Microbiology Commons^™

Development And Characterization Of An In Vitro Four-Species Anaerobic Dental Biofilm Model, Fernando Andrade

Dissertations and Theses (Open Access)

Dental caries is the most common chronic disease worldwide. It is characterized by the demineralization of tooth enamel caused by acid produced by cariogenic dental bacteria growing on tooth surfaces, termed bacterial biofilms. Cariogenesis is a complex biological process that is influence by multiple factors and is not attributed to a sole causative agent. Instead, caries is associated with multispecies microbial biofilm communities composed of some bacterial species that directly influence the development of a caries lesion and other species that are seemingly benign but must contribute to the community in an uncharacterized way. Clinical analysis of dental caries and …

Functionalized Nanomaterials And Their Biological Applications, Pallavi Vedantam

All Dissertations

Bionanomaterials have been used in drug delivery, cancer therapy and biodiagnosis of pathogens based on their size and surface functionalization. In this present work, different kinds of nanoparticles (NPs), their cellular interactions, cytotoxicity profiles, and finally role of gold nanoparticles (GNPs) in biodetection of E. coli was investigated.
Firstly, cytotoxicity profiles of commercial, laser ablation, and green synthetic NPs were studied. Induction of apoptosis in cancer cells was found to be size dependent. The plain 80 nm GNPs and AgNPs enhanced toxic effects in cancer cells when compared to 20 nm ones. Apoptotic profiles of ALB- or FBS-coated NPs were …

Coccidia Of Gerbils From Mongolia, Ethan Thomas Jensen

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

In this study, gerbils collected in the Mongolia over the summers of 2009-2012 were examined for coccidia. In total, 171 gerbils of three species from 22 localities were examined for coccidia. Coccidian oocysts were identified from 21 gerbils, but those found in 1 of those gerbils were probably pseudoparasites of the host from which they were recovered. From the remaining 20 gerbils, 7 morphotypes of Eimeria and 1 morphotype of Isospora were identified. Four of the 7 morphotypes of Eimeria were attributed to new species which were described in this study. In addition, 10 previously described species of Eimeria were …

Analysis Of Human Papillomavirus Capsid Proteins: Insights Into Capsid Assembly, Willie A. Hughes

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

Papillomaviruses (PVs) are double stranded (ds)-DNA viruses (~8-kbp), which infect mucosal and cutaneous epithelial cells from various mammalian species, causing tumors in both epithelial cell-types. During the late-phase, the capsid proteins (L1 and L2), are expressed to encapsidate the viral genome generating infectious virion particles required for PV. Natural PV infections produce morphologically homogenous progeny virions 55-nm in diameter. Transient transfection systems allow individual expression of the capsid proteins, which are able to produce low-levels of infectious virion-like particles (VLPs) and non-infectious VLPs that have the capacity to resemble and function as wild-type virions.

Results: The research herein demonstrates …

Divergent Mechanisms Of Interaction Of Helicobacter Pylori And Campylobacter Jejuni With Mucus And Mucins, Julie Ann Naughton, Karina Mariño, Brendan Dolan, Colm Reid, Ronan Gough, Mary Gallagher, Michelle Kilcoyne, Jared Gerlachscience,, Lokesh Joshi, Pauline Rudd, Stephen Carrington, Billy Bourke, Marguerite Clyne

Articles

Helicobacter pylori and Campylobacter jejuni colonize the stomach and intestinal mucus, respectively. Using a combination of mucus-secreting cells, purified mucins, and a novel mucin microarray platform, we examined the interactions of these two organisms with mucus and mucins. H. pylori and C. jejuni bound to distinctly different mucins. C. jejuni displayed a striking tropism for chicken gastrointestinal mucins compared to mucins from other animals and preferentially bound mucins from specific avian intestinal sites (in order of descending preference: the large intestine, proximal small intestine, and cecum). H. pylori bound to a number of animal mucins, including porcine stomach mucin, but …

Population Genetics And Drug Resistance Markers: An Essential For Malaria Surveillance In Pakistan, Afsheen Raza, Mohammad Asim Beg

Department of Pathology and Laboratory Medicine

Plasmodium (P.) vivax is the prevalent malarial species accounting for 70% of malaria cases in Pakistan. However, baseline epidemiological data on P. vivax population structure and drug resistance are lacking from Pakistan. For population structure studies, molecular genetic markers, circumsporozoite protein (csp) and merozoite surface protein-1 (msp-1) are considered useful as these play an important role in P. vivax survival under immune and environmental pressure. Furthermore, these genes have also been identified as suitable candidates for vaccine development. While efforts for effective vaccine are underway, anti-malarial agents remain the mainstay for control. Evidence of resistance against commonly used anti-malarial agents, …

