Microbiology Commons^™

Assessing The Effects Of Titanium Dioxide Nanoparticles On Microbial Communities In Stream Sediment Using Artificial Streams And High Throughput Screening, Alexandra Ozaki

Master's Theses

Nano-titanium dioxide (nano-TiO2) is an engineered nanomaterial used in a wide array of commercial products. The production and use of large amounts of nano-TiO2 is resulting in the unintended release to the environment. Nano-TiO2 is known to be cytotoxic due primarily to its ability to generate reactive oxygen species, and negative impacts on a variety of organisms have been demonstrated, but the effects of nano-TiO2 on complex microbial communities under ecologically relevant conditions have rarely been tested. We conducted a controlled manipulative experiment using recirculating model streams dosed with a one-time amendment of 1mg L-1 nano-TiO2 (specifically P25). Within one …

Antibodies To Inhibit Clostridium Difficile Adhesion To Human Gut Epithelial Cell Line, Wonbeom Paik

Master's Theses

Clostridium difficile infection (CDI) is a major hospital-acquired diarrhea that can cause life-threatening complications such as pseudomembranous colitis. CDI is caused by colonization of host with C. difficile, a Gram positive, anaerobic bacterium known to produce toxins that cause disease. Normally, the gut microbiota protects the host from CDI, but disruption of the microbial composition through antibiotic treatment can leave one vulnerable for CDI. To date, no vaccines for preventing CDI are available.

In this study, the potential of antibodies directed against specific surface molecules of C. difficile to block bacterial adherence to host gut epithelial cells was studied, in …

Functional Characterization Of The Cholera Toxin Promoter Of Vibrio Cholerae, Jennifer Dittmer

Wayne State University Dissertations

Vibrio cholerae is the bacterium responsible for the severe diarrheal disease cholera. The disease is directly caused by cholera toxin, which is secreted by the bacterium in the upper small intestinal lumen during the course of infection. Expression of cholera toxin, along with other virulence genes, is activated by the positive transcriptional regulator, ToxT. ToxT binds to DNA sequences known as toxboxes that are found within promoters of virulence genes and subsequently ToxT activates transcription. However, the toxboxes have not been previously characterized in arguably the most important virulence promoter in V. cholerae, the cholera toxin promoter (PctxAB). …

Dinitrogen Fixation In Aphotic Oxygenated Marine Environments, Eyal Rahav, Edo Bar-Zeev, Sarah Ohayon, Hila Elifantz, Natalia Belkin, Barak Herut, Margaret R. Mulholland, Iiana Berman-Frank

OES Faculty Publications

We measured N₂ fixation rates from oceanic zones that have traditionally been ignored as sources of biological N₂fixation; the aphotic, fully oxygenated, nitrate (NO¯₃)-rich, waters of the oligotrophic Levantine Basin (LB) and the Gulf of Aqaba (GA). N₂ fixation rates measured from pelagic aphotic waters to depths up to 720 m, during the mixed and stratified periods, ranged from 0.01 nmol N L^-1 d^-1 to 0.38 nmol N L^-1 d^-1. N₂ fixation rates correlated significantly with bacterial productivity and heterotrophic diazotrophs were identified from aphotic as well as …

Free-Living Amoebae In Sediments From The Lascaux Cave In France, Angela M. Garcia-Sanchez, Concepcion Ariza, Jose M. Ubeda, Pedro M. Martin-Sanchez, Valme Jurado, Fabiola Bastian, Claude Alabouvette, Cesareo Saiz Jimenez

International Journal of Speleology

The Lascaux Cave in France is an old karstic channel where the running waters are collected in a pool and pumped to the exterior. It is well-known that water bodies in the vicinity of humans are suspected to be reservoirs of amoebae and associated bacteria. In fact, the free-living amoebae Acanthamoeba astronyxis, Acanthamoeba castellanii, Acanthamoeba sp. and Hartmannella vermiformis were identified in the sediments of the cave using phylogenetic analyses and morphological traits. Lascaux Cave sediments and rock walls are wet due to a relative humidity near saturation and water condensation, and this environment and the presence of abundant bacterial …

Cure From The Cave: Volcanic Cave Actinomycetes And Their Potential In Drug Discovery, Naowarat (Ann) Cheeptham Dr., Tara Sadoway, Devon Rule, Kent Watson, Paul Moote, Laiel C. Soliman, Nicholas Azad, Kingsley Donkor, Derrick Horne

International Journal of Speleology

Volcanic caves have been little studied for their potential as sources of novel microbial species and bioactive compounds with new scaffolds. We present the first study of volcanic cave microbiology from Canada and suggest that this habitat has great potential for the isolation of novel bioactive substances. Sample locations were plot ted on a contour map that was compiled in ArcView 3.2. Over 400 bacterial isolates were obtained from the Helmcken Falls cave in Wells Gray Provincial Park, British Columbia. From our preliminary screen, of 400 isolates tested, 1% showed activity against extended spectrum ß-lactamase E. coli, 1.75% against Escherichia …

