Microbiology Commons^™

Chlorovirus Skp1 And Core Ankyrin-Repeat Protein Interplay And Mimicry Of Cellular Ubiquitin Ligase Machinery, Eric Andrew Noel

School of Biological Sciences: Dissertations, Theses, and Student Research

The ubiquitin-proteasome system is a common target of several unrelated viruses that have evolved convergent strategies to redirect host ubiquitin machinery to serve their own needs. Members of the genus Chlorovirus, a group of large dsDNA viruses that infect certain freshwater chlorella-like green algae, encode a conserved Skp1 homolog and ankyrin-repeat (ANK) proteins, some of which contain C-terminal domains characteristic of cellular F-boxes or related viral PRANC domains. These observations suggested that this unique combination of chlorovirus proteins either interact with or imitate the key components of the SCF (Skp1-Cul1-F-box) ubiquitin ligases. Using mass spectrometry, we identified two functional …

The Role Of The N-Terminus On The Enzymatic Activity Of Dutpase From Dictyostelium Discoideum, Kyle C. Varon

School of Biological Sciences: Dissertations, Theses, and Student Research

The enzyme deoxyuridine triphosphatase (dUTPase) (EC 3.6.1.23) converts dUTP to dUMP, thus shifting the dUTP to dUMP ratio in the cell. The molecule dUTP is subject to mis-incorporation into DNA due to lack of distinguishing by DNA polymerase. Uracil incorporation can be repaired with base excision repair mechanisms but may create overwhelming DNA strand breaks proving to be detrimental to the cell. Most dUTPases of eukaryotes are homotrimeric and contain five highly conserved motifs responsible for catalysis and substrate binding. Many dUTPases of eukaryotes possess a leading and core region in their sequence. The core region is composed of the …

Biological Surveys Of Selected Lower Grand River Streams: Ionia, Kent, Muskegon, And Ottawa Counties, Michigan, August-September 2014, Michigan Department Of Environmental Quality Water Resources Division

Faculty and Professional Research

The biologic integrity and physical habitat conditions of the lower Grand River (Hydrologic Unit Code (HUC) 04050006) and selected tributaries were surveyed during August and September 2014 by staff of the Surface Water Assessment Section (SWAS), Water Resources Division (WRD). The objectives of this study were to: 1. Evaluate the attainment status of the other indigenous aquatic life and wildlife (OIALW) designated use. 2. Identify and investigate effects of nonpoint sources (NPS) of pollution. 3. Satisfy monitoring requests submitted by internal and external customers.

Analysis Of Nucleosome Mobility, Fragility, And Recovery: From Embryonic Stem Cells To Invitrosomes, Ashley Nicolle Wright

Theses and Dissertations

Several factors direct the placement of specific nucleosomes, which in turn have the ability to regulate DNA accessibility. These factors include, but are not limited to, nucleotide sequence preference, nucleotide modifications, the type of histones present within the nucleosome, and the presence of additional transcription factor or chromatin remodelers. A combination of these and other factors are responsible for tightly controlled efficient transcription within the eukaryotic cell. In order to contribute to the understanding of these complicated processes, three separate hypothesis-driven investigations were carried out. First, we looked into nucleosome positioning and phasing within closely related cells lines. Second, we …

Temporal Variations In The Abundance And Composition Of Biofilm Communities Colonizing Drinking Water Distribution Pipes, John J. Kelly, Nicole Minalt, Alessandro Culotti, Marsha Pryor, Aaron Packman

Biology: Faculty Publications and Other Works

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities …

Identification And Characterization Of Phytoplankton In Barnegat Bay, New Jersey, Nicole L. Elia

Seton Hall University Dissertations and Theses (ETDs)

Barnegat Bay is a marine estuary that encompasses 670-square miles of the eastern coast of New Jersey. The bay serves as a home to thousands of species of plants, animals, and microorganisms. During the summer months, the population of the bay increases from 576,000 to over 1.5 million residents. In 2011, the Barnegat Bay Partnership reported that environmental conditions of the bay are declining due to increased pollutants from nutrient fertilizers and runoff. Increased nitrogen levels have led to eutrophication and proliferation of phytoplankton algal blooms. Harmful algal blooms (HABs) cause a decrease in dissolved oxygen levels in the water …

The Use Of Natural Products As Potential Anti-Pseudomonas Agents, Margaret B. Bell

Seton Hall University Dissertations and Theses (ETDs)

