Microbiology Commons^™

Strategies For Long-Term Renal Allograft Survival In Iga Nephropathy Patients, Erin E. Lintz

Browse all Theses and Dissertations

IgA nephropathy is one of the most common kidney diseases worldwide. Most IgA nephropathy patients will undergo a kidney transplant as a treatment. Treatment currently includes the use of immunosuppressants which are necessary to prevent graft rejection but present harmful side-effects when taken long-term. This review focuses on strategies which have the ability to promote tolerance of both donor and recipient cells within a transplant recipient. Such strategies allow development of mixed chimerism and thereby alleviate the need for long-term immunosuppressant usage in allograft recipients. These strategies could be applied to IgA nephropathy patients to allow kidney allograft acceptance without …

Amino Acid Substitutions Created In Reverse Transcriptase And Their Influence On Hiv-1 Mutation Frequencies, Amani Saud Alhejely

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As research has shown, a high mutation rate occurs during the reverse transcription RT process because HIV reverse transcriptase fails to correct erroneously incorporated nucleotides during the reverse transcription process. Based on various research articles, a series of amino acid substitutions created in RT were collected to find out their influence on virus mutation frequencies. Two tables were used; one for amino acid substitutions created in RT that increased the HIV-1 mutation rate and another for amino acid substitutions created in RT that decreased the HIV-1 mutation rate. The tables show which amino acid substitutions created in RT decreased or …

Developing A Quantitative Pcr Assay For Detecting Viral Vector Shedding From Animals, Swathee Chinnasamy

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Replication deficient viruses have been used widely for replacing, repairing, and deleting target genes. These recombinant viruses are tested on research animals or patients in clinical trials. Although viral vectors distribute in the body, they are also disseminated into the environment through secretion and excretion processes. By studying the extent of shedding, a proper risk assessment can be performed and appropriate biocontainment can be achieved. Adenoviral and lentiviral vectors were produced from commercially available kits. The transgene present in both vector systems was the lacZ reporter gene encoding for β-galactosidase. Primers and probes were designed for the encapsidation region of …

Detection Of Autoreactive Cd4 T Cells Using Major Histocompatibility Complex Class Ii Dextramers, Chandirasegaran Massilamany, Bijaya Upadhyaya, Arunakumar Gangaplara, Charles Kuszynski, Jay Reddy

Nebraska Center for Virology: Faculty Publications

Background: Tetramers are useful tools to enumerate the frequencies of antigen-specific T cells. However, unlike CD8 T cells, CD4 T cells - especially self-reactive cells - are challenging to detect with major histocompatibility complex (MHC) class II tetramers because of low frequencies and low affinities of their T cell receptors to MHCpeptide complexes. Here, we report the use of fluorescent multimers, designated MHC dextramers that contain a large number of peptide-MHC complexes per reagent.

Results: The utility of MHC dextramers was evaluated in three autoimmune disease models: 1) proteolipid protein (PLP) 139-151-induced experimental autoimmune encephalomyelitis in SJL/J (H-2 …

Tetherin Inhibits Prototypic Foamy Virus Release, Fengwen Xu, Juan Tan, Ruikang Liu, Dan Xu, Yue Li, Yunqi Geng, Chen Liang, Wentao Qiao

Nebraska Center for Virology: Faculty Publications

Background: Tetherin (also known as BST-2, CD317, and HM1.24) is an interferon- induced protein that blocks the release of a variety of enveloped viruses, such as retroviruses, filoviruses and herpesviruses. However, the relationship between tetherin and foamy viruses has not been clearly demonstrated.

Results: In this study, we found that tetherin of human, simian, bovine or canine origin inhibits the production of infectious prototypic foamy virus (PFV). The inhibition of PFV by human tetherin is counteracted by human immunodeficiency virus type 1 (HIV-1) Vpu. Furthermore, we generated human tetherin transmembrane domain deletion mutant (delTM), glycosyl phosphatidylinositol (GPI) anchor …

Robust Rnai-Based Resistance To Mixed Infection Of Three Viruses In Soybean Plants Expressing Separate Short Hairpins From A Single Transgene, Xiuchun Zhang, Shirley Sato, Xiaohong Ye, Anne E. Dorrance, Thomas Jack Morris, Thomas E. Clemente, Feng Qu

