Microbiology Commons^™

Inhibition Of Burkholderia Multivorans Adhesion To Lung Epithelial Cells By Bivalent Lactosides, Ciara Wight, Rosaria Leyden, Paul V. Murphy, Máire Callaghan, Trinidad Velasco-Torrijos, Siobhan Mcclean

Articles

Burkholderia cepacia complex (Bcc) is an opportunistic pathogen in cystic fibrosis patients which is inherently resistant to antimicrobial agents. The mechanisms of attachment and pathogenesis of Bcc, a group of 17 species, are poorly understood. The most commonly identified Bcc species in newly colonised patients, Burkholderia multivorans, continues to be acquired from the environment. Development of therapies which can prevent or reduce the risk of colonization on exposure to Bcc in the environment would be a better alternative to antimicrobial agents. Previously, it has been shown that Bcc strains bound to many glycolipid receptors on lung epithelia. Using a …

Amyloid-Beta42 Toxicity Reduction In Human Neuroblastoma Cells Using Cholera Toxin B Subunit-Myelin Basic Protein Expressed In Chloroplasts, Alexandra Ayache

HIM 1990-2015

Alzheimer's disease (AD) is an age progressive neurodegenerative brain disorder, affecting 37 million people worldwide. Cleavage of amyloid precursor protein by ?- and ?-secretase produces the amyloid-beta (A?) protein, which significantly contributes to AD pathogenesis. The A? aggregates, formed at the surface of neurons and intracellularly, cause neurotoxicity and decrease synaptic function. Inhibiting or degrading A? accumulation is a key goal for development of new AD treatments. Evidence shows that human Myelin Basic Protein (MBP) binds to and degrades A? thereby, preventing cytotoxicity. A potential method for oral drug delivery that will allow plant-derived bioencapsulated MBP to pass through intestinal …

Multiple Aspects Of Natural Killer Cell Expansion In Relevance To Immunotherapy For Hematologic Malignancies, Dominic Colosimo

HIM 1990-2015

Natural Killer (NK) cells are a subset of lymphocytes that regulate adaptive immune responses and utilize "missing self" recognition to activate anti-tumor and anti-viral cytotoxicity. Clinical research, as well as murine and ex vivo models, have shown that a variety of NK cell applications have proven useful as immunotherapeutic treatments for patients with hematologic malignancies. However, the selective expansion of NK cells to yield relevant amounts of these lymphocytes has been a major hurdle in the development of methods for clinical therapeutic use. Here, we demonstrate a novel ex vivo expansion method utilizing k562 leukemic cell lines and soluble cytokines …

Systems Biology Approaches To Probe Gene Regulation In Bacteria, Diogo F. Troggian Veiga

Dissertations and Theses (Open Access)

Mechanisms that allow pathogens to colonize the host are not the product of isolated genes, but instead emerge from the concerted operation of regulatory networks. Therefore, identifying components and the systemic behavior of networks is necessary to a better understanding of gene regulation and pathogenesis. To this end, I have developed systems biology approaches to study transcriptional and post-transcriptional gene regulation in bacteria, with an emphasis in the human pathogen Mycobacterium tuberculosis (Mtb).

First, I developed a network response method to identify parts of the Mtb global transcriptional regulatory network utilized by the pathogen to counteract phagosomal stresses …

Host-Microbe-Diet Interplay: Dietary Modulation Of The Gut Microbiota In Relation To Health, Inés Martínez

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Vertebrates are associated with trillions of bacteria, with the densest populations residing in the large intestine. The symbiosis between vertebrates and their gut microbiota has resulted in important implications of the gut microbiome on host health. Diet is an important factor that shapes gut microbiota composition, and because of the interplay between host-microbiome-diet, dietary strategies that modulate gut microbiome structure are deemed a relevant tool to improve host health. However, gaps in knowledge exist with respect to these interactions, and it is essential to obtain a mechanistic understanding of how these relations take place to develop successful therapeutic strategies that …

