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Initiation Of Chloroplast Dna Replication, Michael Zundel, Dr. Brent Nielson Oct 2013

Initiation Of Chloroplast Dna Replication, Michael Zundel, Dr. Brent Nielson

Journal of Undergraduate Research

Deoxyribonucleic acid (DNA) is the macromolecule found in cells that carries all of our genetic information. Eukaryotic cells contain a nucleus, where the DNA is housed. Plant cells also contain chloroplasts. Chloroplasts convert light energy into chemical energy, typically in the form of sugar. Chloroplasts contain DNA, which is thought to have evolved from an early symbiotic relationship between a eukaryotic cell and a prokaryotic cell, or bacterium. The eukaryotic cell engulfed the prokaryotic cell and used it for the conversion of light energy. Chloroplast DNA replicates independent of the cell cycle and the nuclear DNA.

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Detection Of Positive Selection In The Gp120 Protein Of Human Immunodeficiency Virus In Relation To Vaccine Trials, Theodore L. Oliphant, Dr. Keith A. Crandall Oct 2013

Detection Of Positive Selection In The Gp120 Protein Of Human Immunodeficiency Virus In Relation To Vaccine Trials, Theodore L. Oliphant, Dr. Keith A. Crandall

Journal of Undergraduate Research

This project’s purpose is to determine sites of positive selection in the gp120 envelope protein of the Human Immunodeficiency Virus (HIV). Positive selection is defined as the fixation of changes in amino acid composition in a population. A data set containing the envelope sequence from patients who contracted HIV while participating in a phase 3 efficacy trial of the AIDSVAXTM HIV vaccine was obtained from Vaxgen, the vaccine’s developer. This data is being compared with data sets taken from Genbank to identify sites along the gp120 protein which have mutated, to allow the virus to escape the antibodies generated by …

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Phosphorylation Dependent Conformational Changes Of Phob In Escherichia Coli, Allison Sparks, Dr. William Mccleary Oct 2013

Phosphorylation Dependent Conformational Changes Of Phob In Escherichia Coli, Allison Sparks, Dr. William Mccleary

Journal of Undergraduate Research

All bacteria must have a way to control cell functions when their outside environment changes. E.coli uses a phosphate signaling pathway to accomplish this. In the bacterial cell membrane, there are proteins that take up phosphate from the environment, transports it into the cell, and triggers transcription of certain genes. The system is comprised of an ATP-dependent transport system which consists of a periplasmic substrate binding protein, PstS, three membrane proteins, PstC, PstA, and PstB, a regulator, PhoU, a transmembrane histidine kinase, PhoR, and a response regulator PhoB. In this system, the response regulator, PhoB is phosphorlated and then activates …

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Purification And Characterization Of A Putative Single-Stranded Dna Binding Protein From Arabidopsis Thaliana, Andrew C. Edmondson, Dr. Brent L. Nielsen Oct 2013

Purification And Characterization Of A Putative Single-Stranded Dna Binding Protein From Arabidopsis Thaliana, Andrew C. Edmondson, Dr. Brent L. Nielsen

Journal of Undergraduate Research

DNA recombination is the exchange of segments between homologous molecules of DNA, resulting in expanded genetic diversity. Recombination provides essential genetic variation, but can also cause harmful rearrangements, resulting in genetic disorders in plants, mammals and yeast. The mechanisms and results of these events are still the subject of much research. A variety of evidence supports DNA recombination in plants, but the mechanisms are poorly understood. Researchers have proposed a bacterial RecA-mediated mechanism for DNA recombination in mitochondria based on evidence of an evolutionary relationship between bacteria and mitochondria. However, until recently, plant mitochondria had not been shown to contain …

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Creating Nutritionist Software To Aid A Poor Community In Northeastern Brazil, Jacob D. Durrant, David D. Busath Oct 2013

Creating Nutritionist Software To Aid A Poor Community In Northeastern Brazil, Jacob D. Durrant, David D. Busath

Journal of Undergraduate Research

Virgem dos Pobres is an impoverished community on the banks of lake Mundaú in the Brazilian state of Alagoas. Its dirt roads are lined with houses made of mud and plaster, and sewage is disposed of by means of an open canal that runs through the community’s center. The neighborhood’s population is afflicted with many of the diseases common to extreme poverty: bacterial infections like impetigo, malnourishment, measles, mumps, etc. It was a great privilege to be able to work in some small way to help these wonderful people.

