Microbiology Commons^™

Systematic Analysis Of Diguanylate Cyclases That Promote Biofilm Formation By Pseudomonas Fluorescens Pf0-1, Peter D. Newell, Shiro Yoshioka, Kelli L. Hvorecny, Russell D. Monds, George A. O'Toole

Dartmouth Scholarship

Cyclic di-GMP (c-di-GMP) is a broadly conserved, intracellular second-messenger molecule that regulates biofilm formation by many bacteria. The synthesis of c-di-GMP is catalyzed by diguanylate cyclases (DGCs) containing the GGDEF domain, while its degradation is achieved through the phosphodiesterase activities of EAL and HD-GYP domains. c-di-GMP controls biofilm formation by Pseudomonas fluorescens Pf0-1 by promoting the cell surface localization of a large adhesive protein, LapA. LapA localization is regulated posttranslationally by a c-di-GMP effector system consisting of LapD and LapG, which senses cytoplasmic c-di-GMP and modifies the LapA protein in the outer membrane. Despite the apparent requirement for c-di-GMP for …

Emerging Dynamics Of Human Campylobacteriosis In Southern Ireland, Susan Bullman, Daniel Corcoran, James O'Leary, Derry O'Hare, Brigid Lucey, Roy D. Sleator

Department of Biological Sciences Publications

Infections with Campylobacter spp. pose a significant health burden worldwide. The significance of Campylobacter jejuni/Campylobacter coli infection is well appreciated but the contribution of non-C. jejuni/C. coli spp. to human gastroenteritis is largely unknown. In this study, we employed a two-tiered molecular study on 7194 patient faecal samples received by the Microbiology Department in Cork University Hospital during 2009. The first step, using EntericBio® (Serosep), a multiplex PCR system, detected Campylobacter to the genus level. The second step, utilizing Campylobacter species-specific PCR identified to the species level. A total of 340 samples were confirmed as Campylobacter genus positive, 329 of …

Mechanical Test Methods For Assessing Porcine Carotid And Uterine Artery Burst Pressure Following Ex Vivo Ultrasonic Ligature Seal And Transection, Carissa M. Krane, Margaret Pinnell, Courtney Gardner, Mercedes Thompson, James Coleman, Robert Wilkens

Biology Faculty Publications

A test method was developed to identify those variables important for assessing the performance of ultrasonic surgical devices in ex vivo ligature sealing of porcine carotid and uterine arteries. Ruggedness testing using a small sample size in pilot experiments was conducted using a newly developed test method in an effort to assess the usefulness of this methodology and to identify test variables that might warrant further testing. The development of this test method included the use of a custom-designed prototypic tension device for load-controlled ex vivo vessel stretching during saline perfusion and subsequent seal and transection of porcine arteries with …

Generation Of A Kupffer Cell-Evading Adenovirus For Systemic And Liver-Directed Gene Transfer, Reeti Khare, Shannon M. May, Francesco Vetrini, Eric A. Weaver, Donna Palmer, Amanda Rosewell, Nathan Grove, Philip Ng, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

As much as 90% of an intravenously (i.v.) injected dose of adenovirus serotype 5 (Ad5) is absorbed and destroyed by liver Kupffer cells. Viruses that escape these cells can then transduce hepatocytes after binding factor X (FX). Given that interactions with FX and Kupffer cells are thought to occur on the Ad5 hexon protein, we replaced its exposed hypervariable regions (HVR) with those from Ad6. When tested in vivo in BALB/c mice and in hamsters, the Ad5/6 chimera mediated >10 times higher transduction in the liver. This effect was not due to changes in FX binding. Rather, Ad5/6 appeared to …

In Situ Enrichment Of Ocean Crust Microbes On Igneous Minerals And Glasses Using An Osmotic Flow‐Through Device, Amy Renee Smith, Martin Fisk, Radu Popa, Mark Nielsen, C. Geoffrey Wheat, Hans W. Jannasch, Andrew T. Fisher, Keir Becker, Stefan M. Sievert, Gilberto Flores