Quorum Sensing And Other Aspects Of The Biology Of Candida Albicans, Kenneth W. Nickerson

Kenneth Nickerson Papers

Most dimorphic fungi exhibit cell density dependent effects in that they grow as yeasts when inoculated at > 10⁶ cells per ml and as mycelia when inoculated at < 10⁶ cells per ml. For Candida albicans, we discovered (2001) that this phenomenon (quorum sensing) is due to the production and secretion of the C₁₅ isoprenoid trans-trans farnesol. Since then, we found that C. albicans cells treated with sublethal levels of zaragozic acid (2003) or fluconazole (2004) produced 10-40X more farnesol and that these fluconazole treated cells were ca. 5X more toxic to mice following tail vein injection. This suggestion …

Simplified Microbial Mats: Unraveling A Complex Community One Alga At A Time., Donna A. Dela Calzada, Brad M. Bebout, Angela Detweiler

STAR Program Research Presentations

Microbial mats are the oldest known ecosystems with an over 3.4 billion-year fossil record. Understanding their structure and function will help us better understand the biological evolution of life on early earth. They are rich in diversity (phylogenetically and physiologically) ranking amongst the most complex systems on earth. In this investigation, we aim to develop an effective method to study microbial mat organisms in relatively uncomplicated ecosystems that mimic the way they grow in nature. By growing “simplified microbial mats” on polypropylene cloth, we are able to observe the range of biogeochemical processes of a single species in a biogeochemical …

Regulation Of To Xin Synthesis By Clostridium Difficile, Charles Darkoh

Dissertations and Theses (Open Access)

Clostridium difficile is the leading definable cause of nosocomial diarrhea worldwide due to its virulence, multi-drug resistance, spore-forming ability, and environmental persistence. The incidence of C. difficile infection (CDI) has been increasing exponentially in the last decade. Virulent strains of C. difficile produce either toxin A and/or toxin B, which are essential for the pathogenesis of this bacterium. Current methods for diagnosing CDI are mostly qualitative tests that detect the bacterium, the toxins, or the toxin genes. These methods do not differentiate virulent C. difficile strains that produce active toxins from non-virulent strains that do not produce toxins or produce …

Effects Of Moisture Augmentation Of Municipal Solid Waste Through Addition Of Food Waste Or Wastewater Treatment Biosolids On Bio-Gas Formation For Power Generation, Jared Michael Gore

UNLV Theses, Dissertations, Professional Papers, and Capstones

An investigation into the effect of moisture augmentation by manipulation of food waste proportion or wastewater treatment plant biosolids proportion was undertaken to determine the effects on production of methane and other biogases from municipal solid waste (MSW). Laboratory microcosm experiments were performed to determine the effect of various proportions of influent waste streams on the production of biogas. Results indicated that moisture augmentation through the addition of food waste to MSW increases the overall bio-gas and hydrogen gas formed during fermentation. Moisture augmentation through addition of wastewater treatment bio-solids lead to inconclusive results. Addition of food waste to MSW …

Characterization Of Binding And Fusion Efficiencies Mediated By The V1–V5 Env Derived From Transmitted And Non-Transmitted Viruses Isolated From A Perinatal Transmission Cohort From Zambia, Mackenzie Waltke

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

Human Immunodeficiency Virus Type 1 (HIV-1) is the etiological agent of acquired immunodeficiency syndrome (AIDS), which affects over 34 million people worldwide. In sub-Saharan Africa where access to antiretroviral therapies (ART) is limited, mother-to-child transmission (MTCT) rates remain high and represent a major concern in the global HIV/AIDS epidemic. Little is known about the biological properties of viruses that are transmitted perinatally, including how the biological functions of envelope (Env) influence transmissibility. Previously, transmitted viruses were found to have an advantage in replicative fitness mediated by Env V1-V5. In this study viruses derived from transmitting mother infant pairs (MIPs) were …