Nebraska Center for Virology: Faculty Publications

Transgenic plants expressing double-stranded RNA (dsRNA) of virus

origin have been previously shown to confer resistance to virus infections

through the highly conserved RNA-targeting process termed RNA silencing

or RNA interference (RNAi). In this study we applied this strategy to

soybean plants and achieved robust resistance to multiple viruses with a

single dsRNA-expressing transgene. Unlike previous reports that relied

on the expression of one long inverted repeat (IR) combining sequences

of several viruses, our improved strategy utilized a transgene designed to

express several shorter IRs. Each of these short IRs contains highly conserved

sequences of one virus, forming dsRNA of …

Kaposi Sarcoma-Associated Herpesvirus Degrades Cellular Toll-Interleukin-1 Receptor Domain-Containing Adaptor-Inducing Β-Interferon (Trif), Humera Ahmad, Rachel Gubbels, Florencia Meyer, Thomas Waterbury, Rongtuan Lin, Luwen Zhang

Nebraska Center for Virology: Faculty Publications

Kaposi sarcoma-associated herpesvirus (KSHV) is a human ƴ - herpesvirus associated with several human malignancies. The replication and transcription activator (RTA) is necessary and sufficient for the switch from KSHV latency to lytic replication. Toll-interleukin-1 receptor (TIR) domain-containing adaptorinducing β-interferon (TRIF, also called TIR-domain-containing adaptor molecule-1 (TICAM-1)) is a signaling adaptor molecule that is critically involved in the Toll-like receptor 3 (TLR-3) and TLR-4 signaling pathways for type I interferon (IFN) production, a key component of innate immunity against microbial infection. In this report, we find a new mechanism by which RTA blocks innate immunity by targeting cellular TRIF. RTA …

Human Papillomavirus 16 Variants From Zambian Women With Normal Pap Smears, Yan Jun Lei, Kgomotso Makhaola, Daraporn Pittayakhajonwut, Charles Wood, Peter C. Angeletti

Nebraska Center for Virology: Faculty Publications

Human papillomavirus (HPV) type 16 is the most prevalent high-risk viral genotype associated with cervical cancer. Six distinct phylogenetic clusters of HPVs have been identified and are distributed differently across five continents. HPV16 DNA was extracted from cervico-lavage samples from women with normal pap smears. The LCR regions were amplified in triplicate, cloned, sequenced, and analyzed from a total of 11 recovered HPV16 positive samples [Ng’andwe et al. (2007): BMC Infect Dis 7:77] were analyzed for sequence variation. The HPV16 LCR variants were assessed for promoter activity by use of a luciferase reporter gene. Six novel HPV16 variants with nucleotide …

Hiv-1 Clade B And C Isolates Exhibit Differential Replication: Relevance To Macrophage-Mediated Neurotoxicity, Agnes A. Constantino, Yunlong Huang, Hong Zhang, Charles Wood, Jialin C. Zheng

Nebraska Center for Virology: Faculty Publications

HIV-associated neurocognitive disorders (HAND) continue to be a consequence of HIV-1 infection among clade B-infected individuals. In contrast, the incidence of severe neurological impairment is lower among clade C-infected patients in regions of Sub-Saharan Africa and India. Biological aspects such as replication, cytopathicity, inflammatory response, and neurotoxicity unique to each clade influence neuropathogenicity and ultimately affect the clinical outcome of the disease. We hypothesize that productive infection by clade C isolates leads to macrophagemediated neurotoxicity, although to a lesser extent than clade B isolates. Using a panel of primary isolates of clades B and C we demonstrated that clade B …

The Zambia Children's Ks-Hhv8 Study: Rationale, Study Design, And Study Methods, Veenu Minhas, Kay L. Crabtree, Ann Chao, Janet M. Wojcicki, Adrian M. Sifuniso, Catherine Nkonde, Chipepo Kankasa, Charles D. Mitchell, Charles Wood

