Biochemistry, Biophysics, and Structural Biology Commons^™

Regulation Of Trypanosoma Brucei Hexokinase 1 And 2 On Multiple Levels: Transcript Abundance, Protein Expression And Enzyme Activity, Heidi Dodson

All Dissertations

Trypanosoma brucei, a unicellular eukaryotic parasite, is the causative agent of African sleeping sickness in sub-Saharan Africa. The parasite encounters two main environments as it progresses through its life cycle: the tsetse fly and the mammalian
bloodstream. Nutrient availability is distinct in the two environments, requiring the parasite to utilize diverse metabolic pathways to efficiently produce ATP for survival. Bloodstream form parasites (BSF), residing in a glucose rich environment, rely solely on
glycolysis for energy, while procyclic form (PF) parasites metabolize readily available proline and threonine in addition to glucose.
T. brucei expresses two hexokinases, the first enzyme in the …

Stealth Carbon Nanotubes: Strategies To Coat Carbon Nanotubes To Prevent Opsonization And Improve Biodistribution, Nalinikanth Kotagiri

Graduate Theses and Dissertations

Carbon nanotubes (CNT) have recently been in the limelight for its potential role in disease diagnostics and therapeutics. Even before these medical applications can be realized, there is a need to address issues like opsonization, phagocytosis by macrophages and sequestration to liver and spleen for eventual elimination from the body. We believe coating CNT with biocompatible and opsonin resistant moieties will not only help CNT in traversing the blood stream to reach the target organ, but also improve biodistribution tremendously. We set out to achieve this by firstly identifying a new compound, mAmp, which is a fluorescent derivative of the …

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 …

The Role Of Albino3 And The Lipid Environment In Chloroplast Signal Recognition Particle Targeting, Nathan Lewis

Graduate Theses and Dissertations

Signal recognition particles (SRPs) in pro- and eukaryotes function in cotranslational targeting of nascent poplypeptides to an SRP receptor at the target membrane. A unique chloroplast SRP (cpSRP) functions post-translationally to direct light-harvesting chlorophyll-binding proteins (LHCPs) to the receptor cpFtsY at the thylakoid membrane for LHCP insertion in a process involving the integral membrane protein Albino3 (Alb3) and requiring GTP. Work here focuses on understanding cpSRP targeting events at the thylakoid membrane, specifically those involving Alb3 and the lipid environment.

We show an interaction between the novel cpSRP subunit cpSRP43 and the soluble, stromal-exposed C terminus of Albino3 (Alb3-Cterm). We …

Ancient Mitochondrial Dna From Pre-Historic Southeastern Europe: The Presence Of East Eurasian Haplogroups Provides Evidence Of Interactions With South Siberians Across The Central Asian Steppe Belt, Jeremy R. Newton

Masters Theses

Studies of mitochondrial DNA (mtDNA) polymorphism have provided valuable insights for understanding patterns of human migration and interaction. The ability to recover ancient mtDNA sequence data from post-mortem bone and tissue samples allows us to view snapshots of historic gene pools firsthand, provided that great care is taken to prevent sample contamination. In this study, we analyzed the DNA sequence of the first hypervariable segment (HVSI) of the mtDNA control region, as well as a portion of the coding region, in 14 individuals from three collective burials from the Neolithic Dnieper-Donetz culture and three individuals from Bronze Age Kurgan burials, …

Transplantation Of Adult Mouse Ips Cell-Derived Photoreceptor Precursors Restores Retinal Structure And Function In Degenerative Mice, Budd A. Tucker, In-Hyun Park, Sara D. Qi, Henry J. Klassen, Caihui Jiang, Jing Yao, Stephen Redenti, George Q. Daley, Michael J. Young