Pseudomonas is a genus of gram-negative gammaproteobacteria with a large range of diversity. Because of its ability to grow at low temperature, Pseudomonas is a cause of food spoilage. This bacterium is also a very common nosocomial infection of hospital patients. In this study, we investigated the effects of different natural products on Pseudomonas. The products included a polysaccharide, two flavonoids tangeretin and nobiletin and their derivatives, 5’OH-tangeretin and 5’OH-nobiletin, black tea polyphenol – theaflavins (TFs), as well as an herb named Fallopia multiflora (Chinese Knotweed). P. fluorescens and P. aeruginosa were used as model organisms. Antimicrobial effects were …

Identification And Characterization Of Microbial Contaminants And Associated Bacterial Viruses In Bioethanol Production Facilities To Suggest A Potential Alternative To Antibiotic Treatment, Charles Austin Coomer

Mahurin Honors College Capstone Experience/Thesis Projects

In recent years, bioethanol has received worldwide interest as a bioenergy source. This interest has stimulated the production of substantial quantities of ethanol annually. However, the inability to produce bioethanol under sterile conditions plagues the industry, resulting in frequent microbial contamination. Bacterial contamination is one of the more challenging problems facing the bioethanol industry because contaminants drastically lower ethanol yield. Conventional methods of antibiotic application to eradicate bacterial contaminants are expensive and prohibitive. A more sustainable approach to control bacterial contamination of industrial ethanol fermentation systems is to use bacteriophages (phage). The goal of this research was to create a …

Structural Features Of The Pseudomonas Fluorescens Biofilm Adhesin Lapa Required For Lapg-Dependent Cleavage, Biofilm Formation, And Cell Surface Localization, Chelsea D. Boyd, T. Jarrod Smith, Sofiane El-Kirat-Chatel, Peter D. Newell, Yves F. Dufrêne, George A. O'Toole

Dartmouth Scholarship

The localization of the LapA protein to the cell surface is a key step required by Pseudomonas fluorescens Pf0-1 to irreversibly attach to a surface and form a biofilm. LapA is a member of a diverse family of predicted bacterial adhesins, and although lacking a high degree of sequence similarity, family members do share common predicted domains. Here, using mutational analysis, we determine the significance of each domain feature of LapA in relation to its export and localization to the cell surface and function in biofilm formation. Our previous work showed that the N terminus of LapA is required for …

Use Of Cholera Toxin B As A Vaccine Adjuvant Activates Antigen Presenting Cells And Stimulates Production Of Pro-Inflammatory Cytokines, Heather C. Romlein

Seton Hall University Dissertations and Theses (ETDs)

Francisella tularensis is an intracellular pathogen that has been classified as a category “A” bioterrorism agent by the Centers For Disease Control. To date, there is no approved vaccine to provide protection against this pathogen. Previous in vivo studies with mice have shown that a mucosally targeted vaccine preparation of inactivated F. tularensis (iFt) adjuvanted with Cholera toxin “B” (CTB), successfully granted full protection against a less virulent strain (FT LVS) of the bacterium and provided partial protection against a more virulent strain (SchuS4). However, the mechanisms of this protection are not fully understood. In this …

Marine Viral Diversity And Spatiotemporal Variability, Dawn Goldsmith

USF Tampa Graduate Theses and Dissertations

Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 10³⁰. They merit study not only because of their sheer abundance, but also because of the role they play in the Earth's biogeochemical cycles. Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump. Viral diversity is important because most viruses are host-specific. In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carbon and nutrient flows. …

The Role Of Nitrogen And Phosphorus In The Growth, Toxicity, And Distribution Of The Toxic Cyanobacteria, Microcystis Aeruginosa, James Parrish

Master's Projects and Capstones

Microcystis aeruginosa is among the most common harmful algal-blooming species in the world. Potent microcystins released by M. aeruginosa have been linked to liver failure and death in aquatic mammals, like the endangered California sea otter, and provide a serious public health risk to humans. Once characterized as a freshwater problem, M. aeruginosa is expanding on a global scale, making persistent returns in freshwater, brackish, and coastal marine ecosystems. Though commonly observed dominating aquatic ecosystems in low N:P atomic ratios less than 44:1, the reliability of N:P ratios as a tool for managing and predicting M. aeruginosa blooms is explored …

Chemical Profiling And Biological Activity Of Two Tunicate-Associated Marine Bacteria, Lyubina Yankova