Illuminating The Dark Side--Vitamin D Status In Different Localities Of Karachi, Romaina Iqbal, Lena Jafri, Ali Haroon, Aysha Habib Khan

Department of Medicine

This study was conducted to determine the association between place of residence (grouped into neighbourhoods), and 25-hydroxy D (25[OH]D) levels of individuals of Karachi. Addresses of 4788 individuals tested for 25[OH]D at the clinical laboratory of the Aga Khan University (AKU), Karachi, from January 2007 to June 2008 were reviewed. The neighbourhoods were categorized into ten, based on locality attributes. A high overall prevalence (74%) of vitamin D deficiency (VDD) was observed. There was a significant difference (p-value < 0.01) between mean log 25[OH]D levels amongst neighbourhoods grouped according to distinct housing structure attributes and localities. A high frequency of VDD in all the studied localities of an urban city warrant dietary vitamin D supplementation and food fortification.

Antimycobacterial And Cytotoxicity Evaluation Of The Constituents Of Monodora Carolinae, Nyangi Magori, Stephen S Nyandoro, Joan Je Munissi, Matthias Heydenreich

Tanzania Journal of Science

Phytochemical investigation of the stem bark of the recently described species Monodora carolinae (Annonaceae) afforded prenylindole derivatives (E)-4-(1H-indol-6-yl)-but-3-en-2-one (1), 5-formylindole (2), fatty acid (Z)-hexade-7-enoic acid (3) and the lignanamide cannabisin B (4). The structures of the isolated compounds were established using NMR and MS analyses. The antimycobacterial activities of the extracts and isolated compounds were evaluated against Mycobacterium madagascariense (MM) and M. indicus pranii (MIP) using the two-fold microtitre dilution method. While the extracts exhibited minimum inhibitory concentration (MIC) ranging from 500 – 1000 µg/mL, the isolated compounds were 125 – 250 µg/mL, indicating very low activity. Cytotoxic effects were …

Comparative Microbial Community Composition From Secondary Carbonate (Moonmilk) Deposits: Implications For The Cansiliella Servadeii Cave Hygropetric Food Web, Annette Summers Engel, Maurizio G. Paoletti, Mattia Beggio, Luca Dorigo, Alberto Pamio, Tiziano Gomiero, Claudio Furlan, Mauro Brilli, Angelo Leandro Dreon, Roberto Bertoni, Andrea Squartini

International Journal of Speleology

The microbial diversity of moonmilk, a hydrated calcium carbonate speleothem, was evaluated from two Italian caves to provide context for the food web of highly-specialized troglobitic beetles, Cansiliella spp. (Leptodirinae), with distinctive carbon and nitrogen isotope values indicative of a novel food source. The moonmilk and associated percolating waters had low to no extractable chlorophyll, with an average organic C:N ratio of 9, indicating limited allochthonous input and a significant contribution from microbial biomass. The biomass from moonmilk was estimated to be ~10⁴ micro- and meiofaunal individuals per m² and ~10⁷ microbial cells/ml. Betaproteobacteria dominated the …

Nuclear Bmp2 And The Immune Response, Daniel S. Olsen

Theses and Dissertations

Nuclear bone morphogenetic protein 2 (nBMP2) is a nuclear variant of the secreted growth factor BMP2. Experiments in nBmp2NLStm mutant mice, which lack nBMP2 in the nucleus, have shown that nBMP2 affects intracellular calcium transport in skeletal muscle and hippocampal neurons. The objective of this study was to determine whether nBMP2 affects the immune system, since activation of lymphocytes and other immune cells depends on intracellular calcium transport. We found that spleens in nBmp2NLStm mutant mice were 24% smaller than in wild type mice. The white pulp of the spleen contains many immune cells, particularly B and T lymphocytes and …

The Role Of Nuclear Bmp2 In The Cell Cycle And Tumorigenesis, Brandt Alan Nichols