Cell Bioenergetics In Leghorn Male Hepatoma Cells And Immortalized Chicken Liver Cells In Response To 4-Hydroxynonenal Induced Oxidative Stress, Alissa Laura Piekarski

Graduate Theses and Dissertations

Bioenergetic mechanisms responsible for ATP production are essential in carrying out maintenance and cell-specific functions. In this study, hepatocytes (liver cells) were used to test both endogenous and exogenous stress on cellular respiration. The secondary lipid peroxide, 4-hydroxynonenal (HNE), was used because it alters bioenergetics by increasing mitochondrial proton leak that attenuates mitochondrial radical production and, therefore, endogenous oxidative stress. The major objective of this study was to demonstrate effects of HNE-induced oxidative stress on avian hepatocyte bioenergetics. Various chemical which help enable the determination of oxygen (O2) consumption linked to ATP synthesis (oligomycin), maximal O2 consumption (FCCP), and proton …

Line Probe Assay For Detection Of Rifampicin And Isoniazid Resistant Tuberculosis In Pakistan, Joveria Qais Farooqi, Erum Khan, Syed Muhammed Zaheer Alam, Asho Ali, Zahra Hasan, Rumina Hasan

Department of Pathology and Laboratory Medicine

Objective:
To assess the efficacy of a line-probe assay delta (LiPA) as rapid diagnostic test for early detection of drug-resistant tuberculosis compared to conventional susceptibility methods in Pakistan.
Methods:
Resistance to rifampicin (RIF) and isoniazid (INH) in 108 smear-positive pulmonary tuberculosis samples was detected using a line-probe assay [GenoType MTBDRplus (Hain Lifescience, GmbH, Nehren, Germany)] at the clinical microbiology laboratory of Aga Khan University Hospital in May, 2009. Results were compared with susceptibilities performed while using agar proportion.
Results:
In comparison to the agar proportion method, the detection rate and specificity of resistance using MTBDR plus was 92.5% and 98.2% …

Epoxide-Mediated Cifr Repression Of Cif Gene Expression Utilizes Two Binding Sites In Pseudomonas Aeruginosa, Alicia E. Ballok, Christopher D. Bahl, Emily L. Dolben, Allia K. Lindsay, Jessica D. St. Laurent, Deborah Hogan, Dean Madden, George A. O'Toole

Dartmouth Scholarship

Pseudomonas aeruginosa secretes an epoxide hydrolase virulence factor that reduces the apical membrane expression of ABC transporters such as the cystic fibrosis transmembrane conductance regulator (CFTR). This virulence factor, named CFTR inhibitory factor (Cif), is regulated by a TetR-family, epoxide-responsive repressor known as CifR via direct binding and repression. We identified two sites of CifR binding in the intergenic space between cifR and morB, the first gene in the operon containing the cif gene. We have mapped these binding sites and found they are 27 bp in length, and they overlap the -10 and +1 sites of both the cifR …

Serratia Marcescens: The Miracle Bacillus, Alan L. Gillen, Rebekah Gibbs

Faculty Publications and Presentations

The objectives of this article are to explain the mysterious appearance of crimson-colored bacteria on food and communion bread/wafers, over the centuries, as well as to describe the biological basis

Cholesterol Degradation Pathways As Therapeutic Targets In Mycobacterium Tuberculosis, Veronica Escalante, Johnathan Abou-Fadel, Rhone A. Mendoza, Hugues Ouellet

COURI Symposium Abstracts, Summer 2012

Mycobacterium tuberculosis (Mtb) is an intracellular pathogen responsible for about 2 million deaths worldwide annually. During infection, Mtb faces the nutrient-deficient environment of the macrophage phagosome and switches to lipids, including cholesterol, as its main source or carbon and energy. Extensive work has been done on the cholesterol AB rings degradation, but much less is known about the degradation of the CD rings and aliphatic side-chain, which are thought to be shortened by β-oxidation reactions. In this study, we investigate the role of four fadD (fadD3, fadD17, fadD19 and fadD36) and eight fadE ( …