Diversity And Biosynthetic Potential Of Culturable Aerobic Heterotrophic Bacteria Isolated From Magura Cave, Bulgaria, Iva Tomova, Irina Lazarkevich, Anna Tomova, Margarita Kambourova, Evgenia Vasileva-Tonkova

International Journal of Speleology

Biocapacity of bacteria inhabiting karstic caves to produce valuable biologically active compounds is still slightly investigated. A total of 46 culturable heterotrophic bacteria were isolated under aerobic conditions from the Gallery with pre-historical drawings in MaguraCave, Bulgaria. Phylogenetic analysis revealed that most of bacterial isolates affiliated with Proteobacteria (63%), followed by Actinobacteria (10.9%), Bacteroidetes (10.9%), and Firmicutes (6.5%). A strong domination of Gram-negative bacteria (total 81%) belonging to nine genera: Serratia, Pseudomonas, Enterobacter, Sphingobacterium, Stenotrophomonas, Commamonas, Acinetobacter, Obesumbacterium, and Myroides, was observed. Gram-positive isolates were represented by the genera Bacillus, Arthrobacter, and Micrococcus. One isolate …

The Effects Of Uv Light On The Antimicrobial Activities Of Cave Actinomycetes, Devon Rule, Naowarat Cheeptham

International Journal of Speleology

The goal of this study was to determine whether actinomycetes isolated from a volcanic cave in western Canada could produce novel antimicrobial compounds against six multidrugresistant pathogens when exposed to UV light. One hundred and seventy-six actinomycete strains isolated from Helmcken Falls Cave, Wells Gray Provincial Park, BC, were screened against six pathogens using the “plug assay” in UV light and no light conditions. Of the 176 strains tested, 100 or 57% of the cave actinomycete strains had antimicrobial activities against the pathogens in 124 different instances: 35 instances when exposed to UV and no light, 30 when exposed to …

A World Review Of Fungi, Yeasts, And Slime Molds In Caves, Karen J. Vanderwolf, David Malloch, Donald F. Mcalpine, Graham J. Forbes

International Journal of Speleology

We provide a review of fungi, yeasts, and slime molds that have been found in natural solution caves and mines worldwide. Such habitats provide frequent roost sites for bats, and in eastern North America the environmental conditions that support white-nose syndrome, a lethal fungal disease currently devastating bat populations. A list of 1029 species of fungi, slime moulds, and yeasts in 518 genera have been documented from caves and mines worldwide in 225 articles. Ascomycota dominate the cave environment. Most research has been conducted in temperate climates, especially in Europe. A mean of 17.9±24.4SD fungal species are reported per study. …

La Serreta Endokarst (Se Spain): A Sustainable Value?, Antonia D. Asencio, Teodoro Espinosa

International Journal of Speleology

La Serreta endokarst (SE Spain), which UNESCO declared a World Heritage Site in 1998, was considered a sanctuary with cave art and one of the most important archaeological sites in the Mediterranean region for both the remains it hosts and the spectacular karstic landscape at the site.

To coincide with the 40th anniversary of its discovery, the La Serreta cave-chasm was adapted for public use with the intention of showing visitors the remains, which date back to prehistoric times. The solution included attempts to minimize contact with the valuables in the cave in order to alter the existing remains as …

Assessment Of A Modified Double Agar Layer Method To Detect Bacteriophage For Assessing The Potential Of Wastewater Reuse In Rural Bolivia, Sakira N. Hadley

USF Tampa Graduate Theses and Dissertations

Water scarcity is a global concern that impacts many developing countries, forcing people to depend on unclean water sources for domestic, agricultural, and industrial needs. Wastewater is an alternative water source that contains nutrients needed for crop growth. Wastewater reuse for agriculture can cause public health problems because of human exposure to pathogens. Pathogen monitoring is essential to evaluate the compliance of wastewater with established World Health Organization (WHO) and U.S. Environmental Protection Agency (EPA) wastewater reuse guidelines. Indicator organisms are commonly used to detect pathogens in water and wastewater because they are quick and easy to measure, non-pathogenic, and …

Direct And Indirect Effects Of Agrochemicals On Bacterial Pathogens And Fecal Indicator Bacteria, Zachery Staley