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The Role Of Ap-1 And Related Inhibitors In Cortisol Secretion And Inflammation, D. Craig Seager, Dr. Allan Judd Oct 2013

The Role Of Ap-1 And Related Inhibitors In Cortisol Secretion And Inflammation, D. Craig Seager, Dr. Allan Judd

Journal of Undergraduate Research

Interleukin-6 (IL-6) increases the secretion of cortisol from bovine adrenal zona fasciculata (ZF) and human adrenal tumor H295R cells. However, the biochemical mechanisms involved in IL- 6-stimulated cortisol secretion are not well understood. In previous studies, it has been determined that IL-6 increases the phosphorylation of Janus kinases (JAK) and signal transducer and activators of transcription (STATs). In many tissues, the JAK-STAT pathway and the activator protein-1 (AP-1) pathways interact. AP-1 is composed of homodimers and heterodimers of the proteins c-Fos, c-Jun, JunB, and JunD. Therefore, in this study we determined the effects of IL-6 on the cellular content of …

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Permeability And Durability Effects Of Cellulose Polymer Variation In Polymer Inclusion Membranes, Jed Walker Oct 2013

Permeability And Durability Effects Of Cellulose Polymer Variation In Polymer Inclusion Membranes, Jed Walker

Journal of Undergraduate Research

Polymer inclusion membranes (PIMs) have been used as an effective means of separation of ions in solution. Due to their mechanical stability, PIMs provide a more effective method of separation than supported liquid membrane (SLM) and bulk liquid membrane (BLM) systems. PIMs also provide higher efficiency, selectivity and ease of use than the previously mentioned systems1,2. The large surface area to volume ratio that is exhibited by PIMs affords them the potential to be used in nuclear and harmful metal waste remediation on an industrial scale.

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Synthesis And Characterization Of Novel Amino-Retinoid A4-Spermine, Jeffrey Swallow, Dr. Heidi Vollmer-Snarr Oct 2013

Synthesis And Characterization Of Novel Amino-Retinoid A4-Spermine, Jeffrey Swallow, Dr. Heidi Vollmer-Snarr

Journal of Undergraduate Research

Age Related Macular Degeneration (AMD) is the leading cause of vision loss in developed countries. The accumulation of lipofuscin in the eye causes death of the retinal pigment epithelium (RPE) leading to blindness (1,2). The lipofuscin chemical A2E has been shown to have cytotoxic effect in RPE, yet much of lipofuscin has remained uncharacterized (3). We have shown that other compounds exist in lipofuscin through preliminary mass spectroscopy (MS) and high-pressure liquid chromatography (HPLC) data collected from lipofuscin samples. Our lab is working to first characterize these lipofuscin compounds and then we will also study their oxidative products in order …

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Production Of A Novel Anti-Tumor Chemotherapy Agent, Jeffrey Stephens, Dr. Merrit Andrus Oct 2013

Production Of A Novel Anti-Tumor Chemotherapy Agent, Jeffrey Stephens, Dr. Merrit Andrus

Journal of Undergraduate Research

Cancer is a condition unlike any other known to man. It is one of the leading causes of death in the United States. In 2000, over 500,000 deaths resulted from various cancers.1 This has led to an extensive search for improved ways to treat cancer, and has left a daunting challenge to develop new ways to treat this condition. The natural product Geldanamycin (GA), the most potent of the benzoquinone absamycin antibiotics, has shown to have great promise as an anti-tumor agent. The analog of Geldanamycin, 17-Allylanino-GA, is currently in clinical trials2, and the first total synthesis of GA was …

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Isolation, Structure Identification And Cytotoxic Studies Of Biologically Active Compounds In Carica Papaya Of Ghana, Kurtis S. Staples, Dr. Steven G. Wood Oct 2013

Isolation, Structure Identification And Cytotoxic Studies Of Biologically Active Compounds In Carica Papaya Of Ghana, Kurtis S. Staples, Dr. Steven G. Wood

Journal of Undergraduate Research

Carica papaya, commonly known as the papaya plant, is found in large abundance throughout the tropical regions of the planet. The fruit of the plant has been extensively studied with papain, a protease, being the center of research. Preliminary studies showed that compounds found in the leaves of the plant possessed anti-cancer properties. As alternatives for cancer treatment are constantly being sought, plant extracts have risen to the forefront in this hunt.1 An understanding of the structure and mode of activity of the compounds in this plant will further knowledge of how to develop chemotherapeutic agents.

