Microbiology Commons^™

Proteolytic Regulation Of Toxin-Antitoxin Systems By Clppc In Staphylococcus Aureus, Niles P. Donegan, Earl T. Thompson, Zhibiao Fu, Ambrose L. Cheung

Dartmouth Scholarship

Bacterial toxin-antitoxin (TA) systems typically consist of a small, labile antitoxin that inactivates a specific longer-lived toxin. In Escherichia coli, such antitoxins are proteolytically regulated by the ATP-dependent proteases Lon and ClpP. Under normal conditions, antitoxin synthesis is sufficient to replace this loss from proteolysis, and the bacterium remains protected from the toxin. However, if TA production is interrupted, antitoxin levels decrease, and the cognate toxin is free to inhibit the specific cellular component, such as mRNA, DnaB, or gyrase. To date, antitoxin degradation has been studied only in E. coli, so it remains unclear whether similar mechanisms of regulation …

Transcription Analysis Of The Chlorovirus Paramecium Bursaria Chlorella Virus-1, Giane M. Yanai

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

Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNAs from poly A-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 …

Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software For Describing And Comparing Microbial Communities, Courtney Robinson

Department of Biology Faculty Publications

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Gene Expression Profile Of Tumor Cell-Fused Or Noni (Morinda Citrifolia)-Treated Dendritic Cells, Melissa O'Connor

All Dissertations

Dendritic cell-mediated cancer immunotherapy employs several ways to engage tumor antigens. We have demonstrated both in pre-clinical animal studies and early clinical trials that dendritomas, highly purified hybrids between dendritic cells and tumor cells, are superior activators of anti-tumor immunity. In the present study, we examined the expression profile of several inflammatory chemokine and chemokine receptors of dendritomas by RNA microarray and real-time RT-PCR. The results indicate that dendritomas made from immature DCs and tumor cells express higher levels of CCL3, CCL5, and CCL22 and lower levels of CCR2 and CCR5, which mimics LPS matured DCs, while dendritomas made from …

Environmental Implications Of Francisella Tularensis Biofilms, Jeffrey J. Margolis '00

Doctoral Dissertations

Francisella tularensis survives in one of the widest environmental ranges of any pathogen. Numerous mammals and arthropod vectors are infected by this highly virulent organism. How this zoonotic pathogen persists outside of its many hosts remains unexplored. We aimed to examine how F. tularensis interacts with environmental surfaces, and hypothesized that biofilm formation may enable survival of this organism in nature. By understanding the role these surface-attached bacterial communities play in F. tularensis ecology, we hope to gain insight into the mechanisms of environmental persistence and transmission of this pathogen.

We identify chitin as a potential non-host niche for F. …

Erk 1/2 And P38 Mapk Pathways Are Both Invovled In The Expression Of Interleukin-6, -8, And Cyclooxygenase-2 In Thrombocytes Stimulated With Lipopolysaccharide, Candace Hitchcock

All Theses

This study was conducted to determine if the p38 and ERK1/2 MAPK pathways are involved in transcription of IL-6, IL-8, and COX-2 in the chicken thrombocyte response to ligation of Toll-like receptor 4 (TLR4) by Salmonella minnesota lipopolysaccharide (LPS). Thrombocytes were isolated and subsequently treated with either p38 MAPK or ERK inhibitor, and then with LPS during in vitro cell culture. Transcription of IL-6, IL-8, and COX-2 mRNA was determined using real-time PCR. The experiments were repeated using pM, nM and μM concentrations of both inhibitors to test cell sensitivity. Stimulation with LPS induced expression of IL-6, IL-8 and COX-2 …

Designing An Instrument Based On Native Fluorescence To Determine Soil Microbial Content At A Mars Analog Site, Heather D. Smith

