Biochemistry, Biophysics, and Structural Biology Commons^™

Biomarker Signature Classification Of Various Stress Forms, Chana L. Rich

Honors Scholar Theses

Various types of stressful conditions can have unique and important effects on immunity and can lead to dramatic consequences to health. For my University Scholar project, the characteristic biomarker signatures produced from a set of diverse stressors (e.g. psychological, biological and chemical) are being investigated. A biomarker signature is a distinctive biological indicator of a specific condition. High-throughput tools for the measurement of different cellular products have the potential to further our understanding of human disease and facilitated the identification of new biomarkers in all areas of medicine. The hypothesis that each form of stress, psychological, chemical and physical, will …

Characterization Of Arginine-82 Mutants With Non-Native Chromophores, Vivek Alaigh

Honors Scholar Theses

Bacteriorhodopsin, found in most halobacteria, is an integral protein that contains seven transmembrane alpha helices and an organic chromophore, all-trans retinal. Light energy is captured by the protein and results in a series of spectrally discrete intermediates that conclude with a proton being pumped across the membrane from the cytoplasmic side to the extracellular milieu. The most blue-shifted photo-intermediate, the M state, has been of interest for protein-based holographic memory storage devices. Bacteriorhodopsin mutants were prepared with either a 4-hydroxy retinal or 3,4-dihydro retinal analog: R82A, R82C, R82H, R82K, R82N and R82Q. The objective of this research was to investigate …

Expression Of The Porcine Reproductive And Respiratory Syndrome Virus Non-Structural Protein 3 (Nsp 3) In Escherichia Coli, Lidia Beka

Honors Scholar Theses

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is single-stranded, positive-sense RNA virus in the family Arteriviridae, order Nidovirales. PRRSV is the most economically significant viral infection of swine herds in the United States. The single-stranded RNA genome is 15 kb in length and encodes 9 open reading frames (ORF1a, ORF1b, ORF2a, ORF2b and ORFs 3 through 7). ORFs 1a and 1b encode for 13 non-structural proteins (nsp) that are suggested to be involved in transcription and viral genome replication. The exact role of non-structural proteins in PRRSV cycle is still unknown. Moreover, there is a limited availability of reagents such …

Modeling Human Immune Response To The Lyme Disease-Causing Bacteria, Yevhen Rutovytskyy

Honors Scholar Theses

The purpose of this project is to develop and analyze a mathematical model for the pathogen-host interaction that occurs during early Lyme disease.

Based on the known biophysics of motility of Borrelia burgdorferi and a simple model for the immune response, a PDE model was created which tracks the time evolution of the concentrations of bacteria and activated immune cells in the dermis. We assume that a tick bite inoculates a highly localized population of bacteria into the dermis. These bacteria can multiply and migrate. The diffusive nature of the migration is assumed and modeled using the heat equation. Bacteria …

Effects Of Vitamin E Isomer, Gamma Tocotrienol (Gt3), At Inhibiting Cell Growth And Inducing Apoptosis In Colon Cancer Cell Line Hct-116., Havya Dave

Undergraduate Honors Theses

Colorectal cancer is the third most prominent cancer world-wide and it is the second leading cause of cancer deaths in the United States. Many dietary components affect the risk of developing colorectal cancer, such as Vitamin E. Of the eight isomers of Vitamin E, four have a tocotrienol structure. Tocotrienols are found at highest concentrations in palm oil, which is ingested more in areas of Asia where the incidence of colorectal cancer is the lowest, suggesting a role of tocotrienols in the prevention of colorectal cancer. The metabolism of Arachidonic acid pathway produces a host of pro-inflammatory metabolites either by …

The Effects Of The Vitamin E Isomers Gamma Tocopherol And Gamma Tocotrienol On The Nfkb Pathway In The Pc-3 Cell Line., Brittney Rudder

Undergraduate Honors Theses

Regions along the Mediterranean and Southern Asia have lower prostate cancer incidence compared to the rest of the world. It has been hypothesized that one of the potential contributing factors for this low incidence includes a higher intake of vitamin E (tocopherols and tocotrienols). This study examines the potential of gamma tocopherol (GT) and gamma tocotrienol (GT3) to reduce prostate cancer proliferation by examining their effects on the NFκB pathway. NFκB is known to inhibit apoptosis in cancer cells. Our data shows that both GT and GT3 are capable of down regulation of NFκB precursors and up regulation of Caspase …