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Synthesis Of Hiv Integrase Inhibitors, Carl Jones, Dr. Matt A. Peterson Oct 2013

Synthesis Of Hiv Integrase Inhibitors, Carl Jones, Dr. Matt A. Peterson

Journal of Undergraduate Research

We have made significant progress toward the synthesis of one branch of the library of compounds that we plan to synthesize. The scheme we have followed is shown below. Once synthesized, we plan to have the compounds tested by expert collaborators to see how well they bind HTLV integrase. In addition, they will be tested against many viruses and cancers, as well as HIV. Because they are nucleoside based, it is impossible to predict exactly what type of biological activity these compounds will have. They could possibly treat a variety of diseases.

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Preferential Infection Of Germinal Center T Cells By X4 Tropic Hiv, Christopher M. Cherry, Dr. Gregory F. Burton Oct 2013

Preferential Infection Of Germinal Center T Cells By X4 Tropic Hiv, Christopher M. Cherry, Dr. Gregory F. Burton

Journal of Undergraduate Research

HIV infects CD4 T cells through binding to CD4 and an appropriate co-receptor. Two co-receptors of concern in HIV biology are CXCR4 and CCR5 because of their affect on disease progression. The majority of transmittable HIV strains use CCR5 as a co-receptor. However, during the latter stages of disease the virus may shift from using CCR5 to using CXCR4 as its co-receptor. This change is referred to as a shift in tropism, and it is of major concern because it leads to rapid disease progression (3). The site and mechanism by which this shift occurs still elude scientists. Recent findings …

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Use Of Cationic Steroid Antibiotics To Fight Drug Resistance In Gram-Positive And Gram-Negative Bacteria, Thomas Orsak, Dr. Paul Savage Oct 2013

Use Of Cationic Steroid Antibiotics To Fight Drug Resistance In Gram-Positive And Gram-Negative Bacteria, Thomas Orsak, Dr. Paul Savage

Journal of Undergraduate Research

Drug resistance has become an increasing problem for clinical anti-bacterial needs and a major human health threat. Drug resistance emerges through structural or biochemical pathway changes that antibacterial drugs specifically target. Bacteria have the ability to rapidly mutate and gain resistance to antibacterial drugs because of their ability to reproduce rapidly. However some parts of bacterial cells need to stay consistent. The need for consistency for these parts arises from their complexity and their essential biological activities. One of these parts is the bacterial membrane.

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A2e-Dna Interaction: A Possible Mechanism For Dna Damage, Sierra Evelyn Dabell, Dr. Heidi R. Vollmer-Snarr Oct 2013

A2e-Dna Interaction: A Possible Mechanism For Dna Damage, Sierra Evelyn Dabell, Dr. Heidi R. Vollmer-Snarr

Journal of Undergraduate Research

A2E, a common fluorophore found in the retinal pigment epithelial cells of the eye has been shown to have phototoxic properties. For this reason A2E has been implicated in the progressive etiology of Age-related Macular Degeneration (AMD). If the mechanism of cell death can be understood, a possible intervention can be produced. Moreover, the benefits of researching A2E are two-fold. An understanding of bisoxirane-DNA interactions holds the possibility of revealing information about the pathology of AMD and presents itself as a possible chemotherapy through photo-dynamic therapy.