Identification Of Two Functional Sumo Interacting Motifs (Sims) In The Non-Structural Protein Of Influenza A Virus Ns1a, Lorellie M. Lewis, German Rosas-Acosta

COURI Symposium Abstracts, Summer 2012

We have previously shown that the non-structural protein of Influenza A virus NS1A is post-translationally modified by conjugation of the Small Ubiquitin-like MOdifier (SUMO). Our functional studies have also demonstrated that SUMO conjugation (SUMOylation) affects NS1A's ability to neutralize the cellular interferon response of the host cell and other functions associated to NS1A. Importantly, we have also shown that influenza infections trigger a global increase in cellular SUMOylation and have recently demonstrated that such an increase is mediated by NS1A. This observation led us to investigate the molecular mechanism endowing NS1A with the ability to increase global cellular SUMOylation. Sequence …

Assessment Of A Microbicide Candidate Among A Diverse Cohort Of Urban Southern Us Women And Their Male Sexual Partners, Paula M. Frew, Kimberly Parker, Takeia Horton, Brooke Hixson, Lisa Flowers, Frances Priddy, Lisa Grohskopf, Christine Mauck, Kimberly Workowski

Environmental & Global Health Faculty Research

Background: This mixed methods study reports on product acceptance from a Phase I clinical trial of a candidate non-nucleoside reverse transcriptase inhibitor (NNRTI) vaginal microbicide product (UC781). The product was evaluated in the context of a Phase I clinical trial in an area characterized by high HIV prevalence among minority women. The findings will inform the development of an acceptable microbicide that will address the needs of diverse women and their partners. Methods: This is a mixed methods study of 34 racially and ethnically diverse female participants and 10 male partners in Atlanta, Georgia. Chi-square tests for marginal homogeneity and …

Efficacy Comparison Of Various Pcr Master Mixes And Thermal Cycling Parameters For Detection Of Brucella Abortus In Multiplex Assays, Kevin J. Testo, Jason A. Olivas, Alda C. Carrillo, Pejman Naraghi-Arani

STAR Program Research Presentations

Diagnostic testing for bioterrorism agents in food is essential for the safety and welfare of the general populace. Multiplex assays provide the means to test for multiple pathogen signatures with a single polymerase chain reaction (PCR) test. PCR, Luminex xMAP ® infrared fluorophore bead technology, and flow cytometry, multiplex diagnostic assays are incredibly specific and sensitive to highly conserved regions at various loci in a microbe’s genome. In order to increase the effectiveness of the PCR and the resulting fluorescent response of the beads, different PCR master mix commercial kits were compared to the standard AgPath RT-PCR mix. This study …

Microbial Co-Occurrence Relationships In The Human Microbiome, Karoline Faust, J. Fah Sathirapongsasuti, Jacques Izard, Dirk Gevers, Jeroen Raes, Curtis Huttenhower

Department of Food Science and Technology: Faculty Publications

The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles …

The Pseudomonas Syringae Type Iii Secretion System: The Translocator Proteins, Their Secretion, And The Restriction Of Translocation By The Plant Immune System, Emerson Crabill

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

Pseudomonas syringae is a Gram-negative plant pathogen whose virulence is dependent upon its type III secretion system (T3SS), a nanosyringe that facilitates translocation, or injection, of type III effector (T3E) proteins into eukaryotic cells. The primary function of P. syringae T3E proteins is suppression of plant immunity. Bacterial proteins called translocators form a translocon that forms a pore in the host plasma membrane which is traversed by T3Es. HrpK1, a putative P. syringae translocator, is a type III-secreted protein important for virulence and T3E injection, but not secretion of T3Es. Harpins are a group of proteins specific to plant pathogens …