Honors Scholar Theses

Marine natural products have recently been an increasingly abundant source of novel antibiotics. Given that there is an increasing resistance to current drug therapies, finding new sources such as marine natural products is essential. Tunicate-associated marine bacteria can be a significant source of antibacterial compounds. Two tunicates of the species Eudistoma were collected from Portobelo National Park on the Salmedina Reef of Panama in the Caribbean Sea. Bacteria associated with the tunicate were isolated, cultured, extracted, and fractionated. Fractions were tested against an array of clinically relevant bacterial pathogens in the BioMAP assay. Two fractions MB0086E and MB0088E demonstrated activity …

Morphometric Studies On Subadult Liza Subviridis And Sillago Sihama From Sonmiani Bay (Miani Hor), Balochistan, Pakistan, Muhammad A. Gondal, Naureen A. Qureshi, Noor U. Saher

Journal of Bioresource Management

Length-weight relationship of Liza subviridis and Sillago sihama (Family: Mugilidae; Class: Pisces and Family: Sillaginidae; Class: Pisces) in subadults sampled from Somiani Bay Balochistan, Pakistan during 2002, 2003 and 2006 was analyzed. Liza subviridis showed positive allometry (3.23) in 2002, and negative allometry during 2003 (2.95) and 2006 (1.95). Sub adults of Sillago sihama showed positive allometry during 2002 (3.10) and 2003 (3.13). An isometric condition (3.02) was observed in the samples of Sillago sihama collected from Bhaira in 2006.

On Individual, Sex And Age Differentiation Of Indian House Crow (Corvus Splendens) Call: A Preliminary Study In Potohar, Pakistan, Waqas Hameed, Inayat Ullah, Safia Janjua, Fakhar -I- Abbas, Afsar Mian

Journal of Bioresource Management

Considering importance of acoustics studies in population biology, 500 calls of the Indian House Crow (Corvus splendens) were recorded in morning - mid-afternoon hours (January-February, 2009) from 23 sites of urban areas of Potahar (Punjab, Pakistan). Calls were recorded using Sony CFS 1030 S sound records (sampling rate = 48 KHz) and edited using Sound Analysis Pro (Version 1.02). software using FFT method rate 50%, data window 9.27 ms, advanced window 1.36 ms. Through editing of calls, we selected 60 (37 ♂♂, 17 ♀♀, 6 Juvenile ♂♂) good quality spectrograms for detailed analysis. Spectrograms were characterized by rapid frequency modulations …

Review: Pollination, Pollinated And Pollinators Interaction In Pakistan, Mohammad Irshad, Elizabeth Stephen

Journal of Bioresource Management

The agriculture sector is important in the overall economy and export earnings of Pakistan. Pollination is an essential ecosystem service that depends on symbiosis between species, the pollinated and the pollinator. Animal mediated pollination contributes to the sexual production of over 90% species of modern angiosperms. Effective pollination results in increased crop production, quality improvement and more seed production. Many fruits, vegetables, edible oil crops, stimulant crops and nuts are highly dependent on bee pollination. Worldwide value of pollinators is €153 billion (217 billion US dollars). The production value of pollinated dependent crop in Pakistan is quantified to be 1.59 …

Research Note: Contribution To Mushroom Flora Of Rawalpindi-Islamabad, Pakistan, Kishwar Sultana, Naveeda Riaz, Gulshan Irshad, Ali Nauman Khan

Journal of Bioresource Management

Seven hymenomycetous fungi (mushrooms) were collected from the twin cities area during July 2008. These were identified as the members of the order Agaricales, class Basidiomycetes. They belong to five genera: *Clitocybe fragrans, *Collybia cookie, *Coprinus radians, *Coprinus sterculinus, *Volvariella bingensis, Volvariella parvula, and Termitomyces microcarpus. Five of them, marked with asterisk were reported for the first time from Pakistan.

Diagnostic Accuracy Of C-Reactive Protein In Neonatal Sepsis, Sidra Younis, Muhammad Ali Sheikh, Amjad Ali Raza

Journal of Bioresource Management

Sepsis is the most common cause of neonatal mortality and is responsible for 30-50% of total neonatal deaths each year in developing countries. The objective of the study was to determine the diagnostic accuracy of C-reactive protein (CRP) in neonatal sepsis. Fifty nine consecutive patients with risk factors and clinical features suggestive of CRP sepsis were selected as per operational definition and fulfilling the inclusion and exclusion criteria. Detailed physical examination was carried out. Blood sample for culture and CRP was taken from all the patients. Results of blood culture and CRP were noted down in the performa. Statistical analysis …