The Effect Of Ultraviolet Light On Cell Viability, Dna Damage And Repair In Hutchinson-Gilford Progeria Syndrome And Bj Fibroblasts., Mckayla Johnson

Undergraduate Honors Theses

Patients of Hutchinson-Gilford Progeria Syndrome (HGPS) display a rate of aging up to ten times that of normal human populations. It might be expected that HGPS cells would have a decreased ability to repair DNA damage through the cell cycle as compared to normal cells such as those of the BJ cell line since DNA damage accumulation is a hallmark phenotype of aging. On earth, we are exposed to far more ultraviolet-B (UV-B, 280-315 nm) and UV-A (315-400 nm) than UV-C (100-280 nm) radiation, since the latter is filtered-out by the atmospheric ozone layer. The relative sensitivity of prematurely aging …

Modeling Human Immune Response To The Lyme Disease-Causing Bacteria, Yevhen Rutovytskyy

Honors Scholar Theses

The purpose of this project is to develop and analyze a mathematical model

for the pathogen-host interaction that occurs during early Lyme disease.

Based on the known biophysics of motility of Borrelia burgdorferi and a

simple model for the immune response, a PDE model was created which tracks

the time evolution of the concentrations of bacteria and activated immune

cells in the dermis. We assume that a tick bite inoculates a highly

localized population of bacteria into the dermis. These bacteria can

multiply and migrate. The diffusive nature of the migration is assumed and

modeled using the heat equation. Bacteria …

A Predictive Model Which Uses Descriptors Of Rna Secondary Structures Derived From Graph Theory., Alissa Ann Rockney

Electronic Theses and Dissertations

The secondary structures of ribonucleic acid (RNA) have been successfully modeled with graph-theoretic structures. Often, simple graphs are used to represent secondary RNA structures; however, in this research, a multigraph representation of RNA is used, in which vertices represent stems and edges represent the internal motifs. Any type of RNA secondary structure may be represented by a graph in this manner. We define novel graphical invariants to quantify the multigraphs and obtain characteristic descriptors of the secondary structures. These descriptors are used to train an artificial neural network (ANN) to recognize the characteristics of secondary RNA structure. Using the ANN, …

Characterization Of Expression Of The Kcne Gene Family In Zebrafish, Danio Rerio, Lauren Vernlund

Honors Senior Capstones and Theses

The KCNE gene family codes for five transmembrane accessory proteins, "minK related peptides" or Mirps, involved in the modification of voltage-gated potassium (Kv) channels, K+ selective pores vital in the regulation of membrane potential and repolarization in all organisms. In mammals, all five KCNE gene members are conserved and active in the heart. In the zebrafish Danio rerio, there are no apparent orthologs for KCNE2 or KCNE5, yet they contain Kv channels with homologous structure, function, and Mirp regulatory behavior to other organisms. Sequence analysis of wildtype zebrafish KCNE1, 3 and 4, and rtPCR on RNA from zebrafish tissues …

Analysis Of The Mechanism By Which Ykl-40 Promotes Glioma Cell Migration, Bahiya Osrah

Theses and Dissertations

This thesis elucidates the crucial role of YKL-40 in enhancing glioma cell migration and invasion in vitro. Increased levels of YKL-40 are specifically associated with the increased invasive capacity of glioma multiforme (GBM) tumors and lower survival rate of GBM patients. In order to examine the effects of YKL-40 on the migration and invasion of GBM cells, we overexpressed YKL-40 in three different glioma cell lines. The overexpression of YKL-40 significantly enhanced glioma cells migration and invasion in vitro and also increased ERK phosphorylation, which is believed to enhance glioma cell survival, and invasiveness. Although receptors for YKL-40 are still …

Analysis Of Nfi-X3 And Stat3 Interaction And Its Functions, Etsegenet Tizazu

Theses and Dissertations

YKL-40 is a secreted protein that is highly up-regulated in malignant glioblastoma (GBM). Its expression is correlated with the invasive nature of GBMs and poor diagnosis of patients (Nigro et al., 2005). Previous research has shown that in astrocytes and GBM cells, YKL-40 expression is regulated by two transcription factors, NFI-X3 and STAT3, which form a complex with each other (Singh et al., 2011). Here, we show that the N-terminal domain of NFI-X3 is sufficient and required for its interaction with STAT3. We also show that the DNA-binding domain of NFI-X3 is required to induce YKL-40 expression. Thus, the interaction …