Theses and Dissertations

Bone morphogenetic protein 2 (BMP2) is a secreted growth factor that is essential for proper embryonic development and proliferation. Our laboratory discovered a nuclear variant of BMP2 (nBMP2) which is produced when translation is initiated at an alternative start codon within the BMP2 gene. When translation occurs at the downstream start codon, the resulting protein lacks the ER signal peptide, thereby allowing cytoplasmic translation and nuclear localization. Our aim is to distinguish the role of this nuclear localized variant from secreted BMP2. Overexpression of nBMP2 in HEK293 and HT29 cell lines resulted in a higher percentage of cells in proliferative …

Characterization Of The Gut Microbiota And Colitogenic Bacterial Species In Core 1 O-Glycans Deficient Mice, Maria E. Perez-Munoz

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

Mucus is one important component of the intestinal mucosal barrier, and loss of its functionality is associated with colitis in humans and mice. Mice deficient in core 1 O-glycans (TM-IEC C1galt1^-/-) display a thinner mucus layer upon mutation of the glycosyltransferase enzyme (C1GALT1) responsible for core 1 O-glycans attachment, thus constituting an experimental model for human Ulcerative Colitis (UC). Under conventional conditions, these mice experience spontaneous inflammation of the colon. However, the exact role of the microbiota in colitis development in these mice has not been systematically investigated.

Aimed to gain insights into the role of …

In Vitro Selection Of Chloroquine Tolerant Plasmodium Falciparum Parasites, Daniel A. Daley

Biological Sciences Theses & Dissertations

Malaria is among the most devastating human diseases, and a majority of lethal cases are caused by the protozoan parasite, Plasmodiumfalciparum. The emergence of multi-drug resistant P.falciparum is a major obstacle to malaria control and is highlighted by the abandonment of chloroquine (CQ) as a first-line treatment of P.falciparum infections worldwide. Chloroquine resistance (CQR) is associated primarily with mutations in the transmembrane digestive vacuole protein, PfCRT. However, CQR P.falciparum parasites harboring the same mutant pfcrt allele vary in their CQ response, suggesting the CQ response is multigenic in nature. No gene outside of pfcrt is completely associated with CQR. Thus, …

Levels And Chemodynamics Of Pesticides In Soil And Sediments At Kilombero Sugarcane Plantations And Environs, Morogoro Region, Tanzania, James T. Zacharia

Journal of Humanities and Social Sciences

metabolites in soil and sediment samples from Kilombero sugarcane plantations and environs, Morogoro Region, Tanzania. The samples were screened for 56 different pesticide residues and their metabolites using GC-ECD and GC-NPD and the results were confirmed by GC-MS. A total of 31 soil samples and 19 sediment samples were analysed in this study and a total of 16 different pesticides/metabolites were detected in soil samples; and 12 different pesticides/metabolites were detected in sediment samples. o,p’-DDT was shown to have the highest concentration of all the detected pesticides/metabolites in soil samples with a mean concentration of 21.04µg/kg d.w whereas the highest …

Promoter Polymorphisms In Interferon Regulatory Factor 5, Daniel N. Clark

Theses and Dissertations

The promoter region of interferon regulatory factor 5 (IRF5) contains the rs2004640 T or G single nucleotide polymorphism (SNP) and a CGGGG indel. Both of these polymorphisms have been implicated as genetic risk factors for several autoimmune diseases, including systemic lupus erythematosus, whose pathology involves altered apoptosis and cytokine signaling. The polymorphisms' overall effect is to increase IRF5 levels. IRF5 is a transcription factor of several cytokines, including interferon, and is pro-apoptotic. Thus an alteration of cytokine levels and apoptosis signaling due to high IRF5 levels is the proposed source of autoimmune risk. Each of IRF5's four first exons (1A, …

Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy, Joshua Christopher Vert

Theses and Dissertations

From acid seeps and deep-sea thermal vents to glacial ice and hypersaline lakes, extreme environments contain relatively simplified communities consisting of extremophiles that have evolved to survive and thrive under adverse abiotic conditions. In more neutral environments, microorganisms use dormancy as a common life history strategy to weather temporal fluctuations of resources or stresses until more 'optimal' conditions are present. It is unclear if dormancy is an essential survival mechanism for microorganisms in extreme environments; however, recent studies suggest that extreme environments may create stable conditions for extremophiles to the extent that dormancy is of less ecological importance. Using lake …

Thymidine Kinase 1: Diagnostic And Prognostic Significance In Malignancy, Melissa Marie Alegre