Amino Acid Racemase Enzyme Assays, Atanas D. Radkov, Luke A. Moe

Plant and Soil Sciences Faculty Publications

Amino acid racemases are enzymes that invert the α-carbon stereochemistry of amino acids (AAs), interconverting amino acids between their L- and D-enantiomers in a reversible reaction. In bacteria, they are known to have catabolic physiological functions but are also involved in the synthesis of many D-AAs, including D-glutamate and D-alanine, which are necessary components of the peptidoglycan layer of the bacterial cell wall. As such, amino acid racemases represent significant targets for the development of bactericidal compounds. Amino acid racemases are also regarded by the biotechnological industry as important catalysts for the production of economically relevant D-AAs. Here, we provide …

Genetic Basis For The Virulence Of Enterohemorrhagic Escherichia Coli Strain Tw14359, Jason Kyle Morgan

USF Tampa Graduate Theses and Dissertations

Enterohemorrhagic Escherichia coli (EHEC) is a virulent pathotype of E. coli that is associated with major outbreaks of hemorrhagic colitis and the life-threatening kidney disease hemolytic uremic syndrome. For successful host colonization and attachment to the intestinal mucosa, EHEC requires the locus of enterocyte effacement (LEE) pathogenicity island, which encodes a type III secretion system (TTSS) responsible for secreting and translocating effector proteins into host colonocytes. Regulation of the LEE is primarily directed through the first operon, LEE1, encoding the locus encoded regulator (Ler), and occurs through the direct and indirect action of several regulators. The 2006 U.S. spinach outbreak …

Investigating Antibiotic Resistance Levels Of Salmonella Internalized In Lettuce Leaves, Jason B. Thomas

McNair Scholars Research Journal

Contamination of food crops by the human pathogen Salmonella is a food safety threat worldwide. Though using treated wastewater for irrigation is a sustainable practice, it may introduce trace levels of Salmonella that may contaminate food crops. Salmonella could develop resistance to antibiotics present in wastewater. The overall goal of the project is to increase the understanding of the public health risk associated with the use of treated wastewater to irrigate food crops. The objective of this particular study is to determine the antibiotic resistance level of Salmonella internalized in lettuce leaves. In this experiment, thirty-six plants of the lettuce …

Characterization Of A Putative Cephalotoxin From The Hemocytes Of Euprymna Scolopes, Jessie E. Scott

University Scholar Projects

Many organisms have beneficial microbial symbionts, and complex interactions between the immune system and the bacteria must occur to allow these symbioses to persist. The host immune system must recognize and preferentially tolerate the beneficial microorganisms, while simultaneously eliminating harmful pathogens. The Hawaiian bobtail squid, Euprymna scolopes, is a model organism for host-microbe interactions because of the unique light organ symbiosis. Hemocytes, the squid’s primary immune cell, infiltrate and patrol the light organ and continuously interact with the symbiont Vibrio fischeri. Using this model, several innate immunity genes have been shown to be differentially expressed in the hemocytes …

Polymorphic Membrane Protein Expression In Chlamydia/Hsv Co-Infected Cells, Julia S. Colgrove

Undergraduate Honors Theses

The Chlamydiaceae are a bacterial family that contains a single genus: Chlamydia. The genus Chlamydia consists of 9 species that are obligate, intracellular pathogens. Untreated C. trachomatis infections can lead to serious health ramifications, such as ectopic pregnancy, tubal factor infertility, pelvic inflammatory disease, and long-term pelvic pain. In this study, it was found that a primary antibody dilution of 1:400 using methanol fixed HeLA cells, as derived from Carrasco, et al. protocol, was only optimal for PMP-C staining. Pmp-A, Pmp-B, and Pmp-F were found to stain brighter with formaldehyde fixed, infected HeLa cells and using different primary antibody dilutions. …

An Examination Of Keratinophilic Fungal On Eastern Bluebird Eggshells, Edward Anthony Hillman Iii

Undergraduate Honors Theses

This study was designed to evaluate the mycobiota of Eastern Bluebird eggshells and assess the abundance of keratinophilic fungi. Samples of fungi taken from Eastern Bluebird eggshells were subcultured for identification using macroscopic and microscopic characteristics. The occurrence of a significant number of keratinophilic fungi on Eastern Bluebird eggshells poses a potential threat to developing chicks.