Biology Faculty Publications and Presentations

The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge was used in the first long-term deployment of microbial enrichment flow cells using osmotically driven pumps in a subseafloor borehole. Three novel osmotically driven colonization systems with unidirectional flow were deployed in the borehole and incubated for 4 years to determine the microbial colonization preferences for 12 minerals and glasses present in igneous rocks. Following recovery of the colonization systems, we measured cell density on the minerals and glasses by fluorescent staining and direct counting and found some significant differences between mineral samples. …

In Search Of An Uncultured Human-Associated Tm7 Bacterium In The Environment, Jorge Dinis, David Barton, Jamsheed Ghadiri, Deepa Surendar, Kavitha Reddy, Fernando Velasquez, Carol Chaffee, Mei-Chong Lee, Helen Gavrilova, Hazel Ozuna, Samuel Smits, Cleber Ouverney

Faculty Publications, Biological Sciences

We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA gene homology to a group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as TM7a-like) was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites. We speculate that upon further …

Antioxidants In Cancer Research And Prevention: Assay Comparison, Structure-Function Analysis, And Food Product Analysis, Andrew Robert Garrett

Theses and Dissertations

Recent epidemiological studies have suggested that the development and progression of several chronic diseases may be initiated or augmented by oxidative stress. Reactive oxygen species and reactive nitrogen species react readily with and can damage nucleic acids, proteins, and lipids. While biological systems are equipped antioxidant defenses to cope with oxidative stress, oxidative damage may still occur when oxidative stress overwhelms antioxidant defenses. This damage, if left unchecked, may lead to a variety of degenerative diseases, including heart disease, Alzheimer's Disease, Parkinson's Disease and cancer. Several assays have been designed to describe the antioxidant activity of various phytochemicals, vitamins, and …

Growth Phase-Dependent Gene Regulation In Vivo In Sulfolobus Solfataricus, Melissa Deyoung, Michelle Thayer, John Van Der Oost, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Ribosomal genes are strongly regulated dependent on growth phase in all organisms, but this regulation is poorly understood in Archaea. Moreover, very little is known about growth phase-dependent gene regulation in Archaea. SSV1- based lacS reporter gene constructs containing the Sulfolobus 16S/23S rRNA gene core promoter, the TF55a core promoter, or the native lacS promoter were tested in Sulfolobus solfataricus cells lacking the lacS gene. The 42-bp 16S/23S rRNA gene and 39-bp TF55a core promoters are sufficient for gene expression in S. solfataricus. However, only gene expression driven by the 16S/23S rRNA gene core promoter is dependent on …

Effects Of Canola And Corn Oil Mimetic On Jurkat Cells, Gabriela Ion, Kayla Fazio, Juliana A. Akinsete, W. Elaine Hardman

Biochemistry and Microbiology

BACKGROUND: The Western diet is high in omega-6 fatty acids and low in omega-3 fatty acids. Canola oil contains a healthier omega 3 to omega 6 ratio than corn oil. Jurkat T leukemia cells were treated with free fatty acids mixtures in ratios mimicking that found in commercially available canola oil (7% α-linolenic, 30% linoleic, 54% oleic) or corn oil (59% linoleic, 24% oleic) to determine the cell survival or cell death and changes in expression levels of inflammatory cytokines and receptors following oil treatment.

METHODS: Fatty acid uptake was assessed by gas chromatography. Cell survival and cell death were …

Characterization And Regulation Of The Icsp And Ospz Locus In Shigella Flexneri, Krystle Lashell Pew

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella flexneri is a gram negative, rod shaped bacterium that is the causative agent of bacillary dysentery, which is characterized by fever, abdominal pain, and bloody diarrhea. Genes essential to the pathogenicity of S. flexneri are encoded by a virulence plasmid. Shigella has evolved a complex regulatory system to regulate transcription of virulence genes. This involves two regulators, VirF and VirB, which allow the bacterium to respond to environmental stimuli and maximally exploit host niches. An additional factor impacting virulence gene regulation is H-NS, a histone nucleoid structuring protein that globally represses transcription. This work addresses the transcriptional regulation of …