Hypervirulent Chlamydia Trachomatis Clinical Strain Is A Recombinant Between Lymphogranuloma Venereum (L(2)) And D Lineages, Naraporn Somboonna, Raymond Wan, David M. Ojcius, Matthew A. Pettengill, Sandeep J. Joseph, Alexander Chang, Ray Hsu, Timothy D. Read, Deborah Dean

All Dugoni School of Dentistry Faculty Articles

Chlamydia trachomatis is an obligate intracellular bacterium that causes a diversity of severe and debilitating diseases worldwide. Sporadic and ongoing outbreaks of lymphogranuloma venereum (LGV) strains among men who have sex with men (MSM) support the need for research on virulence factors associated with these organisms. Previous analyses have been limited to single genes or genomes of laboratory-adapted reference strain L₂/434 and outbreak strain L₂b/UCH-1/proctitis. We characterized an unusual LGV strain, termed L₂c, isolated from an MSM with severe hemorrhagic proctitis. L₂c developed nonfusing, grape-like inclusions and a cytotoxic phenotype in culture, …

Cerium Oxide Nanoparticles For The Detection Of Antimicrobial Resistance, Alexander J. Noll

HIM 1990-2015

The rise of antimicrobial resistance demands the development of more rapid screening methods for the detection of antimicrobial resistance in clinical samples to both give the patient the proper treatment and expedite the treatment of patients. Cerium oxide nanoparticles may serve a useful role in diagnostics due to their ability to exist in a mixed valence state and act as either oxidizing agents or reducing agents. Considering that cerium oxide nanoparticles have been shown to shift in absorbance upon oxidation, a useful method of antimicrobial resistance detection could be based on the oxidation of cerium oxide nanoparticles. Herein, an assay …

Role Of The Mar-Sox-Rob Regulon In Regulating Outer Membrane Porin Expression, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

Multiple factors control the expression of the outer membrane porins OmpF and OmpC in Escherichia coli. In this work, we investigated the role of the mar-sox-rob regulon in regulating outer membrane porin expression in response to salicylate. We provide both genetic and physiological evidence that MarA and Rob can independently activate micF transcription in response to salicylate, leading to reduced OmpF expression. MarA was also found to repress OmpF expression through a MicF-independent pathway. In the case of OmpC, we found that its transcription was moderately increased in response to salicylate. However, this increase was independent of MarA and Rob. …

Identification Of Physiological Substrates Of Plasmodium Falciparum Pfpk5, A Cdk-Like Kinase, Catherine Sullenberger

HIM 1990-2015

Malaria is one of the most devastating infectious diseases causing 1-3 million fatalities a year. The majority of these cases occur amongst children in developing countries. Malarial strains in these areas are exhibiting increasing resistance to canonical treatments proving the importance of new drug targets for anti-malarials. Identification of new drug targets is dependent upon a better understanding of the molecular biology of the parasitic agent of malaria, Plasmodium. The regulation of Plasmodium's complex life cycle is still not well understood. Elucidation of signaling pathways involved in Plasmodium cell cycle regulation will provide insights into how the parasite thrives in …

An Assessment Of Stable Hydrogen-Isotope Analysis Methods To Assign Geographic Origin To Migratory Red-Tailed Hawks (Buteo Jamaicensis), Carla Marie Ahlschwede

Department of Environmental Studies: Undergraduate Student Theses

Stable-hydrogen isotopes are becoming an increasingly popular method of studying migratory birds, though sample preparation methods may affect results.  In this study I examined feathers from red-tailed hawks (Buteo jamaicensis) to determine the relationship between measure of δD due to inter-feather variation or drying methods, assessed the accuracy of results by using two birds of known-origin and estimated possible natal origins of migratory red-tailed hawks.  Two feathers per individual were taken from 81 wild hawks caught at Hitchcock Nature Center near Crescent IA and from 2 rescued red-tailed hawks, Raptor Recovery Nebraska near Eagle, NE. 119 of the …

Evaluation Of Delivery Conditions For Cutaneous Plasmid Electrotransfer Using A Multielectrode Array, Bernadette Ferraro, Loree C. Heller, Yolmari L. Cruz, Siqi Guo, Amy Donate, Richard Heller

Bioelectrics Publications

Electroporation (EP) is a simple in vivo method to deliver normally impermeable molecules, such as plasmid DNA, to a variety of tissues. Delivery of plasmid DNA by EP to a large surface area is not practical because the distance between the electrode pairs, and therefore the applied voltage, must be increased to effectively permeabilize the cell membrane. The design of the multielectrode array (MEA) incorporates multiple electrode pairs at a fixed distance to allow for delivery of plasmid DNA to the skin, potentially reducing the sensation associated with in vivo EP. In this report, we evaluate the effects of field …