Publications and Research

This study was designed to determine whether adult mouse induced pluripotent stem cells (iPSCs), could be used to produce retinal precursors and subsequently photoreceptor cells for retinal transplantation to restore retinal function in degenerative hosts. iPSCs were generated using adult dsRed mouse dermal fibroblasts via retroviral induction of the transcription factors Oct4, Sox2, KLF4 and c-Myc. As with normal mouse ES cells, adult dsRed iPSCs expressed the pluripotency genes SSEA1, Oct4, Sox2, KLF4, c-Myc and Nanog. Following transplantation into the eye of immunecompromised retinal degenerative mice these cells proceeded to form teratomas containing tissue comprising all three germ layers. At …

Determining The Effect Of Double-Stranded Rna Treatment In Ovarian Cancer, Charlotte Roberts

Theses and Dissertations

DETERMINING THE EFFECT OF DOUBLE-STRANDED RNA TREATMENT IN OVARIAN CANCER By Charlotte Faye Roberts, B.A. A thesis submitted in partial fulfillment of the requirements for the degree of Masters of Science in Biochemistry at Virginia Commonwealth University.Virginia Commonwealth University, 2011Major Director: Jessica K. Bell, Ph.D.Assistant Professor, Department of Biochemistry & Molecular Biology. Epithelial ovarian cancer is a lethal gynecological malignancy. Due to its asymptomatic nature it is typically detected in the latter metastatic stages. Standard treatment protocol involves surgical cytoreduction, followed by a combination of taxane and platinum-based chemotherapeutics. Initially this treatment is successful however, most patients face recurring tumors …

An Exploration Of Pharmacognosy And Its Potential In The Multi-Faceted Solution Required To Address Hiv/Aids In Sub-Saharan Africa, Alexandra Sassi

Pell Scholars and Senior Theses

This work has both both biological and anthropoligcal foci. It addresses research done on the medicinal properties of plants and how this research could make positive contributions to the current social and biological issues surrounding the HIV/AIDS epidemic in sub-Saharan Africa.

Differentiation Of Bacillus Endospores From Gas Chromatography-Mass Spectrometry Of Biomarkers Produced By Thermochemolysis Methylation, Tai Van Truong

Theses and Dissertations

Methods for fast, simple detection of biomarkers to detect and differentiate closely related Bacillus endospores including Bacillus anthracis (BA), Bacillus thuringiensis (BT), Bacillus atrophaeus (BG), and Bacillus cereus (BC) using thermochemolysis and methylation (TCM), coiled wire filament (CWF), solid phase micro extraction (SPME) and gas chromatography-mass spectrometry (GC-MS) were developed. The main biomarkers detected and used for differentiation include dipicolinic acid methyl ester (DPAME), fatty acid methyl esters (FAMEs), 3-methyl-2-butenoic acid methyl ester (3M2BAME), 2-butenoic acid methyl ester (2BAME), and several methylated sugars. TCM of endospores was performed based on hydrolysis and methylation at elevated temperature after the endospores were …

Functional Studies Of Human Cellular Detoxification Enzymes, Melanie Neely Willis

Department of Biochemistry: Dissertations, Theses, and Student Research

Cellular detoxification allows for the maintenance of cellular homeostasis and prevention of abnormal cell growth by clearing harmful xenobiotics and endobiotics. After oxygenation by phase I enzymes, phase II enzymes such as glucuronosyltransferases and glutathione-s-transferases conjugate a small molecule to the compound, marking it for subsequent export. Many up-stream enzymes are also essential to cellular detoxification by supplying the small compounds for conjugation. These up-stream enzymes include UDP-glucose dehydrogenase, which synthesizes UDP-glucuronate, and glutamate cysteine ligase, which catalyzes the first and rate-limiting step in the synthesis of glutathione.
UDP-glucose dehydrogenase (UGDH) is an important enzyme in human development and in …

Epistatic Roles For Pseudomonas Aeruginosa Muts And Dinb (Dna Pol Iv) In Coping With Reactive Oxygen Species-Induced Dna Damage, Laurie H. Sanders, Babho Devadoss, Geraldine V. Raja, Jaime O'Connor, Shengchang Su, Daniel J. Wozniak, Daniel J. Hassett, Anthony J. Berdis, Mark D. Sutton