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For this research project we designed an instrument to detect bacteria via biomolecular fluorescence. We introduce the current understanding of astrobiology, our knowledge of life beyond Earth, and the commonality of Earth life as it pertains to the search for life on Mars. We proposed a novel technique for searching for direct evidence of life on the surface of Mars using fluorescence. We use the arid region of the Mojave Desert as an analog of Mars. Results indicate the fluorescence of the biotic component of desert soils is approximately as strong as the fluorescence of the mineral component. Fluorescence laboratory …

Drosophila Adult Eye Model To Teach Scanning Electron Microscopy In An Undergraduate Cell Biology Laboratory, Meghana Tare, Oorvashi Roy Puli, Sarah M. Oros, Amit Singh

Biology Faculty Publications

We have devised an undergraduate laboratory exercise to study tissue morphology using fruit fly, Drosophila melanogaster, as the model organism. Drosophila can be reared in a cost effective manner in a short period of time. This experiment was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of scanning electron microscopy (SEM) technique to study the morphology of adult eye of Drosophila. The adult eye of Drosophila is a compound eye, which comprises of 800 unit eyes, and serves as an excellent model for SEM studies. We used flies that …

Biodiversity And Antimicrobial Activity Of Cold-Adapted Soil Microfungi From: Deception Island, Wilhelmina Bay And Yankee Bay, Maritime Antarctica., Mohammed Ahmed Mohammed Abneuf

Student Works (2010-2019)

Decades ago, the Antarctic regions have been exploited for cold-tolerant microorganisms, prospecting various biological benefits, mainly psychrophilic enzymes and bioactive compounds. The first half of the present research aimed to study the occurrence of microfungi in samples of soil taken from Deception Island, Wilhelmina Bay and Yankee Bay, Maritime Antarctica. Attempt made to screen the biodiversity using conventional media and soil plating technique, yielded population of 27 species from the total of 14 soil samples. Of that, 13 fungal species were recorded from Deception Island, 8 from Wilhelmina Bay and 6 from Yankee Bay. Among the genera were Aspergillus, …

Sequence Analysis And Characterization Of The Dihydrodiol Dehydrogenase And Aldehyde Dehydrogenase Genes In'' Sphingomonas Paucimobilis'' Epa505, Jaleh Jalili

All Dissertations

A bacterial artificial chromosome (BAC) library was previously constructed from genomic DNA of Sphingomonas paucimobilis EPA505 at Clemson University Genomic institute (CUGI). To isolate and identify the bphB gene from the genome of S. paucimobilis EPA505, a set of primers was designed based on conserved regions of the bphB gene encoding dihydrodiol dehydrogenase of Sphingomonas CHY-1 and Sphingomonas yanoikuyae B1. Routine PCR was performed and a PCR fragment of approximately 500 bp that confirmed the presence of pbhB gene in Sphingomonas paucimobilis EPA505 was produced. Hybridization of the PCR product with BAC library was performed and one hundred two positive …

Prevalence And Biological Control Of Salmonella Contamination In Rendering Plant Environments And The Finished Rendered Meals, Brandon Kinley

All Dissertations

Although the rendering process serves as invaluable means for the disposal of inedible animal by-products, the finished products often harbor pathogenic and opportunistic microorganisms such as Salmonella and enterococci, respectively. The temperatures used during the rendering process far exceed the heat tolerance threshold of most bacterial species, so cross-contamination from the environment and/or from the incoming raw material is the proposed source of the contamination. Research has demonstrated that the raw material coming into the rendering facility is highly contaminated with pathogenic bacteria including Salmonella. While not in a rendering facility, studies have also demonstrated that bacteria such as Salmonella …

Bpv Entry And Trafficking In Ebtr Cells, Enkhmart Dudleenamjil

Theses and Dissertations

Bovine Parvovirus (BPV) belongs to the genus Bocavirus, family Parvoviridae. BPV is the leading etiologic agent among the pathogens that cause primary gastroenteritis of cattle. Many of the intracellular events associated with virus replication are unknown. In this research project, we investigated BPV internalization into the host cell and trafficking in the cytosol. Preliminarily, EBTr cells had abundant clathrin, virus attached to purified clathrin, and EM micrographs revealed virus in endocytic vacuoles. Assays detecting virus infectivity (i.e. viral protein synthesis), virus production (completion of the replication cycle), and quantitative PCR (qPCR) to detect viral transcripts were used to evaluate …