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The Role Of A2e In Amd And Chemotherapy, D. Joshua Cameron, Dr. Heidi Vollmer-Snarr Oct 2013

The Role Of A2e In Amd And Chemotherapy, D. Joshua Cameron, Dr. Heidi Vollmer-Snarr

Journal of Undergraduate Research

A2E is implicated in the etiology of AMD. We have found significant concentrations of A2E present in both lipofuscin and melanolipofuscin of human retinal pigment epithelial (RPE) cells, meaning that A2E is likely more involved in AMD than originally thought. Evidence shows that A2E, in small concentrations, is not cytotoxic alone, but becomes toxic when exposed to blue light. The light mechanism involved in A2E toxicity can be controlled and used to trigger cytotoxicity in cancer cell lines. The implications of A2E in AMD and the applications of A2E’s light triggered cytotoxicity as a possible chemotherapeutic treatment were further elucidated …

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Is Dna A Good Model Polymer?, Douglas R. Tree, Abhiram Muralidhar, Patrick S. Doyle, Kevin D. Dorfman Oct 2013

Is Dna A Good Model Polymer?, Douglas R. Tree, Abhiram Muralidhar, Patrick S. Doyle, Kevin D. Dorfman

Faculty Publications

The details surrounding the crossover from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy, and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike …

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The Luteolytic Potential Of Reduced Doses Of Prostaglandin Administered In The Ischiorectal Fossa (Irf), Jacob Brinkerhoff, Dr. Roy Silcox Oct 2013

The Luteolytic Potential Of Reduced Doses Of Prostaglandin Administered In The Ischiorectal Fossa (Irf), Jacob Brinkerhoff, Dr. Roy Silcox

Journal of Undergraduate Research

During the past few years of my education at BYU, I have had the opportunity to study and learn about the dairy industry and what types of management programs are in place to help ensure higher production and lower costs. One of the most important and beneficial reproductive management techniques used on modern dairies is called induced luteolysis or induced destruction of a corpus luteum. This management practice, which can optimize reproductive performance in cattle, involves administration of a hormone called prostaglandin F2µ (PGF).

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“The Role Of Gaba Electrical Networks In Brain Stimulation Reward”, Seth Gunderson, Dr. Scott Steffensen Oct 2013

“The Role Of Gaba Electrical Networks In Brain Stimulation Reward”, Seth Gunderson, Dr. Scott Steffensen

Journal of Undergraduate Research

The basis for my project is predicated on the rewarding properties of alcohol and other substances of abuse. We set out to further our understanding the neural system that is involved in intracranial self stimulation (ICSS) and how this system is mediated by γ-aminobutyric acid (GABA) neurons. Studies involving intravenous self administration (SA) of opiates and psychostimulants have identified specific neural substrates that mediate the reinforcing actions of these drugs and they constitute part of the same central nervous reward system that has evolved for mediating natural motivated behaviors, the mesocorticolimbic dopamine (DA) system.1,2

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The Phylogenetic Relationship Among Endangered Malagasy Astacoides Crayfish, Cynthia Del Carmen Penaflor Diaz, Dr. Keith A. Crandall Oct 2013

The Phylogenetic Relationship Among Endangered Malagasy Astacoides Crayfish, Cynthia Del Carmen Penaflor Diaz, Dr. Keith A. Crandall

Journal of Undergraduate Research

Freshwater crayfishes are taxonomically distributed among three families; two Northern Hemisphere families, Astacidae and Cambaridae and one Southern Hemisphere family, Parastacidae,which includes the Astacoides species. The phylogenetic relationships among the freshwater crayfish families and their relationships to lobster-like ancestors has generated considerable debate for at least 100 years. Because of this ongoing debate, the phylogenetic position of Parastacidae is unresolved. This study represents the first step in exploring the genetic resources of the endangered Malagasy Astacoides crayfish, and is the first large-scale phylogenetic analysis of this complex group. The results of this project will provide a phylogenetic estimate of relationships …

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The Phylogeny Of The Ephemerellidae (Ephemeroptera) Based On Molecular And Morphological Data, Jonathan Osborne, Dr. Michael Whiting Oct 2013

The Phylogeny Of The Ephemerellidae (Ephemeroptera) Based On Molecular And Morphological Data, Jonathan Osborne, Dr. Michael Whiting

Journal of Undergraduate Research

A prior analysis of the families of Ephemerelloidea, based on 49 morphological characters, supported Ephemerellidae diverging basal to all other Ephemerelloid families (McCafferty and Wang, 2000). The family Ephemerellidae contains twenty genera in two subfamilies (McCafferty and Wang, 2000) and comprises the largest family among the pannote mayflies. Members of this family are distributed throughout Holarctic and Oriental regions.