Chemistry Faculty Publications

Pseudomonas aeruginosa is especially adept at colonizing the airways of individuals afflicted with the autosomal recessive disease cystic fibrosis (CF). CF patients suffer from chronic airway inflammation, which contributes to lung deterioration. Once established in the airways, P. aeruginosa continuously adapts to the changing environment, in part through acquisition of beneficial mutations via a process termed pathoadaptation. MutS and DinB are proposed to play opposing roles in P. aeruginosa pathoadaptation: MutS acts in replication-coupled mismatch repair, which acts to limit spontaneous mutations; in contrast, DinB (DNA polymerase IV) catalyzes error-prone bypass of DNA lesions, contributing to mutations. As part of …

Accumulation Of Polonium-210 In Different Species Of Fish In Lake Mead, Suraj Ghevarghese John, Shungmugam Nallaperumal, Vernon Hodge

Festival of Communities: UG Symposium (Posters)

Discovered by Pierre Curie and Marie Skłodowska-Curie in 1898, polonium is a chemical element with an atomic number of 84. This rare naturally occurring radioactive element is chemically similar to bismuth and tellurium, and forms in uranium ores. Polonium-210 is an naturally occurring radioactive element with a half-life of 138.376 days(1). This element is found in trace amounts in most organisms. Our research is focused on the accumulation of polonium-210 in fish that occupy in Lake Mead.

The sample species is chosen based on varying lake stratification (layers of the lake). This gives us a good idea of the difference …

Construction And Use Of A Direct Calorimeter To Estimate Energy Expenditure In Hibernators, Mark S. Burger, Frank Van Breukelen

Festival of Communities: UG Symposium (Posters)

Metabolic rates have traditionally been estimated through indirect calorimetry (gas exchange or respirometry) due to its ease and availability. Oxygen consumption neglects the contributions of anaerobic metabolism, while direct calorimetry (heat production) estimates both anaerobic and aerobic metabolism. Walsberg and Hoffman (2005) report anaerobic metabolism may be more important to small rodents than was previously thought. During the non-steady state of mammalian hibernation, we hypothesize that anaerobic processes may play an even greater role in fueling metabolism. To address this question, we constructed a very sensitive calorimeter that utilizes the Seebeck effect from a thermoelectric element (Peltier device). We describe …

The Release Of Calcium In Bacillus Anthracis Pathogenicity Methods, Natiera Magnuson, Manomita Patra Bhowmik, Maria Elena Reynaga, Ernesto Abel-Santos

Festival of Communities: UG Symposium (Posters)

Anthrax infection starts with germination of Bacillus anthracis spores in macrophages. Some bacteria, including B. anthracis, can sporulate in response to environmental stress, such as starvation. During germination, large concentrations of calcium ions are released from the B. anthracis spore. Calcium ions are hydrophilic secondary messengers, and may therefore interfere with detection of the spore by confusing the cell signaling pathways. We investigated calcium release on infected macrophage viability by replacing the calcium stored in B. anthracis spores for other cations via demineralization/remineralization. It was discovered that calcium ions typically out-performed other cations in germination of B. anthracis.

Characterization Of Ips Pini Ipsdienol Dehydrogenase (Idol Dh), Heidi Pak, Claus Tittiger, William Welch

Festival of Communities: UG Symposium (Posters)

Ipsdienol is an important pheromone component for pine engraver beetle, Ips pini. Ipsdienol is a ten carbon monoterpenoid secondary alcohol and ipsdienone is the corresponding ketone. We are characterizing the activity of recombinant IDOL DH produced in Sf9 (insect) cells. The enzyme has a high stereospecificity: (-) ipsdienol was found to be a substrate while (+)-ipsdienol was neither a substrate nor inhibitor. Closely related monoterpenoids, such as nerol, geraniol, and citral, were neither substrates nor inhibitors. Smaller compounds, such as 2-propanol, also failed to act as an inhibitor or substrate. This indicates the binding site of this enzyme is highly …

Effect Of Temperature And Oxygen Levels On Lactate Production In Palaemonetes Pugio, Robin Schofield, Teresa Mika, Carl Reiber

