Microbiology Commons^™

The Use Of Antibiotic Resistance Profiles To Access The Source Of Fecal Contamination In The Rowan County, Kentucky Watershed, Logan Harrison Burns

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Logan Harrison Burns on December 15, 2005.

The Role Of Viruses In Fe Recycling In The World's Oceans, Leo Poorvin

Doctoral Dissertations

Viral lysis is responsible for a significant fraction of bacterioplankton mortality in marine systems. This work shows that viral lysis of both heterotrophic bacterial and autotrophic cyanobacterial plankton releases iron (Fe) at a greater rate than is released from unlysed cells. These studies also show that the Fe released is bound to organic ligands, these ligands are not siderophores, and that these ligands have Fe binding stability constants similar to organic ligands found in seawater. Further, these studies have shown Fe released via viral lysis to be highly bioavailable to a range of model marine plankton and may potentially satisfy …

Understanding Immune Response In Mycobacterium Ulcerans Infection, Sarojini Adusumilli

Doctoral Dissertations

Buruli ulcer is a necrotizing skin infection and is the third most important mycobacterial disease in immune competent individuals after tuberculosis and leprosy in humid tropical countries. The causative agent Mycobacterium ulcerans is unlike other mycobacterial pathogens in that it appears to maintain an extracellular location during infection. Another unusual feature of the bacterium is that it is the only mycobacterium known to produce a dermo-necrotic polyketide toxin called mycolactone. A single Buruli ulcer, which can cover 15% of a person's skin surface, contains huge numbers of extracellular bacteria. The infection is characterized by massive necrosis at the site of …

Studies On The Role Of Specific Residues Of The Saccharomyces Α-Factor Pheromone Receptor (Ste2p) In The Inactive And Active State, Yong-Hun Lee

Doctoral Dissertations

G protein-coupled receptors (GPCRs) are a class of integral membrane receptor proteins that are characterized by seven-transmembrane (7TM) domains connected by intracellular and extracellular loops, an extracellular N-terminus, and an intracellular C-terminus. To date more than 1000 GPCRs have been identified, and these proteins recognize neurotransmitters, sensory molecules and chemotactic agents. These receptors are involved in the control of many aspects of metabolism and play important roles in diverse processes such as pain perception, growth and blood pressure regulation, and viral pathogenesis. Therefore, these proteins became important target for therapeutic agents and recent reports indicate that nearly 40% of drugs …

The Bovine Coronavirus 2'-O-Methyltransferase Binds Cis-Acting Stem-Loop Iv In The 5-Prime Untranslated Region Of The Viral Genome, Tara Beth Tucker

Masters Theses

The positive-stranded coronavirus genome, at 32 kilobases in length, is the largest known viral RNA genome, and internal cis-signaling elements directing its replication have been described only within the last ten years. The bovine coronavirus genome encodes 26 proteins in the region between the 5’-terminal 210-nt untranslated region and the 3’-terminal 298-nt untranslated region. Here, genes for 5 of the 26 proteins were cloned into bacterial expression plasmids for the long-term goals of characterizing enzymatic and RNA binding properties. These genes encode enzymes postulated to interact directly with the cis-acting RNA elements and carry out RNA synthesis, namely, the …

Rdr6 Has A Broad-Spectrum But Temperature-Dependent Antiviral Defense Role In Nicotiana Benthamiana, Feng Qu, Xiaohong Ye, Guichuan Hou, Shirley Sato, Thomas E. Clemente, Thomas Jack Morris

Nebraska Center for Virology: Faculty Publications

SDE1/SGS2/RDR6, a putative RNA-dependent RNA polymerase (RdRP) from Arabidopsis thaliana, has previously been found to be indispensable for maintaining the posttranscriptional silencing of transgenes, but it is seemingly redundant for antiviral defense. To elucidate the antiviral role of this RdRP in a different host plant and to evaluate whether plant growth conditions affect its role, we down-regulated expression of the Nicotiana benthamiana homolog, NbRDR6, and examined the plants for altered susceptibility to various viruses at different growth temperatures. The results we describe here clearly show that plants with reduced expression of NbRDR6 were more susceptible to all viruses tested …

Aids And Associated Malignancies, Charles Wood, William Harrington Jr.