The Applications Of Graphene And Its Derivatives For Heavy Metal Removal, Clemonne John Madarang

Theses, Dissertations and Culminating Projects

Heavy metal pollution is very prevalent in our environment. The entire removal of heavy metal and organic contaminants in natural water resources will not only affect the environment itself, but also can block the toxic contaminant transfers in food chains. Currently, there are many studies being done to remove these heavy metal ions from our water, such as reduction reactions, chemical precipitation, reverse osmosis and electrolytic recovery. One of the promising techniques is adsorption. The focus of this research is using graphene and its derivatives, such as silylated graphene oxide (GO), to adsorb heavy metals, specifically, lead. This research describes …

Investigation Of Charge Recombination In Escherichia Coli Photolyase And Vibrio Cholera Cryptochrome Dash, Agnieszka Zieba

Theses, Dissertations and Culminating Projects

Proton-coupled electron-transfer (PCET) is a mechanism of great importance in protein electron transfer and enzyme catalysis, and the involvement of aromatic amino acids in this process is of much interest. The DNA repair enzyme photolyase provides a natural system that allows for the study of PCET using a neutral radical tryptophan (Trp‘). In Escherichia coli photolyase, photoreduction of the flavin adenine dinucleotide (FAD) cofactor in its neutral radical semiquinone form (FADH') results in the formation of FADH and Trp . Charge recombination between these two intermediates requires O A/T # the uptake of a proton by ~ Trp . The …

Structural And Functional Characterization Of A Putative Citmhs Protein From Bacillus Anthracis, Qi Wen Li

Renée Crown University Honors Thesis Projects - All

The growing number of strains of antibiotic-resistant bacteria poses a new threat to human health. The development of innovative strategies to treat bacterial infections is essential. The recent discovery of a new class of membrane transporters, CitMHS, unique to bacteria, presents a potential new target for antibacterial therapeutics. CitMHS is a class of secondary metal citrate membrane transporters, with only five members characterized to date (2,3,5,6,7). No crystal structures have been reported. Detailed structural and functional studies of CitMHS are essential to the understanding of infection pathways and, consequently, the ability to block such pathways. Cit_Ba is a CitMHS …

Effects Of Ethanol On Social Behavior & Brain Structure, Lua Jafari

Renée Crown University Honors Thesis Projects - All

Autism spectrum disorders are a developmental disorder characterized by abnormal social behavior. Those with autism have problems with social interactions, repetitive behaviors, and both verbal and non-verbal communication. While the cause of autism is not yet know, studies have shown that there are both genetic and environmental factors linked with autism. The amygdala is considered to be part of the “social brain”, and atypical activation and morphology of the amygdala has been seen in those with autism.

For this research project, I utilized rats subjected to acute ethanol exposure during gestation and examined exposure effects on the anatomy and biochemistry …

Germline Cyst Formation And Development In Zebrafish, Tess Cherlin

Renée Crown University Honors Thesis Projects - All

In developing pre-natal mice, germline cysts are clusters or packages of cells consisting of individual oocytes. They are formed after the primordial germ cells move to the ovary during embryogenesis. The primordial germ cells divide, but do not completely separate. The cells within the cysts are linked by intercellular bridges, which end up breaking down leading to the formation of primordial follicles. The primordial follicles are oocytes surrounded by somatic cells called granulosa cells. Only one third of the original oocytes survive cyst breakdown and become the eggs that will be used by the mouse for her reproduction. This developmental …

Determination Of The Amino Acids Involved In The Interactions Between Dpy-30 And Ash2l, Key Components Of The Mll1 Core Complex, Carey Stuart

Renée Crown University Honors Thesis Projects - All

The human version of the DPY-30 protein is homologous to the DPY-30 protein in Caenorhabditis elegans (nematode), along with other DPY-30 homologous proteins in other organisms. This protein is involved in dosage compensation of X-linked genes, balancing the levels of expression of these genes between the sexes. The mechanism by which the balancing is carried out varies from organism to organism. For example, in C. elegans hermaphrodites (XX), transcript levels of the X-linked genes are cut in half. In Drosophila, the genes on the male’s (XY) X chromosome are transcribed at twice the rate of the female’s (XX) genes. …