The Human Gut Microbiome: Ecology And Recent Evolutionary Changes, Jens Walter, Ruth Ley

Department of Food Science and Technology: Faculty Publications

The human gastrointestinal tract is divided into sections, allowing digestion and nutrient absorption in the proximal region to be separate from the vast microbial populations in the large intestine, thereby reducing conflict between host and microbes. In the distinct habitats of the gut, environmental filtering and competitive exclusion between microbes are the driving factors shaping microbial diversity, and stochastic factors during colonization history and in situ evolution are likely to introduce intersubject variability. Adaptive strategies of microbes with different niches are genomically encoded: Specialists have smaller genomes than generalists, and microbes with environmental reservoirs have large accessory genomes. A shift …

Molecular Analysis Reveals Unique Microbiome In Ileal Pouch During Pouchitis Compared To Healthy Pouches In Ulcerative Colitis And Familial Adenomatous Polyposis, Tiffany Wallingford Glavan

Master's Theses

In severe cases of ulcerative colitis (UC) unresponsive to current treatment options, patients require a complete proctocolectomy, or surgical removal of the colon. Ileal pouch anal anastomosis (IPAA) has become the preferred surgical technique for patients who require surgery, as this method restores rectal function. This procedure is also used to treat colorectal cancers such as adenocarcinoma and familial adenomatous polyposis (FAP). The surgery involves an abdominal colectomy with the construction of an ileal pouch created from folded tissue recovered from the ileal portion of the small intestine. Up to 50% of patients who require IPAA surgery experience an episode …

Novel Model For Multispecies Biofilms That Uses Rigid Gas-Permeable Lenses, Rebecca Peyyala, Sreenatha S. Kirakodu, Jeffrey L. Ebersole, Karen F. Novak

Center for Oral Health Research Faculty Publications

Oral biofilms comprise complex multispecies consortia aided by specific inter- and intraspecies interactions occurring among commensals and pathogenic bacterial species. Oral biofilms are primary initiating factors of periodontal disease, although complex multifactorial biological influences, including host cell responses, contribute to the individual outcome of the disease. To provide a system to study initial stages of interaction between oral biofilms and the host cells that contribute to the disease process, we developed a novel in vitro model system to grow biofilms on rigid gas-permeable contact lenses (RGPLs), which enable oxygen to permeate through the lens material. Bacterial species belonging to early- …

Archaeoparasitology Of Chaco Canyon, Rachel Paseka

Department of Environmental Studies: Undergraduate Student Theses

Ancient cultures of the Colorado Plateau have been a focus of archaeoparasitology since its inception, and a vast parasitological history is recorded in coprolites preserved in this arid region. The inhabitants of Chaco Canyon dominated Ancestral Puebloan culture between 1050 and 1120 AD and were responsible for the construction of great towns, road systems, and early agriculture. Analysis of the parasites preserved in fecal remains contributes to an increased knowledge of ancient Chacoan health and culture. Nineteen coprolites from four sites in Chaco Canyon were rehydrated and analyzed microscopically for parasite remains. Rhabditiform and filariform nematode larvae were found from …

Microbiological Safety Of Organic Fertilizers Used For Produce Production, Cortney Miller

All Theses

Over the last few decades there has been an increase in the use of organic fertilizers due to the rise in popularity of organic food production. However, if the fertilizers are not adequately sanitized there is the possibility of contamination of agricultural crops by foodborne pathogens from the spreading of organic fertilizers onto the crops. This is especially important for animal waste-based fertilizers since animals frequently carry foodborne pathogens. Furthermore, antibiotic use in food animal production may induce antimicrobial resistance in gut bacteria which can be spread to crops and the environment through fertilizer use. The objectives of this study …