Nebraska Center for Virology: Faculty Publications

AIDS associated malignancies (ARL) is a major complication associated with AIDS patients upon immunosuppression. Chronically immunocompromised patients have a markedly increased risk of developing lymphoproliferative disease. In the era of potent antiretrovirals therapy (ARV), the malignant complications due to HIV-I infection have decreased in developed nations where ARV is administered, but still poses a major problem in developing countries where HIV-l incidence is high and ARV is still not yet widely available. Even in ARV treated individuals there is a concern that the prolonged survival of many HIV-l carriers is likely to eventually result in an increased number of malignancies …

Validity Of Frozen Section In The Diagnosis Of Breast Lumps: 5 Years Experience At The Aga Khan University Hospital., Naila Kayani, Nuzhat Sultana

Department of Pathology and Laboratory Medicine

Abstract

Objective: To determine the accuracy of frozen section in the diagnosis of breast lump. Methods: Frozen section diagnosis given in consecutive breast biopsies performed in 5 years in our laboratory was evaluated against the final pathology report of permanent sections. Results: The Aga Khan University Hospital Lab receives more than 400 cases per year for frozen section. Three hundred and nineteen consecutive frozen sections of breast lumps examined from 1999-2003 were considered for analysis. Age of patients ranged between 22 and 90 years (mean age 49 years). In 316 cases (99%) there was no difference between the frozen section …

Pfcg2, A Plasmodium Falciparum Protein Peripherally Associated With The Parasitophorous Vacuolar Membrane, Is Expressed In The Period Of Maximum Hemoglobin Uptake And Digestion By Trophozoites, Roland A. Cooper, Janni Papakrivos, Kristen D. Lane, Hisashi Fujioka, Klaus Lingelbach, Thomas E. Wellems

Roland A. Cooper

Characterization Of Metabolism In The Fe(Iii)-Reducing Organism Geobacter Sulfurreducens By Constraint-Based Modeling, Radhakrishnan Mahadevan, Daniel R. Bond, Jessica E. Butler, Abraham Esteve-Núñez, Maddalena V. Coppi, Bernhard O. Palsson, Christopher H. Schilling, Derek Lovley

Derek Lovley

Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism and electron transport, a metabolic model which integrated genome-based predictions with available genetic and physiological data was developed via the constraint-based modeling approach. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed that energy conservation with extracellular electron acceptors, such as Fe(III), was limited relative to that associated …

Interspecies Transmission Of Chronic Wasting Disease Prions To Squirrel Monkeys (Saimiri Sciureus), Richard F. Marsh, Anthony E. Kincaid, Richard A. Bessen, Jason C. Bartz

Nebraska Center for Virology: Faculty Publications

Chronic wasting disease (CWD) is an emerging prion disease of deer and elk. The risk of CWD transmission to humans following exposure to CWD-infected tissues is unknown. To assess the susceptibility of nonhuman primates to CWD, two squirrel monkeys were inoculated with brain tissue from a CWD-infected mule deer. The CWD-inoculated squirrel monkeys developed a progressive neurodegenerative disease and were euthanized at 31 and 34 months postinfection. Brain tissue from the CWD-infected squirrel monkeys contained the abnormal isoform of the prion protein, PrP-res, and displayed spongiform degeneration. This is the first reported transmission of CWD to primates.

Potential For Quantifying Expression Of The Geobacteraceae Citrate Synthase Gene To Assess The Activity Of Geobacteraceae In The Subsurface And On Current-Harvesting Electrodes, Dawn E. Holmes, Kelly P. Nevin, Regina A. O'Neil, Joy E. Ward, Lorrie A. Adams, Trevor L. Woodard, Helen A. Vrionis, Derek Lovley

Kelly Nevin

The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current …

Rhamnolipids Modulate Swarming Motility Patterns Of Pseudomonas Aeruginosa, Nicky C. Caiazza, Robert M. Q. Shanks, G. A. O'Toole

Dartmouth Scholarship

Pseudomonas aeruginosa is capable of twitching, swimming, and swarming motility. The latter form of translocation occurs on semisolid surfaces, requires functional flagella and biosurfactant production, and results in complex motility patterns. From the point of inoculation, bacteria migrate as defined groups, referred to as tendrils, moving in a coordinated manner capable of sensing and responding to other groups of cells. We were able to show that P. aeruginosa produces extracellular factors capable of modulating tendril movement, and genetic analysis revealed that modulation of these movements was dependent on rhamnolipid biosynthesis. An rhlB mutant (deficient in mono- and dirhamnolipid production) and …

Empirical Analysis Of The Str Profiles Resulting From Conceptual Mixtures, David R. Paoletti, Travis E. Doom, Carissa M. Krane, Michael L. Raymer, Dan E. Krane

Biology Faculty Publications

Samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors can be challenging and associated uncertainties can have dramatic effects on the interpretation of testing results. Using an FBI genotypes dataset, containing complete genotype information from the 13 Combined DNA Index System (CODIS) loci for 959 individuals, all possible mixtures of three individuals were exhaustively and empirically computed. Allele sharing between pairs of individuals in the original dataset, a randomized dataset and datasets of generated cousins and siblings was evaluated as were the number of loci that were necessary to reliably …