Nebraska Center for Virology: Faculty Publications

The epidemic of human immunodeficiency virus in Zambia has led to a dramatic rise in the incidence of human herpesvirus-8 (HHV-8)–associated Kaposi's sarcoma in both adults and children. However, there is a paucity of knowledge about the routes of HHV-8 transmission to young children. The Zambia Children's KS-HHV8 Study, a large, prospective cohort study in Lusaka, Zambia, was launched in 2004 to investigate the role of household members as a source of HHV-8 infection in young children and social behaviors that may modify the risk of HHV-8 acquisition. This cohort is distinct from other epidemiologic studies designed to investigate HHV-8 …

Prevalence Of Human Herpesvirus 8 (Hhv8) And Hepatitis C Virus (Hcv) In A Rural Community With High Risk For Blood Borne Infections In Central China, Tiejun Zhang, Na He, Yingying Ding, Kay L. Crabtree, Veenu Minhas, Charles Wood

Nebraska Center for Virology: Faculty Publications

Former illegal blood donation in the past decade has caused HIV outbreaks in some rural areas in China. Other HIV associated virus infections, such as human herpesvirus 8 (HHV8) in such areas are still not well defined. In order to explore HHV8 and HCV seroprevalence and potential risk factors in such areas, a cross-sectional study with 305 HIV positive and 315 HIV negative subjects recruited from a rural county in Shanxi province was conducted, where illegal blood collection was reported. Interview questionnaires and serum testing were carried out with these participants. HCV and HHV8 seroprevalence were found to be higher …

Comparison Of Adenoviruses As Oncolytics And Cancer Vaccines In An Immunocompetent B Cell Lymphoma Model, Eric A. Weaver, Christopher Y. Chen, Shannon M. May, Mary E. Barry, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

We have screened human adenoviruses (Ads) for oncolytic activity against a variety of mouse and hamster cell lines and have found a number that are susceptible to a variety of Ad serotypes. A20 lymphoma is derived from BALB/c mice and is susceptible to infection and killing by a variety of human Ads. A20 is also a suitable cancer vaccine model, because these cells express a unique immunoglobulin variable region that can be targeted by vaccination. To compare Ads as cancer vaccines versus Ads as oncolytics, A20 tumors were initiated in im- munocompetent BALB/c mice. Mice immunized with first-generation Ad5 expressing …

Advances And Future Challenges In Adenoviral Vector Pharmacology And Targeting, Reeti Khare, Christopher Y. Chen, Eric A. Weaver, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Adenovirus is a robust vector for therapeutic applications, but its use is limited by our understanding of its complex in vivo pharmacology. In this review we describe the necessity of identifying its natural, widespread, and multi-faceted interactions with the host since this information will be crucial for efficiently redirecting virus into target cells. In the rational design of vectors, the notion of overcoming a sequence of viral “sinks” must be combined with re-targeting to target populations with capsid as well as shielding the vectors from pre-existing or toxic immune responses. It must also be noted that most known adenoviral pharmacology …

Species D Adenoviruses As Oncolytics Against B-Cell Cancers, Christopher Y. Chen, Julien S. Senac, Eric A. Weaver, Shannon M. May, Diane F. Jelinek, Philip Greipp, Thomas Witzig, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Purpose: Oncolytic viruses are self-amplifying anticancer agents that make use of the natural ability of viruses to kill cells. Adenovirus serotype 5 (Ad5) has been extensively tested against solid cancers, but less so against B-cell cancers because these cells do not generally express the coxsackie and adenoviral receptor (CAR). To determine whether other adenoviruses might have better potency, we "mined" the adenovirus virome of 55 serotypes for viruses that could kill B-cell cancers.

Experimental Design: Fifteen adenoviruses selected to represent Ad species B, C, D, E, and F were tested in vitro against cell lines and primary patient B-cell cancers …

Regulation Of The Latency–Reactivation Cycle By Products Encoded By The Bovine Herpesvirus 1 (Bhv-1) Latency-Related Gene, Clinton Jones, Leticia Frizzo Da Silva, Devis Sinani

School of Veterinary and Biomedical Sciences: Faculty Publications

Like other α-herpesvirinae subfamily members, the primary site for bovine herpesvirus 1 (BHV-1) latency is ganglionic sensory neurons. Periodically BHV-1 reactivates from latency, virus is shed, and consequently virus transmission occurs. Transcription from the latency-related (LR) gene is readily detected in neurons of trigeminal ganglia (TG) of calves or rabbits latently infected with BHV-1. Two micro-RNAs and a transcript encompassing a small open reading frame (ORF-E) located within the LR promoter can also be detected in TG of latently infected calves. A BHV-1 mutant that contains stop codons near the beginning of the first open reading frame (ORF2) within the …