Microrna Regulation Of Prostate Cancer Desensitization To Androgen Receptor Antagonist Drugs During Androgen Deprivation Therapy, Robert A. Lorch

HIM 1990-2015

The current standard treatment of prostate cancer by androgen deprivation therapy involves using drugs such as bicalutamide (Casodex) to antagonistically block androgen receptors that are normally present within prostate cells. Usually, the therapy is successful in the short run at limiting the growth of prostate cancer. However, in virtually all cases tumors begin to grow aggressively again after several months of treatment and new therapies must be started. The mechanism by which these prostate cells transform from androgen sensitive to androgen independent and anti-androgen resistant is unclear. In this study, we investigated the role of microRNAs, small 15 to 18 …

Cross-Talk Of Retinoic Acid And Adrenergic Hormone Signaling May Influence Development Of Cardiac Conduction And Rhythmicity In Utero, Sabikha Alam

HIM 1990-2015

Stress hormones, adrenaline and noradrenaline, have been shown to be critical for heart development. Mice lacking dopamine greek lower case letter beta]-hydroxylase (Dbh), an enzyme responsible for synthesis of these adrenergic hormones, die during mid-gestation due to cardiac failure. Prior research showed that adrenergic cells are found within the electrical conduction system of the heart, and adrenergic deficiency leads to slowed cardiac conduction during embryogenesis. Microarray analysis of wild-type (Dbh+/+) and knockout (Dbh-/-) mouse hearts revealed significant differences in expression of retinoic acid (RA) signaling genes. RA signaling has also been shown to be critical for heart development. These data …

Analysis Of The Repair Of Topoisomerase Ii Dna Damage, Eric D. Goldstein

HIM 1990-2015

A large number of anti-cancer chemotherapeutics target DNA topoisomerases. Etoposide is a specific topoisomerase II poison which causes reversible double strand DNA breaks. The focus of this project is to analyze the repair of DNA damage induced by etoposide.. Double strand DNA break repair is mediated by through either non-homologous end joining (NHEJ) or homologous recombination. NHEJ repairs through direct ligation of a double stranded break while homologous recombination utilizes a homologous template to recover the wild type sequence. A reporter cassette, RYDR-GFP, has been stably integrated into HeLa cells. This reporter contains an ultra-high affinity topoisomerase II cleavage site …

A Tripartile Biosensor For Real-Time Snss Detection In Dna Hairpin Motif, Camha Nguyen

HIM 1990-2015

The hybridization between two complementary strands of nucleic acid is the basis for a number of applications in DNA and RNA analysis, including in vivo RNA monitoring, microarrays, SNPs detection, and so on. The short oligonucleotide probes form Watson/Crick base pairs (A-T and G-C) with the analyzed nucleic acid. Molecular beacon (MB) probe is one of the most advantageous tools for nucleic acid analysis in real-time. A traditional MB probe consists of a DNA strand folded in hairpin motif with a fluorophore attached to the 5'end and a quencher attached to the 3' end. The loop segment is complementary to …

Plant-Made Oral Vaccines Evaluation Of Capsules, James Stewart New

HIM 1990-2015

Antigen expression through the Chloroplast Transformation Technology (CTT) produces bioencapsulated subunit-vaccines, capable of eliciting immune responses when delivered orally. Considerable challenges to effective plant-based vaccines are the normalization of dosage and preservation of accumulated antigen, which is complicated by variable high water content and protease activity. This study critically examines the efficacy of lyophilization in dehydrating plant-tissues and preserving plant-derived antigens with vaccine potential. Lyophilization was optimized through gravimetric analysis using lettuce expressing Protective Antigen (PA) of Bacillus anthracis (LS-HPAG) and the human autoantigen Proinsulin (Pins) fused to Cholera toxin subunit B (LS-CTB-Pins). Lyophilization for 48-hours was sufficient treatment to …

Molecular Evolution And Historical Biogeography Of New World Birds, Brian T. Smith

UNLV Theses, Dissertations, Professional Papers, and Capstones

Deciphering the patterns of how biodiversity has evolved across time and space has remained a fundamental objective for biologists for the last 200 years. Researchers are faced with the challenge of interpreting the complexity of evolutionary patterns that have been generated over the deep history of the Earth. The advancement of DNA sequencing technology has yielded a new and powerful genetic toolkit that has allowed biologists to address novel evolutionary questions. For my dissertation research, I used molecular genetics and a statistical framework to study the evolution and historical biogeography of birds distributed in North and South America. My dissertation …