Aids And Associated Malignancies, Charles Wood, William Harrington

Papers in Virology

AIDS associated malignancies (ARL) is a major complication associated with AIDS patients upon immunosuppression. Chronically immunocompromised patients have a markedly increased risk of developing lymphoproliferative disease. In the era of potent antiretrovirals therapy (ARV), the malignant complications due to HIV-1 infection have decreased in developed nations where ARV is administered, but still poses a major problem in developing countries where HIV-l incidence is high and ARV is still not yet widely available. Even in ARV treated individuals there is a concern that the prolonged survival of many HIV-l carriers is likely to eventually result in an increased number of malignancies …

Metanephric Adenoma: A Rare Benign Renal Tumour, Nausheen Yaqoob, Jai Pal Paryani, Naila Kayani, Mohammad Zafar Rafique, Raziuddin Biyabani

Department of Pathology and Laboratory Medicine

Metanephric adenoma is a rare benign renal tumour. We are reporting one histologically proven such case in a 23 year old male from Afghanistan. He presented with severe right flank pain since 3 weeks. Nephrectomy was done and histopathology was consistent with the diagnosis of metanephric adenoma. This novel renal mass has been reported to have benign clinical course despite its symptomatic presentation and large tumour size. There is no distinguishing radiological feature with can differentiate it from malignant tumours. So far, a uniformly benign clinical course has been associated with Metanephric adenoma, but given its relatively recent identification and …

Heterotopic Glial Tissue In Tonsil: A Case Report, Nausheen Yaqoob, Zubair Ahmed, Akhtar Husain

Department of Pathology and Laboratory Medicine

We describe a six month old boy with a mass in the left tonsil. It was present since birth and was enlarging progressively. It was completely excised. Histopathology showed a choristoma of neural origin composed of glial cells--astrocytes in a fibrillary background, and a choroid plexus. Immunohistochemistry confirmed the findings.

16s Rrna Gene Sequence And Phylogenetic Tree Of Lactobacillus Species From The Vagina Of Healthy Nigerian Women, Kingsley Anukam, Emmanuel Osazuwa, Ijeoma Ahonkhai, Gregor Reid

Kingsley C Anukam

Lactobacilli are ubiquitous in nature and in humans they play a very significant role in the general health maintenance of the host. Identification of Lactobacilli has previously been based on cultutre-dependent methods and recently molecular techniques involving gene sequencing are now the ‘gold standard’. Scarce information exists in Africa on the real identity of Lactobacillus species, albeit phylogenetic distances among the species present in the human vagina. 185 vaginal swabs were collected from healthy premenopausal women (18-48 years). Bacterial DNA was extracted, amplified using PCR, with group specific Lactobacillus primers, and processed by denaturing gradient gel electrophoresis (DGGE). DGGE bands …

Suppressors Of Rna Silencing Encoded By Plant Viruses And Their Role In Viral Infections, Feng Qu, Thomas Jack Morris

Nebraska Center for Virology: Faculty Publications

Published in FEBS Letters 579:26 (October 31, 2005), pp. 5958–5964; doi 10.1016/j.febslet.2005.08.041 Copyright © 2005 Federation of European Biochemical Societies; published by Elsevier B.V. Used by permission. http://www.sciencedirect.com/science/journal/00145793

Genetic Characterization Of A Single Bifunctional Enzyme For Fumarate Reduction And Succinate Oxidation In Geobacter Sulfurreducens And Engineering Of Fumarate Reduction In Geobacter Metallireducens, Jessica E. Bulter, Richard H. Glaven, Cinthia Núñez, Abraham Esteve-Núñez, Evgenya S. Shelobolina, Daniel R. Bond, Derek Lovley

Derek Lovley

The mechanism of fumarate reduction in Geobacter sulfurreducens was investigated. The genome contained genes encoding a heterotrimeric fumarate reductase, FrdCAB, with homology to the fumarate reductase of Wolinella succinogenes and the succinate dehydrogenase of Bacillus subtilis. Mutation of the putative catalytic subunit of the enzyme resulted in a strain that lacked fumarate reductase activity and was unable to grow with fumarate as the terminal electron acceptor. The mutant strain also lacked succinate dehydrogenase activity and did not grow with acetate as the electron donor and Fe(III) as the electron acceptor. The mutant strain could grow with acetate as the electron …