Dur3 Is The Major Urea Transporter In Candida Albicans And Is Co-Regulated With The Urea Amidolyase Dur1,2, Dhammika H. M. L. P Navarathna, Aditi Das, Joachim Morschhauser, Kenneth W. Nickerson, David D. Roberts

Kenneth Nickerson Papers

Hemiascomycetes, including the pathogen Candida albicans, acquire nitrogen from urea using the urea amidolyase Dur1,2, whereas all other higher fungi use primarily the nickel-containing urease. Urea metabolism via Dur1,2 is important for resistance to innate host immunity in C. albicans infections. To further characterize urea metabolism in C. albicans we examined the function of seven putative urea transporters. Gene disruption established that Dur3, encoded by orf 19.781, is the predominant transporter. [¹⁴C]Urea uptake was energy-dependent and decreased approximately sevenfold in a dur3D mutant. DUR1,2 and DUR3 expression was strongly induced by urea, whereas the other putative transporter genes …

Analysis Of Risk Factors Associated With Asymptomatic Colonization Of Methicillin Resistant Staphylococcus Aureus (Mrsa) Among Community College Students, Marilynn Kish-Molina

Walden Dissertations and Doctoral Studies

The bacterium Staphylococcus aureus has been an important human ailment for centuries, and with the overuse of antibiotics, methicillin resistant Staphylococcus aureus (MRSA) has emerged as a deadly, costly pathogen worldwide. Healthy carriers can become sick or can spread MRSA without symptoms. The amount of asymptomatic colonization among healthy college students and risk factors for colonization by MRSA are not well understood. According to the epidemiologic triangle model, the host (students who take antibiotics or have a history of skin infections), the infectious agent (MRSA) and the environment (direct contact with people, animals, or objects that may harbor MRSA) all …

Detection Of The Sire1 Env-Like Protein, A Potential Retroviral Protein In Soybean, Garen Gaston

Master's Theses

Long terminal repeat (LTR) retroelements are mobile DNAs that are ubiquitous in eukaryotic genomes and include retroviruses, endogenous retroviruses and retrotransposons. Though retrotransposons, which are noninfectious, can make up as much as 80% of plant genomes, no traces of retroviral elements have been confirmed in plants. However, the 2000-copy soybean retrotransposon SIRE1 has an extra open reading frame, that has been described as env-like, because its conceptual translation product is predicted to have features of retroviral envelope proteins, which sponsor infectivity. Demonstrating that this region encodes an envelope protein would extend the range of endogenous retroviruses to plants. Demonstrating also …

An Investigation Of The Subtype Diversity Of Clinical Isolates Of Irish Clostridium Difficile Ribotypes 027 And 078 By Repetitive-Extragenic Palindromic Pcr, Denise Drudy, K. Solomon, S. Murray, L. Scott, S. Mcdermott,, A. Martin, C. O’Donoghue, M. Skally, K. Burns, L. Fenelon, F. Fitzpatrick,, L. Kyne, S. Fanning

Articles

A repetitive-extragenic palindromic PCR (rep-PCR) subtyping method (DiversiLab) in conjunction with ribotyping, toxinotyping and antimicrobial-susceptibility testing was used to detect subtypes within Clostridium difficile ribotypes 027 and 078. Clinical isolates of ribotypes 027 (toxinotype III) (n530) and 078 (toxinotype V) (n523) were provided by health-care facilities across the Republic of Ireland over 2 months in 2006 and 1 month in 2009. Ribotype 027 isolates were significantly more related to each other (9 different subtype profiles) when compared to ribotype 078 isolates (14 different profiles) (P50.001; cut-off .90 % similarity). Almost half of ribotype 078 isolates (45.5 %) showed no relationship …

