Microbiology Commons^™

Iron Oxide And Calcite Associated With Leptothrix Sp. Biofilms Within An Estavelle In The Upper Floridan Aquifer, Lee J. Florea, Chasity L. Stinson, Josh Brewer, Rick Fowler, B Joe Kearns, Anthony M. Greco

International Journal of Speleology

In Thornton’s Cave, an estavelle in west-central Florida, SEM, EDS, and XRD data reveal biofilms that are predominantly comprised of FeOOH-encrusted hollow sheaths that are overgrown and intercalated with calcite. Fragments of this crystalline biofilm adhere to the walls and ceiling as water levels vary within the cave. Those on the wall have a ‘cornflake’ appearance and those affixed to the ceiling hang as fibrous membranes. PCR of DNA in the active biofilm, combined with morphologic data from the tubes in SEM micrographs, point to Leptothrix sp., a common Fe-oxidizing bacteria, as the primary organism in the biofilm. Recent discoveries …

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 …

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 …

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 …

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 …

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 …

Characterization Of Photochromogenic Mycobacterium Spp. From Chesapeake Bay Striped Bass Morone Saxatilis, D. T. Gauthier, A. M. Helenthal, M. W. Rhodes, W. K. Vogelbein, H. I. Kator

Biological Sciences Faculty Publications

A large diversity of Mycobacterium spp. has been isolated from striped bass Morone saxatilis in Chesapeake Bay, USA. The new species M. shottsii and M. pseudoshottsii are the dominant isolates, while the classical fish pathogen M. marinum is found much less frequently. M. fortuitum and M. chelonae, other Mycobacterium spp. known to commonly infect fishes, have not yet been aseptically isolated from striped bass within Chesapeake Bay. While M. pseudoshottsii and M. shottsii have been phenotypically and genotypically characterized, other less common mycobacterial isolates have not. In the present study, we describe 17 photochromogenic isolates from Chesapeake …

Human Endogenous Retrovirus Transcription Profiles Of The Kidney And Kidney-Derived Cell Lines, Sonja Haupt, Michele Tisdale, Michelle Vincendeau, Mary Anne Clements, David T. Gauthier, Raymond Lance, O. John Demmes, Adriana Tuqueti-Neves, Elfriede Noessner, Christine Leib-Mösch, Alex D. Greenwood

Biological Sciences Faculty Publications

The human genome comprises approximately 8-9% of human endogenous retroviruses (HERVs) that are transcribed with tissue specificity. However, relatively few organs have been examined in detail for individual differences in HERV transcription pattern, nor have tissue-to-cell culture comparisons been frequently performed. Using an HERV-specific DNA microarray, a core HERV transcription profile was established for the human kidney comparing 10 tissue samples. This core represents HERV groups expressed uniformly or nearly so in non-tumour kidney tissue. The profiles obtained from non-tumour tissues were compared to 10 renal tumour tissues (renal cell carcinoma, RCC) derived from the same individuals and additionally, to …

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 …

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 …

Molecular Mechanisms Of Poly [Adp-Ribose] Polymerase-1 In Hiv-1 Infection, Daniel Reyes

Open Access Theses & Dissertations

Poly (ADP-ribose) polymerase-1 (PARP-1) is a cellular enzyme involved in genome stability and transcriptional regulation. The role of this protein in HIV-1 infection is largely controversial. Some reports indicated a fundamental role of PARP-1 in HIV-1 DNA integration and results from other laboratories do not support these conclusions. An important characteristic in all these experiments is that the HIV-1 target cells that were used express, in addition to PARP-1, the functional homologue PARP-2. We evaluated the role of PARP-1 in the chicken B lymphoblastoid cell line DT40. These cells naturally lack PARP-2 and support the early steps of HIV infection. …

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, …

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 …

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 …

Abundance Of Eukaryotic Microbes In The Deep Subtropical North Atlantic, Danielle Morgan-Smith, Gerhard J. Herndl, Hendrik M. Van Aken, Alexander B. Bochdansky

OES Faculty Publications

The meso- and bathypelagic ocean comprises the largest habitat on earth, yet we know very little about the distribution and activity of protists in this environment. These small eukaryotes are responsible for controlling bacterial abundance in the surface ocean and are major players in the material and energy transfer of pelagic food webs. In this paper, we quantify microbial eukaryotes in the deep North Atlantic, as well as provide a basic characterization of eukaryote community changes through the water column. To this end, we counted organisms using 2 different approaches: (1) catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH, also …

Characterization Of Putative Iron Responsive Genes As Species-Specific Indicators Of Iron Stress In Thalassiosiroid Diatoms, Leann P. Whitney, Jeremy J. Lins, Margaret P. Hughes, Mark L. Wells, P. Dreux Chappell

OES Faculty Publications

Iron (Fe) availability restricts diatom growth and primary production in large areas of the oceans. It is a challenge to assess the bulk Fe nutritional health of natural diatom populations, since species can differ in their physiological and molecular responses to Fe limitation. We assayed expression of selected genes in diatoms from the Thalassiosira genus to assess their potential utility as species-specific molecular markers to indicate Fe status in natural diatom assemblages. In this study, we compared the expression of the photosynthetic genes encoding ferredoxin (a Fe-requiring protein) and flavodoxin (a Fe-free protein) in culture experiments with Fe replete and …