Festival of Communities: UG Symposium (Posters)

Oxygen delivery rates must keep pace with the increased metabolic rate observed in poikilothermic animals exposed to increased temperature if aerobic metabolism is to be maintained. Physical failure of the oxygen delivery system to meet these demands may be a mechanism of cardiac failure in crustaceans at temperature extremes. As part of the determination of the effect of temperature on the cardio-respiratory system, we are measuring whole animal lactate levels in grass shrimp acclimated to 20°C over temperature ranges in normoxic and hyperoxic conditions. Lactate levels are measured as an indicator of a switch from aerobic to anaerobic metabolism. Animals …

Dicarbonyldichloridobis(Trimethylphosphane)Iron(Ii)–Carbonyldichloridotris(Trimethylphosphane)Iron(Ii)–Tetrahydrofuran (1/1/2), Nigam Rath, Meghan Stouffer, Matthew Janssen, John Bleeke

Chemistry & Biochemistry Faculty Works

The asymmetric unit of the title crystal, [FeCl2(C3H9P)3(CO)]·[FeCl2(C3H9P)2(CO)2]·2C4H8O, contains half mol­ecules of the two closely related FeII complexes lying on mirror planes and a tetra­hydro­furan solvent mol­ecule, one C atom of which is disordered over two sets of sites with site occupancy factors 0.633 (9) and 0.367 (9). In both FeII complex mol­ecules, a distorted octa­hedral coordination geometry has been observed around the Fe atoms. Weak intermolecular C-H...O inter­actions are observed in the crystal structure.

Determining The Composition Of The Dwelling Tubes Of Antarctic Pterobranchs, Lukasz J. Sewera

Honors Projects

Pterobranchs are a group of marine invertebrates within the Hemichordata, which share characteristics with both chordates and echinoderms.  Pterobranchs live in colonies of secreted tubes, coenicia, which are composed of a gelatinous material of unknown composition.  Visually, the tubes appear similar to the tunic of tunicates, a group of invertebrates within the Chordata. The nonproteinaceous tunic of tunicates is composed of cellulose, which is unusual.  The goal of this study was to determine the composition of the pterobranch coenicium. Some aspects of pterobranch phylogeny are still unclear even after multiple molecular and morphological studies.  Identification of any new shared characteristics …

Molecular Structures Of Prrsv That Contribute To Prrsv Protective Immunity, Asit K. Pattnaik

School of Veterinary and Biomedical Sciences: Faculty Publications

One of the objectives of the proposal is to delineate the regions of the two glycoproteins (GP2 and GP4) of PRRSV that interact with CD163. Other objectives of the proposal are to generate antibodies to these small regions of the glycoproteins as well as to the full-length proteins for future studies to determine if any of these antibodies possess PRRSV neutralizing activity.

To carry out the studies in the proposed objectives, we generated a series of mutants of GP2 as well as GP4 proteins in which various regions were specifically removed by manipulating the plasmids encoding these proteins. We then …

Activation Of Multiple Apoptotic Pathways In Human Nasopharyngeal Carcinoma Cells By The Prenylated Isoflavone, Osajin, Tsung-Teng Huang, Fu-Guo Liu, Chia-Fong Wei, Chia-Chen Lu, Chang-Chieh Chen, Hung-Chi Lin, David M. Ojcius, Hsin-Chih Lai

All Dugoni School of Dentistry Faculty Articles

Osajin is a prenylated isoflavone showing antitumor activity in different tumor cell lines. The underlying mechanism of osajin-induced cancer cell death is not clearly understood. In the present study, the mechanisms of osajin-induced cell death of human nasopharyngeal carcinoma (NPC) cells were explored. Osajin was found to significantly induce apoptosis of NPC cells in a dose- and time-dependent manner. Multiple molecular effects were observed during osajin treatment including a significant loss of mitochondrial transmembrane potential, release of cytochrome c into the cytosol, enhanced expression of Fas ligand (FasL), suppression of glucose-regulated protein 78 kDa (GRP78), and activation of caspases-9, -8, …