Identification Of Persistent Long Range Interactions In GA95 And GB95 Through Thermal Unfolding Simulations, Milen Redai Tesfamariam

Chemistry & Biochemistry Theses & Dissertations

For over five decades, different experiments have been performed to research how proteins attain their native three dimensional structures. However, the folding problem continues to be a puzzle in modern science. The design of two proteins that have maximal sequence identity but different folds and functions is one method that is being used to study the relationship between protein structure and amino acid sequence. In particular, mutant proteins of Streptococcus protein G, G_A and G_B, have 95% sequence identity and a 3a helix fold and β4/a fold, respectively. Molecular dynamics simulations of G_A95 …

Cyclic Di-Gmp Phosphodiesterases Rmda And Rmdb Are Involved In Regulating Colony Morphology And Development In Streptomyces Coelicolor. Journal Of Bacteriology, Travis D. Hull, Min-Hyung Ryu, Matthew J. Sullivan, Ryan C. Johnson, Nikola T. Klena, Robert M. Gelger, Mark Gomelsky, Jennifer A. Bennett

Biology and Earth Science Faculty Scholarship

Cyclic dimeric GMP (c-di-GMP) regulates numerous processes in Gram-negative bacteria, yet little is known about its role in Gram-positive bacteria. Here we characterize two c-di-GMP phosphodiesterases from the filamentous high-GC Gram-positive actinobacterium Streptomyces coelicolor, involved in controlling colony morphology and development. A transposon mutation in one of the two phosphodiesterase genes, SCO0928, hereby designated rmdA (regulator ofmorphology and development A), resulted in decreased levels of spore-specific gray pigment and a delay in spore formation. The RmdA protein contains GGDEF-EAL domains arranged in tandem and possesses c-di-GMP phosphodiesterase activity, as is evident from in vitro enzymatic assays using the purified protein. …

The Role And Regulation Of Nsars: A Cell-Envelope Stress Sensing Two-Component System In Staphylococcus Aureus, Stacey Lynn Kolar

USF Tampa Graduate Theses and Dissertations

Abstract

S. aureus has 16 predicted two-component systems (TCS) that respond to a range of environmental stimuli, and allow for adaptation to stresses. Of these 16, three have no known function, and are not homologous to any other TCS found in closely related organisms. NsaRS is one such element, and belongs to the intramembrane-sensing histidine kinase (IM-HK) family, which is conserved within the Firmicutes. The regulators are defined by a small sensing domain within their histidine kinase, suggesting that they do not sense external signals, but stress in or at the membrane. Our characterization of NsaRS in this work reveals …

Two Boundaries Separate Borrelia Burgdorferi Populations In North America, Gabriele Margos, Jean I. Tsao, Santiago Castillo-Ramirez, Yvette A. Girard, Anne G. Hoen

Dartmouth Scholarship

Understanding the spread of infectious diseases is crucial for implementing effective control measures. For this, it is important to obtain information on the contemporary population structure of a disease agent and to infer the evolutionary processes that may have shaped it. Here, we investigate on a continental scale the population structure of Borrelia burgdorferi, the causative agent of Lyme borreliosis (LB), a tick-borne disease, in North America. We test the hypothesis that the observed d population structure is congruent with recent population expansions and that these were preceded by bottlenecks mostly likely caused by the near extirpation in the 1900s …

Sigma Factor N (Σn): A Novel Regulator Of Extreme Acid Resistance In Enterohemorrhagic E. Coli O157:H7, Pamela Ann Fay

USF Tampa Graduate Theses and Dissertations

Extreme acid resistance contributes to the successful transmission of enterohemorrhagic E. coli (EHEC) through acidic food matrices and the stomach, allowing it to gain access to the intestine and elicit disease in humans. Alternative sigma factor N (σ^N, encoded by rpoN) was previously identified as a novel regulator of extreme acid resistance in EHEC. This study investigated the role for σ^N and co-expressed products of the rpoN operon in the acid resistance phenotype of EHEC. The results revealed that σ^N primarily controls acid resistance through repression of the glutamate-dependent acid resistance (GDAR) system through control …

