubert, Dr. Julianne Grose

Journal of Undergraduate Research

Nicotinamide adenine dinucleotide (NAD) is a crucial coenzyme used in the production of ATP and general cellular metabolism. Its structure consists of two nucleotides—pyridine and adenine—joined by a pyrophosphate bond. The pyridine allows the molecule to function as an electron carrier in the cell. In this capacity, NAD is involved in over 300 cellular reactions including enzymatic reactions in glycolysis, reactions within the TCA cycle, and especially in the electron transport chain (Grose et al, 2005). Differing levels of NAD have been associated with many pathologies, including diabetes, inflammatory syndromes, neurodegeneration, and cancer (Magni et al., 2008). Current methods of …

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Function Of Novel Nuclear Bone Morphogenetic Protein 2 In Regulating Inositol 1,4,5-Triphosphate Receptor 1 Expression, Broc Mccune, Dr. Laura Bridgewater Aug 2013

Function Of Novel Nuclear Bone Morphogenetic Protein 2 In Regulating Inositol 1,4,5-Triphosphate Receptor 1 Expression, Broc Mccune, Dr. Laura Bridgewater

Journal of Undergraduate Research

Bone morphogenetic protein 2 (Bmp2) is a well-characterized secreted transforming growth factor. Researchers in the lab of Dr. Laura Bridgewater, Brigham Young University, discovered a novel nuclear variant of Bmp2 (nBmp2)1. Preliminary data indicates that mice not expressing nBmp2 have difficulty regulating intracellular Ca2+ (unpublished). Seeking to find a molecular explanation for this observation, I performed a yeast two-hybrid (Y2H) screen to identify putative binding-partners of nBmp2. My results indicate nBmp2 binds Phospholipid scramblase 1 (PLSCR1). Zhou et al2 have shown that PLSCR1 directly binds a 15 DNA base pair sequence (hereafter called P1) ~100 base pairs upstream of the …

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The Contribution Of Ccr9 To The Homing, Migration, And Accumulation Of Iga Antibody Secreting Cells In Mouse Salivary Glands, Susanne Linderman, Dr. Eric Wilson Aug 2013

The Contribution Of Ccr9 To The Homing, Migration, And Accumulation Of Iga Antibody Secreting Cells In Mouse Salivary Glands, Susanne Linderman, Dr. Eric Wilson

Journal of Undergraduate Research

IgA is the most common antibody isotype involved in the immune system’s defense of mucosal membranes. In order to migrate and accumulate at these sites, IgA antibody secreting cells rely on chemokines. These chemokines, which are proteins differentially secreted in different tissues, bind to chemokine receptors on the cell’s surface. By discovering which receptors are important for immune cell migration to specific sites, we can gain a better understanding of how the immune system functions. This could eventually lead to better treatment of autoimmune and immunodeficiency diseases, as well as to the development of better vaccines. My goal was to …

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Assessing The Splicing Variants Of The Interferon Regulatory Factor 5 Risk Haplotype, Jared Lambert, Dr. Brian Poole Aug 2013

Assessing The Splicing Variants Of The Interferon Regulatory Factor 5 Risk Haplotype, Jared Lambert, Dr. Brian Poole

Journal of Undergraduate Research

Systemic lupus erythematosus (SLE) is an autoimmune disease which commences from the immune system producing antibodies which target the body’s own tissues and cells. There are various factors thought to be involved in the development of SLE. In this study I assessed how the splicing variants of the interferon regulatory factor (IRF5) gene are affected by a single nucleotide polymorphism (SNP) associated with risk for systemic lupus erythematosus (SLE). Through this assessment I hoped to more fully determine the mechanisms through which this risk allele affects the development of SLE. IRF5 is a cytoplasmic transcription factor gene responsible for interferon …

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The Role Of Rage In Inflammatory Lung Disease Induced By Diesel Particulate Matter, Karisa Wasley, Dr. Paul Reynolds Aug 2013

The Role Of Rage In Inflammatory Lung Disease Induced By Diesel Particulate Matter, Karisa Wasley, Dr. Paul Reynolds

Journal of Undergraduate Research

The causes of high morbidity and mortality associated with inflammatory respiratory diseases are not well understood. My research project helped to shed light on cellular signaling pathways associated with inflammatory disease, particularly those caused by or worsened by air pollutants. Asthmatics, in particular, have a difficult time dealing with common pollutants found in cities, including diesel particulate matter (PM). I focused specifically on the inflammation induced by air pollutants such as diesel PM and the activation of signaling pathways initiated by their binding with the receptors for advanced glycation end-products (RAGE). RAGE is involved developmentally in the lungs and specifically …

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There’S No Wrong Way For A Cell To Die: Caspase-Independent Programmed Cell Death Pathways Resulting In Apoptotic Characteristics, Katalyn Pickett, Dr. John D. Bell Aug 2013

There’S No Wrong Way For A Cell To Die: Caspase-Independent Programmed Cell Death Pathways Resulting In Apoptotic Characteristics, Katalyn Pickett, Dr. John D. Bell

Journal of Undergraduate Research

There are a number of ways that cells can die. One way is through apoptosis, also known as programmed cell death. This death pathway is characterized by orderly signals and mechanisms that essentially tell the cell to die without “making a mess”. Necrosis, another form of cell death, can be thought of as cell “homicide”; cells, generally in response to some environmental stress, are simply unable to survive and therefore die quickly and seemingly without regulation. Previously, the line between apoptosis and necrosis was thought to be distinct, but recent studies have shown that there are cell death pathways that …

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