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Conservation Implications Of Chukars (Alectoris Chukar) In The United States, Randy T. Larsen, Dr. Jerran T. Flinders Oct 2013

Conservation Implications Of Chukars (Alectoris Chukar) In The United States, Randy T. Larsen, Dr. Jerran T. Flinders

Journal of Undergraduate Research

The Chukar (Alectoris chukar) is a medium-sized gallinaceous bird native to the Middle East and Asia first released in North America in 1893 in Illinois (Cottam et al. 1940). The sheer scale of subsequent releases is astonishing. Between 1931 and 1970 over 800,000 birds were released in 41 states (Hawaii included) and six Canadian provinces (Christensen 1970). Many of the initial introductions failed; however, wild populations were noted in a few western states as early as the 1940’s (Christensen 1996). Currently, persistent self-sustaining wild populations are found in California, Nevada, Arizona, Utah, Colorado, Wyoming, Idaho, Montana, Oregon, Washington, Hawaii and …

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Determination Of Hla Epitopes, Bethany S. Fredline, Dr. Keith Crandall Oct 2013

Determination Of Hla Epitopes, Bethany S. Fredline, Dr. Keith Crandall

Journal of Undergraduate Research

On June 5, 1981, the U.S. Centers for Disease Control and Prevention issued its first warning about a relatively rare form of pneumonia among a small group of young gay men in Los Angeles. Eventually the pneumonia was connected to Acquired Immune Deficiency Syndrome, better known as AIDS. The causative agent of AIDS was a human retrovirus later known as Human Immunodeficiency Virus (HIV). The HIV/AIDS epidemic has contributed to the death of 22 million people since its emergence roughly twenty years ago. Currently, 42 million people worldwide are living with either HIV or AIDS.

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Virulence Of Entomopathogenic Nematodes To The Citrus Root Weevil: A Comparison Between Indigenous And Commercially Produced Nematodes, Douglas Adolphson, Dr. Byron Adams Oct 2013

Virulence Of Entomopathogenic Nematodes To The Citrus Root Weevil: A Comparison Between Indigenous And Commercially Produced Nematodes, Douglas Adolphson, Dr. Byron Adams

Journal of Undergraduate Research

The citrus root weevil is a major pest of citrus crops in Florida and the Caribbean. Currently, entomopathogenic nematodes are being used as an insecticide against the weevil. The nematodes carry bacteria inside of them as they enter the weevil. Once inside, they release the bacteria that kill the weevil; thus providing the nematodes with nutrients to grow and replicate. These commercially produced nematodes introduce foreign organisms into the ecosystem, which could have damaging effects in the long run.

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A Novel Approach To Assessing The Metastatic Potential Of Cancer Cells, Nyall Robert London Jr., Dr. Kim O'Neill Oct 2013

A Novel Approach To Assessing The Metastatic Potential Of Cancer Cells, Nyall Robert London Jr., Dr. Kim O'Neill

Journal of Undergraduate Research

Cancer remains a major cause of death around the world today. A major problem with cancer is metastasis or the spread of cancerous cells from the tumor to a secondary location. This occurs when cancer cells break away from a primary tumor, invade the tissue, and travel through the bloodstream or lymphatic system to other parts of the body. The aim of this study was to develop a cost-effective in vivo model through which metastasis could be explored in more depth.

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Loss Of Scribble Tumor Suppressor In Human Cancers: Atypical Hscrib Expression And Localization In Malignant Breast Cancer, Daniel F. Fuja, Dr. Kim L. O'Neill Oct 2013

Loss Of Scribble Tumor Suppressor In Human Cancers: Atypical Hscrib Expression And Localization In Malignant Breast Cancer, Daniel F. Fuja, Dr. Kim L. O'Neill

Journal of Undergraduate Research

Drosophila Melanogaster has been used for years in basic developmental and genetic research, because of its short life cycle, low cost, and ease of handling. One beneficial consequence of this extensive research is an increased knowledge of human cancer progression. Multiple homologues have been found within the human model for genes initially discovered to be important in the development of Drosophila melanogaster. Three of these homologues (Hugl, hDlg, and hScrib) were initially indicated as potential tumor suppressors because of their Drosophila homologues’ roles in accurate asymmetric protein localization in the developing Drosophila neuroblast. Scribble (human homologue, hScrib), the most recently …