Sex And The Seas: Gene Transfer Agents, Elizabeth Young

USF Tampa Graduate Theses and Dissertations

Gene Transfer Agents (GTAs) are phage-like pthesiss that are produced by many alpha proteobacteria in late stationary growth phase and are capable of transferring chromosomal genes (termed "constitutive transduction"). Examination of alpha proteobacterial genomic sequences indicated widespread occurrence of GTA-like elements. The goal of this study was to investigate gene transfer potential of GTAs of marine alpha proteobacteria in culture as well as in natural marine environments. Another goal was to determine the potential of bacterial symbionts from zooxanthellae and coral to genetically transfer beneficial properties between symbionts. Ruegeria mobilis (ID 45A6) was isolated from cultures of the coral endosymbiotic …

Role Of Type Ii Transmembrane Serine Proteases In Coronavirus Production, Gitanjali Cuckemane Subramanya

Master's Theses

Proteolytic cleavage of Coronavirus spike proteins at the appropriate time and location results in efficient virus entry activation. Type II transmembrane serine proteases (TTSPs), specifically, transmembrane protease serine 2 (TMPRSS2) when expressed on target cells, enhance SARS coronavirus entry by activating spike cleavage. This study investigated the effect of TTSPs expressed in Coronavirus producer cells. Murine Hepatitis Virus strain A59 (MHV A59) viruses produced in the absence of TMPRSS2 required target cell protease activity - either cell surface serine proteases or endosomal acidophilic proteases - for entry. MHV A59 viruses produced in the presence of TMPRSS2 were less infectious overall, …

Assessing The Relationship Of Monocytes With Primary And Secondary Dengue Infection Among Hospitalized Dengue Patients In Malaysia, 2010: A Cross-Sectional Study, Benjamin Glenn Klekamp

USF Tampa Graduate Theses and Dissertations

Dengue, a group of four similar viruses transmitted through the bite of a mosquito, is estimated to infect upwards of 100 million annually in over 100 nations throughout the global equatorial belt. Distribution of global dengue is highly skewed as Southeast Asian and Western Pacific regions endure 75% of the global dengue burden. Similar to other regional countries, Malaysia has been rapidly urbanizing, which has supported a hyperendemic dengue state.

The biological pathway by which dengue infection causes a wide range of clinical manifestations, spanning asymptomatic to life-threatening severe complications, is not comprehensively understood. Historically, severe dengue complications have primarily …

Gastric Malt Lymphoma: A Rarity, Shahid Pervez, Naureen Ali, Hina Aaqil, Khalid Mumtaz, Syed Siddiq Ullah

Department of Pathology and Laboratory Medicine

Association of Helicobacter pylori (H. Pylori) infection with gastric ‘Mucosa Associated Lymphoid Tissue’ (MALT) lymphomas (MALTomas) is well established. In this study the frequency and characteristics of gastric MALToma over a period of 18 years was evaluated. During this period 24 patients with gastric MALToma were diagnosed; out of them, 13 (54.2%) had active H. Pylori infection. The mean and median age was 49.7 and 53.5 years. The male: female ratio was 17:7. The common presenting complaints were epigastric pain (n=10) and dyspepsia (n=9). Endoscopic findings revealed mild gastric hyperemia (n=16), superficial erosions (n=4) and superficial ulcers (n=4). It was …

Microbial Ecology And Functional Genomics Of Deep-Water Coral-Associated Microbes, Julia Parker Galkiewicz

USF Tampa Graduate Theses and Dissertations

Lophelia pertusa is a cosmopolitan cold-water coral, often found in aphotic waters (>200m). Aggregations of L. pertusa (reefs) provide important habitat to many invertebrate and fish species and act as biodiversity hotspots in the deep sea. The health and diversity of these reefs is of vital importance to deep-sea ecosystems, and the microbial consortia associated with L. pertusa form the most basic ecological level. Deciphering the diversity and function of these microbes provides insight into the roles they play in maintaining reef health. This dissertation takes microbiological techniques that are used in shallow-water coral microbial research and applies them …