Part 1: Screening Of Thirty-One Medicinal Plant Species Against Herpes Simplex Virus, Acetone And Methanol Extracts From The Root Tissue Of Kalanchoe Pinnata Interferes With Hsv Types 1 And 2 Dna Replication And Early And Late Gene Expression Preventing The Spread Of Hsv In Vitro. Part 2: Professional Development Curriculum: Integrating Molecular Biology And Microbiology Into The Existing Secondary Biology Curricula, Mary Ruth Greer

Theses and Dissertations

PART 1: Thirty-one medicinal plant species from Hawaii, Morocco, and the Sonoran Desert, USA have been shown in past studies to be highly inhibitory to pathogenic bacteria, fungi, and certain cancer cell lines. However, none were tested for antiviral activity. Acetone and methanol extracts from these species were bio-assayed for antiviral activity against herpes simplex virus types 1 and 2 (HSV 1 and HSV 2) and for cytotoxicity to the Vero C1008 cell line. Extracts from these species were tested in vitro for antiviral activity using an immunoperoxidase mini-plaque reduction assay to detect viral structural protein synthesis. Sulforhodamine B and …

Human Uterine Natural Killer Cells But Not Blood Natural Killer Cells Inhibit Human Immunodeficiency Virus Type 1 Infection By Secretion Of Cxcl12, Teddy F. Mselle, Aexandra L. Howell, Mimi Ghosh, Charles R. Wira, Charles L. Sentman

Dartmouth Scholarship

Natural killer (NK) cells derived from the human female reproductive tract (FRT) are phenotypically and functionally distinct from those obtained from peripheral blood. Because the FRT is a primary site of human immunodeficiency virus type 1 (HIV-1) infection in women, we determined whether soluble factors secreted by uterine-derived NK (uNK) cells inhibit HIV-1 infection. Clonal populations of uNK cells were activated with interleukin-12 (IL-12) and IL-15, and conditioned media (CM) from these cultures evaluated for their ability to inhibit infection of cells by HIV-1_IIIB, HIV-1_NL4.3, and HIV-1_HC4 (X4-tropic) or HIV-1_BaL (R5-tropic) viruses. We found …

Levels Of The Secreted Vibrio Cholerae Attachment Factor Gbpa Are Modulated By Quorum-Sensing-Induced Proteolysis, Brooke A. Jude, Raquel M. Martinez, Karen Skorupski, Ronald K. Taylor

Dartmouth Scholarship

Vibrio cholerae is the etiologic agent of cholera in humans. Intestinal colonization occurs in a stepwise fashion, initiating with attachment to the small intestinal epithelium. This attachment is followed by expression of the toxin-coregulated pilus, microcolony formation, and cholera toxin (CT) production. We have recently characterized a secreted attachment factor, GlcNAc binding protein A (GbpA), which functions in attachment to environmental chitin sources as well as to intestinal substrates. Studies have been initiated to define the regulatory network involved in GbpA induction. At low cell density, GbpA was detected in the culture supernatant of all wild-type (WT) strains examined. In …

Antimicrobial Evaluation Of Novel Fatty Acid Derivatives And Other Natural Antimicrobials, Patricia Nobmann

Doctoral

The food industry has shown increased interest for novel natural antimicrobials due to consumer demand for foods with fewer synthetic additives, increased safety, quality and shelf-life. Concurrently, the emergence of drug resistant bacteria substantiates the need for newer antimicrobial agents. Alternative strategies include the use of novel antimicrobials, such as fatty acid derivatives, essential oils and bacteriocins, with proven antimicrobial properties against a diverse range of bacteria. This study investigated novel carbohydrate fatty acid (CF A) derivatives for their antibacterial activity against a range of pathogenic and spoilage bacteria. A series of mono-substituted CF A derivatives using lauric and caprylic …