Requirement Of Ssdelseed-Motif Of Escherichia Coli F1FO Atp Synthase In Antimicrobial Peptide Binding., Junior Kom Tayou

Electronic Theses and Dissertations

F₁F_O ATP synthase is a membrane bound enzyme capable of synthesizing and hydrolyzing ATP. Lately, α-helical cationic peptides such as melittin and melittin related peptide (MRP) were shown to inhibit E. coli ATP synthase. The proposed but unconfirmed site of inhibition is βDELSEED-motif formed by the residues 380-386, located at the interface of α/β subunit of ATP synthase. This project was a mutagenic analysis of βDELSEED-motif residues to understand the binding mechanism and mode of action of peptide inhibitors. The study addressed 2 main questions: Are the antibacterial/anticancer effects of these peptides related to their inhibitory action …

Using Polymerase Chain Reaction To Detect Nifh And Vnfdgk In A Novel Acidophilic Microbial Community, Samantha L. Flowers

Undergraduate Honors Theses

Acidophiles are widely known for their ability to exploit harsh environments, typically consisting of high temperatures, dissolved metal concentrations, and acidic conditions. Consequently, different acidophilic species are employed industrially in applications such as biomining and bioleaching. However, their full potential in bioremediation, and in industrial practices, has yet to be fully explored because many of these acidophiles are difficult to culture in laboratory conditions or have yet to be properly identified. This investigation focuses on a novel community sampled from the Richmond Mine site in Iron Mountain, California, consisting of a filamentous fungus and prokaryotes. This consortium can be cultured …

An Investigation Of The Composition, Microbial Digestion And Potential Applications Of An Industrial By-Product Of Seaweed Extraction, Juncal Nogales Esteban

Theses

Commercial preparation of seaweed extract from Ascophyllum nodosum, for use as fertilizer and soil improver, produces a residue which requires remediation. This residue is rich in nutrients and offers potential for other added-value products. The residue’s composition and microbial flora were studied, a microbial digestion system was developed, and extracts were screened for anti-hyaluronidase and anti-elastase activities.

The residue had a pH of 8.61±0.39, 16% (w/w) TS which comprised 40.6% minerals, 29.5% fibre, 20.9% lipid, 4.9% protein and 0.48% polyphenols. The microbial digestion included an initial 3-day anaerobic phase during which pH decreased from 9.12 to 7.89. At day 3, …

Stress Response And Pathogenesis Of Salmonella Enterica Serovar Typhimurium, Jigna D. Shah

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Salmonella is a food-borne pathogen that leads to substantial illness worldwide. The clinical syndromes associated with Salmonella infection are enteric (typhoid) fever and gastroenteritis, in healthy humans. Typhoid fever is caused by host-adapted S. Typhi and S. Paratyphi. Gastroenteritis is caused by serovars usually referred to as non typhoidal Salmonellae (NTS). In recent years, an increasing number of outbreaks due to NTS, despite increased efforts in food safety, were reported because of persistence of Salmonella in the food chain. Thus I hypothesized that Salmonella is able to withstand stresses in the environment and treatments used during food processing …

Design Of A Factorial Experiment With Randomization Restrictions To Assess Medical Device Performance On Vascular Tissue, Wiebke Diestelkamp, Carissa M. Krane, Margaret Pinnell

Biology Faculty Publications

Background: Energy-based surgical scalpels are designed to efficiently transect and seal blood vessels using thermal energy to promote protein denaturation and coagulation. Assessment and design improvement of ultrasonic scalpel performance relies on both in vivo and ex vivo testing. The objective of this work was to design and implement a robust, experimental test matrix with randomization restrictions and predictive statistical power, which allowed for identification of those experimental variables that may affect the quality of the seal obtained ex vivo.