Theses and Dissertations

Thymidine kinase 1 (TK1) is a cancer biomarker which has diagnostic and prognostic potential in a variety of malignancies. TK1 is significantly elevated in the serum and tumor tissue of most malignancies. This increase in TK1 can be detected in the very early stages of malignancy, including in pre-malignant disease with an increased risk for progression. Several studies have demonstrated that elevated TK1 is found in serum months before any clinical symptoms of malignancy. It has also been demonstrated that TK1 is elevated months before clinical recurrence of malignancy. This work first sought to demonstrate the early nature of TK1 …

Localization Of Phosphatidylinositol 4,5-Bisphosphate To Lipid Rafts And Uroids In The Human Protozoan Parasite Entamoeba Histolytica, Amrita B. Koushik, Rhonda R. Powell, Lesly A. Temesvari

Publications

Entamoeba histolytica is an intestinal protozoan parasite and is the causative agent of amoebiasis. During invasive infection, highly motile amoebae destroy the colonic epithelium, enter the blood circulation, and disseminate to other organs such as liver, causing liver abscess. Motility is a key factor in E. histolytica pathogenesis, and this process relies on a dynamic actomyosin cytoskeleton. In other systems, phosphatidylinositol 4,5-bisphosphate [PI(4,5)P₂] is known to regulate a wide variety of cellular functions, including signal transduction, actin remodeling, and cell motility. Little is known about the role of PI(4,5)P₂ in E. histolytica pathogenicity. In this study, we …

A Simple Assay To Screen Antimicrobial Compounds Potentiating The Activity Of Current Antibiotics, Junaid Iqbal, Ruqaiyyah Siddiqui, Shahana Urooj Kazmi, Naveed Ahmed Khan

Department of Biological & Biomedical Sciences

Antibiotic resistance continues to pose a significant problem in the management of bacterial infections, despite advances in antimicrobial chemotherapy and supportive care. Here, we suggest a simple, inexpensive, and easy-to-perform assay to screen antimicrobial compounds from natural products or synthetic chemical libraries for their potential to work in tandem with the available antibiotics against multiple drug-resistant bacteria. The aqueous extract of Juglans regia tree bark was tested against representative multiple drug-resistant bacteria in the aforementioned assay to determine whether it potentiates the activity of selected antibiotics. The aqueous extract of J. regia bark was added to Mueller-Hinton agar, followed by …

Escherichia Coli Strain Diversity In Humans: Effects Of Sampling Effort And Methodology, Emily R. Neal

Master's Theses

Studies investigating Escherichia coli strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in E. coli strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. …

Isolation Of Primary Cilia By Shear Force, Kimberly A. P. Mitchell

Faculty Publications and Presentations

The cell’s primary cilium is both a mechanical and chemical sensor involved in many signaling pathways. In order to ascertain protein enrichment in the primary cilium or study sub-ciliary localization of various proteins, it is advantageous to remove the primary cilium from the cell body. The protocol described here gives detailed instructions on purifying primary cilia by separating them from the cell body using shear force. This simple technique avoids using harsh purification conditions that may affect signaling proteins in the cilium or cause the ciliary membrane to disintegrate. In addition, as the cell body remains mostly intact, contamination of …

Functional Annotation, Transcriptional Characterization And Enzymatic Contributions Of Essential Amino Acid Biosynthesis-Related Genes, Teresa J. Clark

Masters Theses

In plants, essential amino acid biosynthesis predominantly or exclusively occurs in the plastid. The plastid in the heterokont alga Nannochloropsis oceanica is surrounded by four membranes, which add great complexity to intracellular trafficking and communication. N. oceanica genes in essential amino acid biosynthesis were functionally annotated. The biosynthesis pathways resemble the pathways in Arabidopsis thaliana, but the gene content seems to be simpler in N. oceanica.

In addition, two A. thaliana mutants with loss-of-function mutations in the aspartate kinase-homoserine dehydrogenase 2 (AK-HSDH2) gene were characterized. These ak-hsdh2 mutants demonstrate unexpected accumulation of aspartate-derived amino acids (ADAAs), particularly threonine, in …

The Role Of Indoleamine 2,3-Dioxygenase In Lp-Bpm5 Murine Retroviral Disease Progression, Megan A. O'Connor, William R. Green