The Role Of Hiv-1 Proteins In Alzheimer's Disease Pathology, Brian Nelson Giunta

USF Tampa Graduate Theses and Dissertations

Prevalence of HIV-associated cognitive impairment is rising, the worst form of which is HIV-associated dementia (HAD). The disease is fuiled by a chronic innate type pro-inflammatory response in the brain which is highly dependent upon the activation of microglia. We first created an in vitro model of HAD composed of cultured microglial cells synergistically activated by the addition of IFN-gamma and the HIV-1 coat glycoprotein, gp120. This activation, as measured by TNF-alpha and NO release, is synergistically attenuated through the alpha7nAChR and p44/42 MAPK system by pretreatment with nicotine, and the cholinesterase inhibitor, galantamine. As these medications have been FDA …

Investigation Of The Optimal Dissolved Co2 Concentration And Ph Combination For The Growth Of Nitrifying Bacteria, Raymond Anthony Morris

USF Tampa Graduate Theses and Dissertations

Ammonium (NH₄⁺) is a biological nutrient that is transformed in a wastewater treatment plant (WWTP) in a process called activated sludge. This is accomplished in an aerobic environment using microorganisms and inorganic carbon that convert the ammonium to nitrate (NO₃^-). This process is termed nitrification. Removal of ammonium is necessary due to its oxygen demand and toxicity to the environment.

Nitrification is considered a slow process due to the slow growth rate of the nitrifying bacteria. Ammonia oxidizing bacteria (AOB) first covert the ammonium (NH₄⁺) to nitrite (NO₂^-) …

Identification And Characterization Of The Human Herpesviruses 6a And 6b Genome Integration Into Telomeres Of Human Chromosomes During Latency, Jesse Herbert Arbuckle

USF Tampa Graduate Theses and Dissertations

While the latent genome of most Herpesviruses persists as a nuclear circular episome, previous research has suggested that Human Herpesvirus 6 (HHV-6) may integrate into host cell chromosomes, and be vertically transmitted in the germ-line. Because the HHV-6 genome encodes a perfect TTAGGG telomere repeat array at the right end direct repeat (DR_R) and an imperfect TTAGGG repeat at the end of the left end direct repeat (DR_L), we established a hypothesis that during latency, the HHV-6A and HHV-6B genome integrates into the telomeres of human chromosomes through homologous recombination with the n(TTAGGG) viral repeats, and …

Development Of An Elisa For Eastern Equine Encephalitis Virus That Can Differentiate Infected From Vaccinated Horses, Andrea Bingham

USF Tampa Graduate Theses and Dissertations

Eastern Equine Encephalitis virus (EEEV) causes a fatal mosquito-borne virus that is vaccine preventable for horses. The conventional serological tests measure antibodies to the structural proteins of EEEV which are also found in the vaccine. This makes it difficult to differentiate infected and vaccinated animals (DIVA). Detection of antibodies to non-structural proteins (NSPs) is a theoretical strategy that would allow you to survey natural infections among vaccinated populations. This test would also allow for more accurate representations of the natural infection rate, vaccination rate, and help identify vaccine failures. The potential uses of the NSPs of Eastern Equine Encephalitis virus …

Microbial Landscapes Of Corals And Ctenophores, Camille Arian Daniels

USF Tampa Graduate Theses and Dissertations

As technology and engineering allow mankind to survey nature at finer scales, the importance of bacteria has been elucidated in their metabolic diversity, ability to transfer genetic information, involvement in biogeochemical cycling, and sheer abundance. With an individual domain of life unto themselves, this diverse group of microorganisms plays an integral role in facilitating life on land and in the oceans, and is second only to viruses in abundance on Earth. They carve niches in a wide range of environments, including those inhospitable to other life forms, and reside in concert or to the detriment of other microbes and/or hosts …

Mechanistic Modeling Of Photocatalytic Water Disinfection, Omatoyo Kofi Dalrymple

USF Tampa Graduate Theses and Dissertations

The main goal of this research was to develop a mechanism-based model for photocatalytic disinfection of bacteria in water using suspended catalyst pthesiss in batch reactors. The photocatalytic disinfection process occurs as a semiconductor photocatalyst, most commonly titanium dioxide (TiO₂), is irradiated with light of wavelength less than 380 nm to produce hydroxyl radicals and other highly reactive oxidants which can inactivate microorganisms. Photocatalytic disinfection involves a complex interaction of many fundamental mechanisms such as light absorption and scattering by semiconductor pthesiss, electrochemical surface reactions, and heterogeneous colloidal stability. Current models, based largely on chemical reacting systems, do …