Comparing The Gut Flora Of Irish Breastfed And Formula-Fed Neonates Aged Between Birth And 6 Weeks Old, Gordon Cooke, John Behan, Nicola Clarke, Winifred Gorman, Mary Costello

Articles

The exact composition of the complex microsystem that constitutes the gut flora continues to be explored as molecular methodology supplements traditional microbiological studies. The current study reports a random analysis of the faecal flora composition for 31 neonates in the 0–1 day age group, 41 neonates aged 2–5 days and 33 6-week-old neonates. All infants, born at the National Maternity Hospital, Ireland, were considered healthy, full-term normal deliveries and were either exclusively breastfed or formula-fed from birth. Microbiological and biochemical analyses of the faecal samples were used to specifically enumerate Lactobacillus spp., Bifidobacterium spp., Enterococcus spp., Staphylococcus spp., Bacteroides spp., …

Effects Of Commercial Diazinon And Imidacloprid On Microbial Urease Activity In Soil And Sod, C. W. Ingram, Mark S. Coyne, David W. Williams

Plant and Soil Sciences Faculty Publications

Diazinon [O,O-diethyl O-2-isopropyl-6-methyl(pyrimidine-4-yl) phosphorothioate] and imidacloprid [1-(1-[6-chloro-3-pyridinyl]methyl)-N-nitro-2-imidazolidinimine] are applied to lawns for insect control simultaneously with nitrogenous fertilizers such as urea, but their potential effect on urease activity and nitrogen availability in turfgrass management has not been evaluated. Urease activity in enzyme assays, washed cell assays, and soil slurries was examined as a function of insecticide concentration. Intact cores from field sites were used to assess the effect of insecticide application on urease activity in creeping bentgrass (Agrostis palustris Huds.) and bluegrass (Poa pratensis L.) sod. Bacterial urease fromBacillus pasteurii and plant …

Adaptation To Disruption Of The Electron Transfer Pathway For Fe(Iii) Reduction In Geobacter Sulfurreducens, Ching Leang, Lorrie A. Adams, Kuk-Jeong Chin, Kelly P. Nevin, Barbara A. Methѐ, Jennifer Webster, Manju L. Sharma, Derek Lovley

Kelly Nevin

Previous studies demonstrated that an outer membrane c-type cytochrome, OmcB, was involved in Fe(III) reduction in Geobacter sulfurreducens. An OmcB-deficient mutant was greatly impaired in its ability to reduce both soluble and insoluble Fe(III). Reintroducing omcB restored the capacity for Fe(III) reduction at a level proportional to the level of OmcB production. Here, we report that the OmcB-deficient mutant gradually adapted to grow on soluble Fe(III) but not insoluble Fe(III). The adapted OmcB-deficient mutant reduced soluble Fe(III) at a rate comparable to that of the wild type, but the cell yield of the mutant was only ca. 60% of that …

Survey Of Extreme Solvent Tolerance In Gram-Positive Cocci: Membrane Fatty Acid Changes In Staphylococcus Haemolyticus Grown In Toluene, Lindsey E. Nielsen, Dana R. Kadavy, Soumitra Rajagopal, Rhae A. Drijber, Kenneth W. Nickerson

Papers in Microbiology

We exploited the unique ecological niche of oil fly larval guts to isolate a strain of Staphylococcus haemolyticus which may be the most solvent-tolerant gram-positive bacterium yet described. This organism is able to tolerate 100% toluene, benzene, and p-xylene on plate overlays and saturating levels of these solvents in monophasic liquid cultures. A comparison of membrane fatty acids by gas chromatography after growth in liquid media with and without toluene showed that in cells continuously exposed to solvent the proportion of anteiso fatty acids increased from 25.8 to 33.7% while the proportion of 20:0 straight-chain fatty acids decreased from …

Extraneural Prion Neuroinvasion Without Lymphoreticular System Infection, Jason C. Bartz, Crista Dejoia, Tammy Tucker, Anthony E. Kincaid, Richard A. Bessen

Nebraska Center for Virology: Faculty Publications

While prion infection of the lymphoreticular system (LRS) is necessary for neuroinvasion in many prion diseases, in bovine spongiform encephalopathy and atypical cases of sheep scrapie there is evidence to challenge that LRS infection is required for neuroinvasion. Here we investigated the role of prion infection of LRS tissues in neuroinvasion following extraneural inoculation with the HY and DY strains of the transmissible mink encephalopathy (TME) agent. DY TME agent infectivity was not detected in spleen or lymph nodes following intraperitoneal inoculation and clinical disease was not observed following inoculation into the peritoneum or lymph nodes, or after oral ingestion. …

Identification And Characterization Of A Selective Inhibitor Of The Pim-1 Kinase, Sheldon Levon Holder

Loma Linda University Electronic Theses, Dissertations & Projects

The PIM-1 kinase is a serine/threonine kinase that has been implicated in the development of many human cancers, including leukemias, lymphomas, and prostate cancer. We have endeavored to identify and characterize a selective inhibitor of the PIM- 1 kinase. Such an inhibitor would have utility as a laboratory tool for the study of PIM-1 kinase function and as a template for the design of molecular therapeutics for diseases in which PIM-1 kinase activity is dysregulated.