Methods: The design of the experiment included three factors: temperature (two levels); the type of solution used to perfuse the …

Endo-Porter–Mediated Delivery Of Phosphorodiamidate Morpholino Oligos (Pmos) In Erythrocyte Suspension Cultures From Cope's Gray Treefrog Hyla Chrysoscelis, Venkateshwar Mutyam, Matthew V. Puccetti, James Frisbie, David L. Goldstein, Carissa M. Krane

Biology Faculty Publications

Cope's gray treefrog, Hyla chrysoscelis, is a freeze-tolerant anuran that accumulates cryoprotective glycerol during cold acclimation. H. chrysoscelis erythrocytes express the aquaglyceroporin HC-3, which facilitates transmembrane glycerol and water movement. Aquaglyceroporins have no pharmacological inhibitors, and no genetic knockout tools currently exist for H. chrysoscelis. A phosphorodiamidate morpholino oligo (PMO)–mediated expression knockdown approach was therefore pursued to provide a model for testing the role of HC-3. We describe a novel procedure optimized for specific, efficient knockdown of HC-3 expression in amphibian erythrocyte suspensions cultured at nonmammalian physiological temperatures using Endo-Porter. Our protocol includes three critical components: pre-incubation at 37°C, …

Knowledge And Beliefs Among Health Care Workers Regarding Hepatitis B Infection And Needle Stick Injuries At A Tertiary Care Hospital, Karachi, Faiza Habib, Durreshahwar K Khan, Shan-E-Abbas, Faiza Bhatti, Afia Zafar

Department of Pathology and Laboratory Medicine

Hepatitis B virus (HBV) infection is a recognized occupational risk for health care workers (HCWs). This study aimed to assess the knowledge and beliefs of HCWs regarding HBV transmission and needle stick injuries (NSIs). A cross-sectional questionnaire based KAP study was conducted at Civil Hospital, Karachi, during the period of January to September 2006. HCWs were inquired about possible modes of HBV transmission and association with NSIs. Data were entered using EpiInfo 6.04d software. Statistical analysis was performed using SPSS 12.5 software. A total of 343 HCWs participated, and those answered at least 5 correct modes of HBV transmission were …

Investigation Of Bovine Herpesvirus 1 (Bhv-1) Encoded Infected Cell Protein 0 (Bicp0), Natasha N. Gaudreault

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

Bovine herpesvirus 1 (BHV-1) is a significant pathogen of cattle.  Following acute infection, BHV-1 establishes a latent infection that persists for the life of the infected host.  Stress induced factors cause the virus to reactivate from latency, resulting in virus transmission and transient immune suppression.  BHV-1 encoded bICP0 is expressed early and constitutively throughout productive infection.  bICP0 is critical for efficient viral replication, virulence, and reactivation in cattle because it stimulates viral transcription and interferes with innate immune responses.  bICP0 potentially interacts with a variety of proteins to activate viral gene expression and inhibit innate antiviral defenses.  bICP0 localizes to …

Role Of Vitamin-D3 And Retinoic Acid In A Human Thp-1 Macrophage Model Of Mycobacterium Tuberculosis Infection, Jaymie L. Estrella

Dissertations and Theses (Open Access)

Mycobacterium tuberculosis (Mtb) replicates within the human macrophages and we investigated the activating effects of retinoic acid (RA) and vitamin D3 (VD) on macrophages in relation to the viability of Mtb. A combination of these vitamins (RAVD) enhanced the receptors on THP-1 macrophage (Mannose receptor and DC-SIGN) that increased mycobacterial uptake but inhibited the
subsequent intracellular growth of Mtb by inducing reactive oxygen species (ROS) and autophagy. RAVD also enhanced antigen presenting and homing receptors in THPs that suggested an activated phenotype for THPs following RAVD treatment. RAVD mediated activation was also associated with a marked phenotypic change in Mtb …

Multiple Posttranscriptional Regulatory Features Control Expression Of Ethanolamine Utilization Genes In Enterococcus Faecalis, Kristina A. Fox

Dissertations and Theses (Open Access)