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The Secondary Phase Of Photorhabdus Luminescens Tt01 Is Closely Tied To The Sexual Form Of Heterorhabditis Bacteriophora, John Chaston, Dr. Byron Adams Oct 2013

The Secondary Phase Of Photorhabdus Luminescens Tt01 Is Closely Tied To The Sexual Form Of Heterorhabditis Bacteriophora, John Chaston, Dr. Byron Adams

Journal of Undergraduate Research

Heterorhabditis bacteriophora and Photorhabdus luminescens are a symbiotically associated nematode/bacterium pair that act together as potent insect killers and have been cultured en masse for distribution as an insect control agent in agricultural settings. Heterorhabditis is a nematode species that acts as a vector to penetrate the insect exoskeleton through existing openings where it subsequently releases Photorhabdus, the bacterial symbiont that it carries in its gut, into the haemocoel of the invaded insect. The bacteria produce a variety of proteases and toxins that digest the insides of the insect into nutrients they use as they rapidly replicate. The nematode then …

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Botox Cleavage Of Snare Proteins That Are Bound Together In Vitro, Josepp D. Walch, Dr. Dixon Woodbury Oct 2013

Botox Cleavage Of Snare Proteins That Are Bound Together In Vitro, Josepp D. Walch, Dr. Dixon Woodbury

Journal of Undergraduate Research

I finished my project last July (2005) just before Dr. Woodbury left for Germany to present his recent work at a few of the academic institutions of Europe. The project commenced in February of 2004.

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Snare Regulation, Deborah Adams, Dr. Dixon Woodbury Oct 2013

Snare Regulation, Deborah Adams, Dr. Dixon Woodbury

Journal of Undergraduate Research

SNARE proteins are involved in transporting molecules within our cells, but their mechanism of action is not well known (Figure 1). It is established that SNARE proteins aid in the process of vesicles docking at target membranes. When neuronal cells are excited calcium enters the cell and the docked vesicles fuse to the target membrane releasing their contents into the intercellular space called the synapse. It is not exactly known by what method calcium induces membrane fusion but it has been shown that syntaxin and synaptobrevin, or VAMP, are minimal machinery for membrane fusion (1).

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Understanding The Pathway Of Steroidogenic Acute Regulatory Protein Using Bioluminescence, Andrew Miner, Dr. Allen Judd Oct 2013

Understanding The Pathway Of Steroidogenic Acute Regulatory Protein Using Bioluminescence, Andrew Miner, Dr. Allen Judd

Journal of Undergraduate Research

Steroidogenic Acute Regulatory Protein (StAR) is a protein involved in the genesis of cortisol, testosterone, estrogen and other steroids. In fact, it is the rate-limiting step in the process of steroidogenesis. StAR is responsible for transporting cholesterol from the outside of the mitochondrial matrix to the inside, where it undergoes chemical processes that turn it into the steroids listed above. The body is thought to increase the amount of StAR in mitochondrial membranes when it receives certain signals in order to create more steroids. My topic involves the mechanism for this upregulation.

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The Effects During Embryogenesis And Tumorigenesis Of Dominant-Active Beta Catenin In Wnt Signaling, Melissa Schmidt, Dr. Jeffery Richard Barrow Oct 2013

The Effects During Embryogenesis And Tumorigenesis Of Dominant-Active Beta Catenin In Wnt Signaling, Melissa Schmidt, Dr. Jeffery Richard Barrow

Journal of Undergraduate Research

Cell communication is crucial in multiceullar organisms. Cells have therefore devised signaling pathways for intracellular communication. One of these is the Wnt signaling pathway. Wnt signaling plays an important role in cell fate decisions during embryogenesis. In the adult, Wnt signaling has been hypothesized to be essential in the maintenance of adult gut, blood, and skin tissues. Interestingly, aberrant Wnt signaling has been found to be the primary defect in all colon cancers and to be the cause of other tumors such as hepatocellular carcinoma (HCC).

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