Dartmouth Scholarship

Indoleamine 2,3-dioxygenase (IDO) is an immunomodulatory intracellular enzyme involved in tryptophan degradation. IDO is induced during cancer and microbial infections by cytokines, ligation of co-stimulatory molecules and/or activation of pattern recognition receptors, ultimately leading to modulation of the immune response. LP-BM5 murine retroviral infection induces murine AIDS (MAIDS), which is characterized by profound and broad immunosuppression of T- and B-cell responses. Our lab has previously described multiple mechanisms regulating the development of immunodeficiency of LP-BM5-induced disease, including Programmed Death 1 (PD-1), IL-10, and T-regulatory (Treg) cells. Immunosuppressive roles of IDO have been demonstrated in other retroviral models, suggesting a possible …

The Effects Of Intestinal Microbial Community Structure On Disease Manifestation In Il-10-/- Mice Infected With Helicobacter Hepaticus, Courtney Robinson

Department of Biology Faculty Publications

BackgroundThe aberrant inflammation that is the hallmark of the inflammatory bowel diseases (IBD) is associated with several factors, including changes in the intestinal microbiota. Here, we confirmed that an intestinal microbiota is needed for development of typhlocolitis in Helicobacter hepaticus infected IL-10-/- C57BL/6 mice, and investigated the role of the microbiota in modulating disease.ResultsWe altered the murine microbiota by treatment with the antibiotics vancomycin or cefoperazone prior to H. hepaticus infection. Through surveys of the 16S rRNA encoding-gene, analyses of histology and changes in expression of host mediators, we correlated alterations in the microbiota with host responses. We found that …

Neuropathogenic Escherichia Coli K1 Does Not Exhibit Proteolytic Activities To Exert Its Pathogenicity, Junaid Iqbal, Mehak Rajan, Ruqaiyyah Siddiqu, Naveed Ahmed Khan

Department of Biological & Biomedical Sciences

Background: Proteases are well-known virulence factors that promote survival, pathogenesis and immune evasion of many pathogens. Several lines of evidence suggest that the blood-brain barrier permeability is a prerequisite in microbial invasion of the central nervous system. Because proteases are frequently associated with vascular permeability by targeting junctional proteins, here it is hypothesized that neuropathogenic Escherichia coli K1 exhibit proteolytic activities to exert its pathogenicity.
Methods: Zymographic assays were performed using collagen and gelatin as substrates. The lysates of whole E. coli K1 strain E44, or E. coli K-12 strain HB101 were tested for proteolytic activities. The conditioned media were …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 91st Annual Virginia Journal of Science Meeting, May 2013

Detection Of Bacterial Retroelements Using Genomics, Sen Mu

Electronic Theses and Dissertations

The reverse flow of genetic information can occur when a special DNA polymerase called Reverse Transcriptase (RT) copies the genetic information in an RNA molecule back into a complementary DNA. One type of RT encoding gene found in bacteria is called a retron element. Recent bacterial genome sequencing projects have revealed many examples of retron RT genes. This gene assignment is based on comparison with a few known retron RT proteins. However, RT proteins are highly diverse in their amino acid sequences, and thus the assigned identity of these RT proteins as retrons in genome databases is questionable. One way …

Aerobic Degradation Of Α-, Β-, Γ-Hexachlorocyclohexane By Narragansett Bay Bacterioplankton, Ian M. Rambo

Senior Honors Projects

Hexachlorocyclohexanes (HCHs) are a family of chlorinated organic compounds that were previously used as agricultural insecticides. HCHs are recognized as persistent organic pollutants due to their toxicity, recalcitrant properties, and tendency to bioaccumulate in food webs. Although HCH was first synthesized in 1825, its use was not widespread until the discovery of the insecticidal activity of the γ-HCH isomer in 1942. γ-HCH and its toxic waste isomers α-HCH and β-HCH were banned from production and use by the United Nations in 2009, yet these chemicals still present environmental problems due to their persistence in soils and surface waters. HCHs continue …

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD …

Interaction Of Bacillus Anthracis Exosporium Protein Bcla With Complement Factor H And Spore Persistence In The Lung, Sarah A. Jenkins

Dissertations and Theses (Open Access)

Anthrax outbreaks in the United States and Europe and its potential use as a bioweapon have made Bacillus anthracis an interest of study. Anthrax infections are caused by the entry of B. anthracis spores into the host via the respiratory system, the gastrointestinal tract, cuts or wounds in the skin, and injection. Among these four forms, inhalational anthrax has the highest lethality rate and persistence of spores in the lungs of animals following pulmonary exposure has been noted for decades. However, details or mechanisms of spore persistence were not known. In this study, we investigated spore persistence in a mouse …