Using phage display techniques we identified the peptide, HGVKKRPHNPYG, as a probable pseudosubstrate of the PIM-1 kinase with inhibitory activity in the low micromolar range …

Lymphoepithelioma-Like Carcinoma Of Urinary Bladder: (Lelca), Nausheen Yaqoob, Naila Kayani, Jaipal Piryani, Mohammad Nasir Sulaiman, Sheema H. Hasan

Department of Pathology and Laboratory Medicine

Lymphoepithelioma-like carcinoma of the bladder (LELCA) is an uncommon neoplasm of the urinary bladder and up till now only 49 cases have been reported in the English literature. It is imperative to distinguish between lymphoepithelioma-like carcinoma and malignant lymphoma as primary bladder lymphoma is extremely rare. We report a case of a 55 year old lady who presented with the complaint of burning micturition and gross hematuria for the past 5 months. There were no other known comorbids. Pelvic ultrasound was normal. Cystoscopy showed a 4x4 cm sessile mass in the bladder. Histopathological examination was consistent with the diagnosis of …

Evolutionary Innovation: A Bone-Eating Marine Symbiosis, Shana K. Goffredi, Victoria J. Orphan, Greg W. Rouse, Linda Jahnke, Tsegeria Embaye, Kendra Turk, Ray Lee, Robert C. Vrijenhoek

Shana Goffredi

Symbiotic associations between microbes and invertebrates have resulted in some of the most unusual physiological and morphological adaptations that have evolved in the animal world. We document a new symbiosis between marine polychaetes of the genus Osedax and members of the bacterial group Oceanospirillales, known for heterotrophic degradation of complex organic compounds. These organisms were discovered living on the carcass of a grey whale at 2891 m depth in Monterey Canyon, off the coast of California. The mouthless and gutless worms are unique in their morphological specializations used to obtain nutrition from decomposing mammalian bones. Adult worms possess elaborate posterior …

Atypical Pkciota Contributes To Poor Prognosis Through Loss Of Apical-Basal Polarity And Cyclin E Overexpression In Ovarian Cancer, Astrid M. Eder, Xiaomei Sui, Daniel G. Rosen, Laura K. Nolden, Kwai Wa Cheng, John P. Lahad, Madhuri Kango-Singh, Karen H. Lu, Carla L. Warneke, Edward N. Atkinson, Isabelle Bedrosian, Khandan Keyomarsi, Wen-Lin Kuo, Joe W. Gray, Jerry C. P. Yin, Jinsong Liu, Georg Halder, Gordon B. Mills

Biology Faculty Publications

We show that atypical PKCι, which plays a critical role in the establishment and maintenance of epithelial cell polarity, is genomically amplified and overexpressed in serous epithelial ovarian cancers. Furthermore, PKCι protein is markedly increased or mislocalized in all serous ovarian cancers. An increased PKCι DNA copy number is associated with decreased progression-free survival in serous epithelial ovarian cancers. In a Drosophila in vivo epithelial tissue model, overexpression of persistently active atypical PKC results in defects in apical-basal polarity, increased Cyclin E protein expression, and increased proliferation. Similar to the Drosophila model, increased PKCι proteins levels are associated with …

Outer Membrane C-Type Cytochromes Required For Fe(Iii) And Mn(Iv) Oxide Reduction In Geobacter Sulfurreducens, Teena Mehta, Maddalena V. Coppi, Susan E. Childers, Derek Lovley

Derek Lovley

The potential role of outer membrane proteins in electron transfer to insoluble Fe(III) oxides by Geobacter sulfurreducens was investigated because this organism is closely related to the Fe(III) oxide-reducing organisms that are predominant in many Fe(III)-reducing environments. Two of the most abundant proteins that were easily sheared from the outer surfaces of intact cells were c-type cytochromes. One, designated OmcS, has a molecular mass of ca. 50 kDa and is predicted to be an outer membrane hexaheme c-type cytochrome. Transcripts for omcS could be detected during growth on Fe(III) oxide, but not on soluble Fe(III) citrate. The omcS mRNA consisted …