Killing Of Treponema Denticola By Mouse Peritoneal Macrophages, P. Gaibani, C. Vocale, S. Ambretti, F. Cavrini, Jacques Izard, L. Miragliotta, M. T. Pellegrino, V. Sambri

Department of Food Science and Technology: Faculty Publications

Treponema denticola has been identified as an important cause of periodontal disease and hypothesized to be involved in extra-oral infections. The objective of this study was to investigate the role of T. denticola cell length and motility during mouse peritoneal macrophages in vitro uptake. Macrophages, incubated under aerobic and anaerobic conditions, produced a similar amount of TNF-α when stimulated with Escherichia coli LPS. The uptake of FlgE- and CfpA-deficient mutants of T. denticola was significantly increased compared with the wild-type strain, due to cell size or lack of motility. Opsonization with specific antibodies considerably improved the treponemes’ uptake. …

The Pentameric Vertex Proteins Are Necessary For The Icosahedral Carboxysome Shell To Function As A Co2 Leakage Barrier, Fei Cai, Balaraj B. Menon, Gordon C. Cannon, Kenneth J. Curry, Jessup M. Shively, Sabine Heinhorst

Faculty Publications

Background

Carboxysomes are polyhedral protein microcompartments found in many autotrophic bacteria; they encapsulate the CO₂ fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) within a thin protein shell and provide an environment that enhances the catalytic capabilities of the enzyme. Two types of shell protein constituents are common to carboxysomes and related microcompartments of heterotrophic bacteria, and the genes for these proteins are found in a large variety of bacteria.

Methodology/Principal Findings

We have created a Halothiobacillus neapolitanus knockout mutant that does not produce the two paralogous CsoS4 proteins thought to occupy the vertices of the icosahedral carboxysomes and related microcompartments. Biochemical …

Biomarker Changes Associated With Tuberculin Skin Test (Tst) Conversion: A Two-Year Longitudinal Follow-Up Study In Exposed Household Contacts, Rabia Hussain, Najeeha Talat, Firdaus Shahid, Ghaffar Dawood

Department of Pathology and Laboratory Medicine

Background:A high prevalence (50-80%) of Tuberculin Skin Test Positivity (TST+ >or=10 mm indurations) has been reported in TB endemic countries. This pool forms a huge reservoir for new incident TB cases. However, immune biomarkers associated with TST conversion are largely unknown. The objective of this study was to identify immune biomarkers associated with TST conversion after acute Mycobacterium tuberculosis (MTB)
Methodology/Principal Findings:A 24 month longitudinal study was carried out in a recently MTB exposed cohort of household contacts (HC = 93, 75% TST+). Control group consisted of unexposed community controls (EC = 59, 46%TST+). Cytokine secretion was assessed …

Protection Against Mucosal Shiv Challenge By Peptide And Helper-Dependent Adenovirus Vaccines, Eric A. Weaver, Pramod N. Nehete, Bharti P. Nehete, Stephanie J. Buchl, Donna Palmer, David C. Montefiori, Philip Ng, K. Jagannadha Sastry, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Groups of rhesus macaques that had previously been immunized with HIV-1 envelope (env) peptides and first generation adenovirus serotype 5 (FG-Ad5) vaccines expressing the same peptides were immunized intramuscularly three times with helperdependent adenovirus (HD-Ad) vaccines expressing only the HIV-1 envelope from JRFL. No gag, pol, or other SHIV genes were used for vaccination. One group of the FG-Ad5- immune animals was immunized three times with HD-Ad5 expressing env. One group was immunized by serotype-switching with HD-Ad6, HD-Ad1, and HD-Ad2 expressing env. Previous work demonstrated that serum antibody levels against env were significantly higher in the serotype-switched group than in …

Flagellar Formation In C-Ring-Defective Mutants By Overproduction Of Flii, The Atpase Specific For Flagellar Type Iii Secretion, Manabu Konishi, Masaomi Kanbe, Jonathan L. Mcmurry, Shin-Ichi Aizawa