Lapg, Required For Modulating Biofilm Formation By Pseudomonas Fluorescens Pf0-1, Is A Calcium-Dependent Protease, Chelsea D. Boyd, Debashree Chatterjee, Holger Sondermann, George A. O'Toole

Dartmouth Scholarship

Biofilm formation by Pseudomonas fluorescens Pf0-1 requires the cell surface adhesin LapA. We previously reported that LapG, a periplasmic cysteine protease of P. fluorescens, cleaves the N terminus of LapA, thus releasing this adhesin from the cell surface and resulting in loss of the ability to make a biofilm. The activity of LapG is regulated by the inner membrane-localized cyclic-di-GMP receptor LapD via direct protein-protein interactions. Here we present chelation and metal add-back studies demonstrating that calcium availability regulates biofilm formation by P. fluorescens Pf0-1. The determination that LapG is a calcium-dependent protease, based on in vivo and in vitro …

A Novel Virus Genome Discovered In An Extreme Environment Suggests Recombination Between Unrelated Groups Of Rna And Dna Viruses, Geoffrey S. Diemer, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.

Results: Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar …

Investigation Into The Mechanism Of Salicylate-Associated Genotypic Antibiotic Resistance In Staphylococcus Aureus, Nada Salah Helal

USF Tampa Graduate Theses and Dissertations

Growth of Staphylococcus aureus with the NSAID salicylate increases phenotypic resistance (SAPAR), and the frequency at which heritable resistance occurs to various antibiotics (SAGAR). This study describes the effect of salicylate on heritable and phenotypic resistance to a set of antibiotics for laboratory and multi-drug resistant strains of S. aureus and investigates the link between resistance and SAGAR. Drug gradient plates were used to determine phenotypic resistance to antibiotics targeting DNA replication, transcription, translation and the cell wall in the presence or absence of salicylate. To measure heritable resistance, mutation frequencies were determined for each antibiotic in the presence and …

Effect Of Antioxidants And Oxidative Stress On Different Cancer Cell Types, Gaytri Devi Gupta Elera

Theses and Dissertations

Vaccinium cyanococcus, most commonly known as blueberry, is a fruit native to North America that is known for its unique taste and high antioxidant content. The skin, seed and juice of both organically and conventionally grown blueberry extract were analyzed for antioxidant content using both the Hydrophilic and Lipophilic Oxygen Radical Absorbance Capacity (ORAC) assays. Results from the Hydrophilic ORAC test showed that conventionally grown blue berries had a higher antioxidant capacity across all samples, while the Lipophilic ORAC assay showed that the antioxidant concentration of organically cultivated blueberry juice was highest, but conventionally grown blueberry seed and skin …

Enhanced Hydrocarbon Biodegradation Using Bioaugmentation With Biowish™-Aqua Fog, Michael Robert Lehrer

Master's Theses

This study was done to determine the effectiveness of a commercially available bioaugmentation product, BiOWiSH^TM-Aqua FOG, for remediating petroleum-contaminated sandy soil. Biodegradation enhancement by BiOWiSH^TM-Aqua FOG was evaluated in laboratory microcosms by directly measuring total petroleum hydrocarbon (TPH) and indirectly using respirometry. Attempts were made to enrich hydrocarbon-degrading bacteria in BiOWiSH^TM-Aqua FOG, and the resulting enrichment cultures were screened using respirometry as well. Potential hydrocarbon-degrading bacteria in BiOWiSH^TM-Aqua FOG were isolated. Experiments were performed at bench-scale using microcosm bottles containing sand contaminated with either motor oil or No. 2 diesel fuel. The …