USF Tampa Graduate Theses and Dissertations

The presence of agrochemical residues in both urban and agricultural water bodies has become ubiquitous, often producing deleterious effects in the impacted watershed including reductions in biodiversity, alterations in species interactions, and toxicity to non-target organisms. While these effects have been studied on metazoan consumers, the consequences of agrochemical contamination on microorganisms, such as bacteria, protozoa, and viruses, are poorly understood. Agrochemicals could act directly on microorganisms, including pathogens, by either facilitating their survival or decreasing their abundance. Further, a multitude of indirect effects of agrochemicals on microorganisms are possible, whereby agrochemicals alter predation, competition, or parasitism on or available …

Mycoplasma Feriruminatoris Sp. Nov., A Fast Growing Mycoplasma Species Isolated From Wild Caprinae, Joerg Jores, Anne Fischer, Pascal Sirand-Pugnet, Andreas Thomann, Elisabeth M. Liebler-Tenorio, Christiane Schnee, Ivette Santana-Cruz, Martin Heller, Joachim Frey

All Peer-Reviewed Publications

Five Mycoplasma strains from wild Caprinae were analyzed: four from Alpine ibex (Capra ibex) which died at the Berlin Zoo between 1993 and 1994, one from a Rocky Mountain goat collected in the USA prior to 1987. These five strains represented a population different from the populations belonging to the 'Mycoplasma mycoides cluster' as tested using multi locus sequence typing, Matrix-assisted laser desorption/ionization time of flight mass spectrometry analysis and DNA-DNA hybridization. Analysis of the 16S rRNA gene (rrs), genomic sequence based in silico as well as laboratory DNA-DNA hybridization, and the analysis of phenotypic traits in particular their exceptionally …

Prenatal Stress, Depression, And Herpes Viral Titers, Pao-Chu Hsu

USF Tampa Graduate Theses and Dissertations

Recent studies suggest that some cases of prenatal depression may be associated with reactivation of latent infections of the herpesvirus family. The possible relationships among stress, prenatal depression, and herpes viral reactivation in pregnancy are understudied and the molecular pathways such as the neuroimmune biogenic amine pathway are unidentified. Chronic stress shifts the T helper-1 cell (Th1) cytokine profile to a Th2 profile, which favors virus induced pathogenesis and survival. Pregnancy is also associated with a similar Th2 dominance. In non-pregnant individuals, exposure to psychological or physical stress may be associated with latent herpes viral reactivation and could result in …

Innate Immune Responses To Respiratory Syncytial Virus: Age-Associated Changes, Terianne Maiko Wong

USF Tampa Graduate Theses and Dissertations

Respiratory syncytial virus (RSV) infection causes ~64 million cases of respiratory disease and 200,000 deaths annually worldwide, yet there is no broadly effective prophylactic or treatment regimen. RSV can produce acute respiratory illness in patients of all ages but strikes the age extremes, infants and the elderly, with highest frequency presumably due to innate immune deficiencies. A higher morbidity and mortality has been reported for the elderly above 65 years of age, which has been attributed to immune senescence. Efforts to generate an effective vaccine have thus far been unsuccessful.

The innate immune system provides the first line of defense …

Persistent Infection With Human Herpesvirus-6 In Patients With An Inherited Form Of The Virus: A Newly Described Disease, Shara Pantry

USF Tampa Graduate Theses and Dissertations

Human Herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are ubiquitous betaherpesviruses. Both viruses are associated with a variety of adult disorders including neurological disorder, such as multiple sclerosis and chronic fatigue syndrome. HHV-6 viruses are capable of establishing latency by integration into the telomeres of the host chromosome and are transmitted in a Mendelian manner in approximately one percent of the population. To date little is known about the immunological and neurological consequences of HHV-6 inheritance. This study focused on a unique population of individuals that inherited HHV-6 and present with chronic fatigue-like symptoms, including hypersomnia, generalized fatigue, headache, and short …

Complete Genome Sequences And Phylogeny Of West Nile Virus Isolates From Southeastern United States, 2003-2012, Crystal Wedin

USF Tampa Graduate Theses and Dissertations

The study of the evolution and phylogeny of West Nile virus (WNV) has been an important area of research since the introduction of WNV in 1999. However, genome sequencing of isolates from the Southeastern part of the United States has been somewhat limited. To determine how WNV has evolved at a more localized level, ten isolates from Florida and Georgia from 2003-2012 were completely sequenced using Illumina's next-generation technology. In addition, a phylogenetic comparison of both the complete genome and select partial genomes was completed to ensure consistency among the results. This study further demonstrated the dominance of the North …

Clinicopathological Spectrum Of Ovarian Sex Cord-Stromal Tumors; 20years' Retrospective Study In A Developing Country, Saroona Haroon, Aleena Zia, Romana Idrees, Aisha Memon, Saira Fatima, Naila Kayani