Faculty Articles

The flagellar cytoplasmic ring (C ring), which consists of three proteins, FliG, FliM, and FliN, is located on the cytoplasmic side of the flagellum. The C ring is a multifunctional structure necessary for flagellar protein secretion, torque generation, and switching of the rotational direction of the motor. The deletion of any one of the fliG, fliM, and fliN genes results in a Fla - phenotype. Here, we show that the overproduction of the flagellum-specific ATPase FliI overcomes the inability of basal bodies with partial C-ring structures to produce complete flagella. Flagella made upon FliI overproduction were paralyzed, indicating that an …

Identification Of The [Fefe]-Hydrogenase Responsible For Hydrogen Generation In Thermoanaerobacterium Saccharolyticum And Demonstration Of Increased Ethanol Yield Via Hydrogenase Knockout, A. Joe Shaw, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

Three putative hydrogenase enzyme systems in Thermoanaerobacterium saccharolyticum were investigated at the genetic, mRNA, enzymatic, and phenotypic levels. A four-gene operon containing two [FeFe]-hydrogenase genes, provisionally termed hfs (hydrogenase-Fe-S), was found to be the main enzymatic catalyst of hydrogen production. hfsB, perhaps the most interesting gene of the operon, contains an [FeFe]-hydrogenase and a PAS sensory domain and has several conserved homologues among clostridial saccharolytic, cellulolytic, and pathogenic bacteria. A second hydrogenase gene cluster, hyd, exhibited methyl viologen-linked hydrogenase enzymatic activity, but hyd gene knockouts did not influence the hydrogen yield of …

The Role Of Human Endogenous Retroviruses In Renal Cell Carcinoma, Michele D. Tisdale

Biological Sciences Theses & Dissertations

Human endogenous retroviruses make up approximately 8-9% of the human genome. A number of expressed HERVs, those that are actively transcribing, have been associated with various cancers. Suppression mechanisms that control HERV expression often fail or become more permissive in tissues where expression should be restricted. Previous studies have identified HERV expression in breast cancer tissues, whereas normal tissue HERV expression remained suppressed. In addition, studies of DNA hypermethylation have correlated with the ability to contribute to cancer development. Hypermethylation of several tumor suppressor genes occurs frequently in cancers and alterations in promoter regions could contribute to the development of …

Breast Carcinoma Grading, Estimation Of Tumor Size, Axillary Lymph Node Status, Staging, And Nottingham Prognostic Index Scoring On Mastectomy Specimens., Zubair Ahmad, Amna Khurshid, Asim Qureshi, Romana Idress, Nasira Asghar, Naila Kayani Naila Kayani

Department of Pathology and Laboratory Medicine

Introduction: Breast carcinoma is the most common malignant tumor and the leading cause of cancer death in women. In western countries, a sharp increase in the detection of breast carcinoma, largely due to widespread use of mammography, has recently led to a fall in breast cancer mortality. This, however, is not true for less developed countries, in which mortality continues to rise.
Objective:The aim of this study was to acquire information about the extent and spread of breast carcinoma in our Patients by grading the tumors, determining the tumor size, and axillary lymph node status, staging of the tumors …

Calcifying Fibrous Pseudotumor In Association With Hyaline Vascular Type Castleman's Disease., Muhammad Azam, Yousuf A Husen, Shahid Pervez

Department of Pathology and Laboratory Medicine

Calcifying fibrous pseudotumor is a recently described rare entity. It is considered as sclerosing end stage of inflammatory myofibroblastic tumor. An association with hyaline vascular type Castleman's disease has also been described. We report a case of a 13-year-old boy who presented with pain in epigastrium. Computed tomography scan of abdomen revealed a circumscribed mass arising from the gastric wall along the greater curvature. Histology revealed a tumor composed of spindle cells present within the dense hyalinized collagenous tissue. Lymphoplasmacytic infiltrate was seen along with lymphoid follicles, dystrophic and ossifying calcification. Tumor cells were focally positive for alpha smooth muscle …