Plant-Microbial Interactions Change Along A Prairie Restoration Chronosequence, Anna Herzberger

Undergraduate Honors Theses

Soil microbial communities are critical in determining the performance and density of species in plant communities. However, their role in regulating the success of restorations is much less clear. This study assessed the ability of soil microbial communities to regulate the growth and performance of two potentially dominant grasses and two common forbs in prairie restorations. Specifically, I examined the effects of soil microbial communities along a restoration chronosequence from agricultural fields to remnant prairies using experimentally inoculated soils. The two grass species, Andropogon gerardii and Sorghastrum nutans, produced larger biomass with the agricultural inoculates and experienced a decline …

Cell Kinase Inhibitor Panel Reveals Multiple Targets To Prevent Replication Of Varicella-Zoster Virus, Bryan Egan Bunnell

Renée Crown University Honors Thesis Projects - All

The alphaherpesvirus that causes chicken pox and shingles, varicella-zoster virus (VZV), infects skin fibroblasts and keratinocytes. These cells are typically quiescent and it is known that VZV manipulates their intracellular environment to activate MAPK signaling cascades, cell cycle regulators, and many transcription factors for its replication. We hypothesized that inhibition of cell kinases would prevent VZV replication and also elucidate which pathways are most important. We evaluated 80 kinase inhibitors for cytotoxicity and anti-proliferative effects on human foreskin fibroblasts, and then determined their antiviral efficacy against VZV-ORF9-Luc strain. Ten well-tolerated, potent kinase inhibitors whose targets are critical mediators of VZV …

Population Dynamics Of Triticum Mosaic Virus In Various Host Species, Melissa S. Bartels

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

It has been established that RNA viruses should be genetically diverse, due to the high error rate of their RNA-dependent RNA polymerases and the lack of proof-reading capabilities. Plant RNA viruses are not as genetically diverse as expected. Evolutionary factors, such as purifying selection and bottlenecks that favor genetic stability, might be affecting plant viral populations. Otherwise RNA virus populations, with their potential for extreme diversity, might acquire a lethal number of mutations leading to the collapse of the population.

Triticum mosaic virus (TriMV) populations maintained in a controlled greenhouse environment displayed genetic stability. The mutation frequency per nucleotide of …

Fruiting Bodies Of The Social Amoeba Dictyostelium Discoideum Increase Spore Transport By Drosophila, Jeff Smith, David C. Queller, Joan E. Strassmann

Biology Faculty Research

Background: Many microbial phenotypes are the product of cooperative interactions among cells, but their putative fitness benefits are often not well understood. In the cellular slime mold Dictyostelium discoideum , unicellular amoebae aggregate when starved and form multicellular fruiting bodies in which stress-resistant spores are held aloft by dead stalk cells. Fruiting bodies are thought to be adaptations for dispersing spores to new feeding sites, but this has not been directly tested. Here we experimentally test whether fruiting bodies increase the rate at which spores are acquired by passing invertebrates.
Results: Drosophila melanogaster accumulate spores on their surfaces more quickly …

Study Of The Function Of The Mold Specific Gene Ms95 In Dna Repair In The Pathogenic, Dimorphic Fungus Histoplasma Capsulatum, Erin M. Smith

Honors Theses

Histoplasma capsulatum (Hc) is a dimorphic fungus that is the etiologic agent of the respiratory infection Histoplasmosis that is mediated by a shift from the mold phase to the pathogenic yeast phase. Genes have been identified that are specific to the mold or yeast phase in order to study the molecular biology of this shift. MS95 was identified in a subtractive cDNA library that was enriched for mold-specific genes, and has been found to be homologous to the DNA damage-responsive gene DDR48, which functions in DNA repair in Saccharomyces cerevisiae. In order to elucidate the function of MS95, a …

Effect Of Preanalytical Processing Of Thinprep Specimens On Detection Of High-Risk Human Papillomavirus By The Aptima Hpv Assay, Erik Munson, Elizabeth R. Schroeder, Kevin C. Ross, Connie Yauck, Theresa Bieganski, Robert D. Amrhein, Maureen Napierala, April L. Harkins

Clinical Lab Sciences Faculty Research and Publications

Two important preanalytical protocols performed on liquid-based cytological specimens, namely, automated cytology processing and glacial acetic acid (GAA) treatment, may occur prior to the arrival of specimens in a molecular diagnostics laboratory. Ninety-two ThinPrep vials previously positive for high-risk human papillomavirus (HPV) via the Cervista HPV HR test were preselected and alternated with 92 previously negative ThinPrep vials. The specimen set was processed in a consecutive fashion by an automated cytology processor without fastidious decontamination precautions. Carryover potential was subsequently assessed by performance of the Aptima HPV assay on aliquots from reprocessed ThinPrep vials. All previously negative ThinPrep vials yielded …