Department of Pathology and Laboratory Medicine

Background:
Ovarian sex cord stromal tumors are rare neoplasms as compared to epithelial tumors. No large study has been done in Pakistan to find out the frequencies of various sex cord stromal tumors and their clinicopathological behavior in our region. The purpose of our study was to determine the various histological patterns and clinical features of ovarian sex cord stromal tumors along with follow-up in our set-up.
Methods:
It is a retrospective observational study. The study was conducted in section of Histopathology, Aga Khan University Hospital, Karachi, Pakistan. All reported cases of sex cord stromal tumors of ovary during 1992 …

Frequency And Outcome Of Graft Versus Host Disease After Stem Cell Transplantation: A Six-Year Experience From A Tertiary Care Center In Pakistan, Natasha Ali, Salman Naseem Adil, Mohammad Usman Shaikh, Nehal Masood

Department of Pathology and Laboratory Medicine

Objective: The objective of this study was to evaluate the frequency and outcome of graft versus host disease after stem cell transplantation for various haematological disorders in Pakistan.
Materials and Methods: Pretransplant workup of the patient and donor was performed. Mobilization was done with G-CSF 300 mu g twice daily for five day. Standard GvHD prophylaxis was done with methotrexate 15mg/m(2) on day +1 followed by 10mg/m(2) on days +3 and +6 and cyclosporine. Grading was done according to the Glucksberg classification.
Results: A total of 153 transplants were done from April 2004 to December 2011. Out of these were …

Identification Of Non-Tuberculous Mycobacteria Isolated From Clinical Specimens At A Tertiary Care Hospital: A Cross-Sectional Study, Imran Ahmed, Kauser Jabeen, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background:
Non-tuberculous mycobacteria (NTM) are opportunistic pathogens in immuno-compromised patients. They are also increasingly recognized as pathogens in immuno-competent individuals. Globally, an increase in NTM isolation is being reported with a varied geographic prevalence of different species around the world. There is lack of data on species distribution of these organisms from Pakistan. Treatment options differ according to the species isolated and its susceptibility profile. Knowledge of local species variation would help targeted therapy. This study was performed to determine frequencies of different NTM species isolated from various clinical specimens submitted at a tertiary care hospital laboratory.
Methods:
NTM isolated …

Overview Of Benign And Malignant Prostatic Disease In Pakistani Patients: A Clinical And Histopathological Perspective, Huma Arshad, Zubair Ahmad

Department of Pathology and Laboratory Medicine

Background: To present the overall clinical and histological perspective of benign and malignant prostatic disease as seen in our practice in the Section of Histopathology, Department of Pathology and Microbiology, Aga Khan University Hospital, Karachi, Pakistan.
Materials and Methods: All consecutive prostate specimens (transurethral resection or TUR, enucleation, needle biopsies) received between July 1, 2012 and December 31, 2012 were included in the study.
Results: Of the total of 785 cases, 621 (79.1%) were TUR specimens, 80 (10.2%) enucleation specimens, and 84 (10.7%) needle biopsies. Some 595 (75.8%) were benign, while 190 (24.2%) were malignant. Mean weight of BPH specimens …

Peripheral T-Cell Lymphoma Presenting As Testicular Mass; A Diagnostic Challenge, Saroona Haroon, Arsalan Ahmed

Department of Pathology and Laboratory Medicine

Background: T-cell lymphomas involve the testis infrequently, which deserve special attention because of the poor prognosis and the need to make an appropriate diagnosis, which could lead to a better therapeutic strategy.
Case Presentation: A 40-year-old man presented with right testicular swelling for past three months. The swelling was painless, hard and rubbery. Testicular ultrasound showed diffuse increase in size of the testicle, with alteration in its echogenicity. The patient underwent orchidectomy, and based on histopathological and immunohistochemical tests, a peripheral T-cell lymphoma, not otherwise specified was diagnosed.
Conclusion: Testicular peripheral T-cell lymphomas are rare and aggressive cancers, with clinical …

Prevalence Of Drug Resistance Associated Mutations In Plasmodium Vivax Against Sulphadoxine-Pyrimethamine In Southern Pakistan, Afsheen Raza, Najia K. Ghanchi, Muhammad Shahzeb Khan, Mohammad Asim Beg

Department of Pathology and Laboratory Medicine

Background: In Pakistan, Plasmodium vivax and Plasmodium falciparum co-exist and usage of sulphadoxine-pyrimethamine (SP) against P. falciparum exposes P. vivax to the drug leading to generation of resistant alleles. The main aim of this study was to investigate frequency distribution of drug resistance associated mutations in pvdhfr, pvdhps genes and provide baseline molecular epidemiological data on SP-associated resistance in P. vivax from southern Pakistan.
Methods: From January 2008 to May 2009, a total of 150 samples were collected from patients tested slide-positive for P. vivax, at the Aga Khan University Hospital, Karachi, or its collection units located in Baluchistan and …