Transitions To And From The Cd4-Bound Conformation Are Modulated By A Single-Residue Change In The Human Immunodeficiency Virus Type 1 Gp120 Inner Domain, Aemro Kassa, Navid Madani, Arne Schön, Hillel Haim, Andrés Finzi, Shi-Hua Xiang, Liping Wang, Amy Princiotto, Marie Pancera, Joel Courter, Amos B. Smith Iii, Ernesto Freire, Peter D. Kwong, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

Binding to the primary receptor CD4 induces conformational changes in the human immunodeficiency virus type 1 (HIV-1) gp120 envelope glycoprotein that allow binding to the coreceptor (CCR5 or CXCR4) and ultimately trigger viral membrane-cell membrane fusion mediated by the gp41 transmembrane envelope glycoprotein. Here we report the derivation of an HIV-1 gp120 variant, H66N, that confers envelope glycoprotein resistance to temperature extremes. The H66N change decreases the spontaneous sampling of the CD4-bound conformation by the HIV-1 envelope glycoproteins, thus diminishing CD4-independent infection. The H66N change also stabilizes the HIV-1 envelope glycoprotein complex once the CD4-bound state is achieved, decreasing the …

Transcriptome Analysis Of Frog Virus 3, The Type Species Of The Genus Ranavirus, Family Iridoviridae, Sai Majji, V. Thodima, R. Sample, D. Whitley, Y. Deng, J. Mao, V. Gregory Chinchar

Faculty Publications

Frog virus 3 is the best characterized species within the genus Ranavirus, family Iridoviridae. FV3's large (similar to 105 kbp) dsDNA genome encodes 98 putative open reading frames (ORFs) that are expressed in a coordinated fashion leading to the sequential appearance of immediate early (IE), delayed early (DE) and late (L) viral transcripts. As a step toward elucidating molecular events in FV3 replication, we sought to identify the temporal Class Of Viral messages. To accomplish this objective an oligonucleotide microarray containing 70-mer probes corresponding to each of the 98 FV3 ORFs was designed and used to examine viral gene expression. …

Evidence Base For The Use Of Selected Complementary And Alternative Therapies By Patients With Diabetes: Preface, Ruth Lindquist, Byron Hoogwerf

University Faculty Publications and Creative Works

No abstract provided.

Microbial Nad Metabolism: Lessons From Comparative Genomics, Francesca Gazzaniga, Rebecca Stebbins, Sheila Z. Chang, Mark A. Mcpeek, Charles Brenner

Dartmouth Scholarship

NAD is a coenzyme for redox reactions and a substrate of NAD-consuming enzymes, including ADP-ribose transferases, Sir2-related protein lysine deacetylases, and bacterial DNA ligases. Microorganisms that synthesize NAD from as few as one to as many as five of the six identified biosynthetic precursors have been identified. De novo NAD synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. Salvage NAD synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, and nicotinic acid riboside occurs via modules of different genes. Nicotinamide salvage genes nadV and pncA, found in distinct bacteria, appear to have spread throughout the tree of life …

Characterization Of Two Outer Membrane Proteins, Flgo And Flgp, That Influence Vibrio Cholerae Motility, Raquel M. Martinez, Madushini N. Dharmasena, Thomas J. Kirn, Ronald K. Taylor

Dartmouth Scholarship

Vibrio cholerae is highly motile by the action of a single polar flagellum. The loss of motility reduces the infectivity of V. cholerae, demonstrating that motility is an important virulence factor. FlrC is the sigma-54-dependent positive regulator of flagellar genes. Recently, the genes VC2206 (flgP) and VC2207 (flgO) were identified as being regulated by FlrC via a microarray analysis of an flrC mutant (D. C. Morris, F. Peng, J. R. Barker, and K. E. Klose, J. Bacteriol. 190:231-239, 2008). FlgP is reported to be an outer membrane lipoprotein required for motility that functions as a colonization factor. The study reported …