Enterococcus faecalis is a Gram-positive bacterium that lives as a commensal organism in the mammalian gastrointestinal tract, but can behave as an opportunistic pathogen.  Our lab discovered that mutation of the eutK gene attenuates virulence of E. faecalis in the C. elegans model host.  eutK is part of the ethanolamine metabolic pathway which was previously unknown in E. faecalis.  I discovered the presence of two unique posttranscriptional regulatory features that control expression of eut locus genes.  The first feature I found is an AdoCBL riboswitch, a cis-acting RNA regulatory element that acts as a positive regulator of gene …

Activities Of Muscadine Grape Skin And Polyphenolic Constituents Against Helicobacter Pylori, Joseph Brown

All Dissertations

Helicobacter pylori is a microaerophilic, gram-negative bacterium and among the most persistent of all human pathogens. Its presence in the gastric environment is corre-lated with diseases such as gastritis, peptic ulcers, mucosa-associated lymphoid tissue lymphoma, and gastric carcinoma. Multiple factors are believed responsible for disease progression and outcome including infecting strain(s) genetic composition, age of acqui-sition, host immune response, environment, and diet. Due to the complexity of H. pylori infection, all possible host-pathogen interactions should be considered. One important factor frequently underplayed is host dietary habits which may serve a more important role during and immediately following infection with H. …

Identification, Cloning And Characterization Of Van Operon In Cyanobacterium Synechococcus Sp. Iu 625, Robert Newby Jr.

Seton Hall University Dissertations and Theses (ETDs)

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Knowledge And Beliefs Among Health Care Workers Regarding Hepatitis B Infection And Needle Stick Injuries At A Tertiary Care Hospital, Karachi, Faiza Habib, Durreshahwar K Khan, Shan-E Abbas, Faiza Bhatti, Afia Zafar

Department of Pathology and Laboratory Medicine

Hepatitis B virus (HBV) infection is a recognized occupational risk for health care workers (HCWs). This study aimed to assess the knowledge and beliefs of HCWs regarding HBV transmission and needle stick injuries (NSIs). A cross-sectional questionnaire based KAP study was conducted at Civil Hospital, Karachi, during the period of January to September 2006. HCWs were inquired about possible modes of HBV transmission and association with NSIs. Data were entered using EpiInfo 6.04d software. Statistical analysis was performed using SPSS 12.5 software. A total of 343 HCWs participated, and those answered at least 5 correct modes of HBV transmission were …

Elevated Expression Of Squamous Cell Carcinoma Antigen (Scca) Is Associated With Human Breast Carcinoma, Joseph M. Catanzaro, Jennifer L. Guerriero, Jingxuan Liu, Namratha Sheshadri, John J. Chen, Wei-Xing Zhong

Department of Molecular Genetics and Microbiology Faculty Publications

Squamous cell carcinoma antigen (SCCA) belongs to the serine protease inhibitor (Serpin) family of proteins. Elevated expression of SCCA has been used as a biomarker for aggressive squamous cell carcinoma (SCC) in cancers of the cervix, lung, head and neck, and liver. However, SCCA expression in breast cancer has not been investigated. Immunohistochemical analysis of SCCA expression was performed on tissue microarrays containing breast tumor tissues (n = 1,360) and normal breast epithelium (n = 124). SCCA expression was scored on a tiered scale (0-3) independently by two evaluators blind to the patient's clinical status. SCCA expression was observed in …

Reactivation Phenotypes Of Parent Strain And Four Viral Constructs In The Murine Hyperthermia Reactivation Model For Herpes Simplex Virus-1, Jason Hardcastle

Student Theses and Dissertations

Herpes simplex virus-1 (HSV-1) is the source of non-genital herpes infections in humans. The host typically suffers an acute infection followed by latency, in which the host appears asymptomatic as the virus remains present within the host. The virus can reactivate, usually due to physiological stress of the host, which once again becomes symptomatic of herpes. This study examines the role of the reactivation critical region (RCR) by removing a 348-base pair (bp) region transcribing latency-associated transcripts (LAT) from the wild-type HSV-1 strain (17syn+). Upon reactivation, the mice infected with the 17syn+ strain exhibited an 89% reactivation rate while the …