Microbiology Commons^™

Quantitative Pcr Assay For Mycobacterium Pseudoshottsii And Mycobacterium Shottsii And Application To Environmental Samples And Fishes From The Chesapeake Bay, D. T. Gauthier, K. S. Reece, J. Xiao, M. W. Rhodes, H. I. Kator, R. J. Latour, C. F. Bonzek, J. M. Hoenig, W. K. Vogelbein

Biological Sciences Faculty Publications

Striped bass (Morone saxatilis) in the Chesapeake Bay are currently experiencing a very high prevalence of mycobacteriosis associated with newly described Mycobacterium species, Mycobacterium pseudoshottsii and M. shottsii. The ecology of these mycobacteria outside the striped bass host is currently unknown. In this work, we developed quantitative real-time PCR assays for M. pseudoshottsii and M. shottsii and applied these assays to DNA extracts from Chesapeake Bay water and sediment samples, as well as to tissues from two dominant prey of striped bass, Atlantic menhaden (Brevoortia tyrannus) and bay anchovy (Anchoa mitchilli). Mycobacterium …

Response Surface Optimization Of Crystal Violet Decolorization By Pellets Of Pyncnoporus Sanguineus., Siti Suhana Sulaiman

Student Works (2010-2019)

Ligninolytic enzymes of white-rot fungi have broad specificities and have been implicated in transformation and mineralization of organo-pollutant with chemical structure similar to lignin e.g. synthetic dyes. This study was carried out to optimize selected parameters for decolorization of Crystal violet by Pycnoporus sanguineus in shake flasks. The parameters studied were initial dye concentration (ppm), agitation speed (rpm) and process time. They were optimized using response surface methodology (RSM). Subsequent to the optimization, the decolorization process was scaled up in stirred tank reactor (STR). Effect of different geometry of impellers on the decolorization process was studied. Curved blade and angled …

Isolation And Characterization Of Actinobacteria From Soil Samples Of Signy Island, Antarctica., Pan Shing Yi

Student Works (2010-2019)

In this study, ninety five actinobacterial isolates were cultured from seven soils samples collected on Signy Island, maritime Antarctica. Nine different isolation media were used and the isolates plates were incubated at 15ºC for up to four months. SCN agar serves as the better media for the isolation of actinobacteria. Presence of actinobacteria in the soil samples was also detected using PCR with actinobacteria specific primers. The actinobacterial isolates were characterized based on morphology (Gram-stain, coverslip examination, colour grouping), analysis of DAP isomers, antibacterial activities and by molecular methods (ARDRA, analysis of 16S rRNA sequence and detection of NRPS gene). …

Enterobacterial Repetitive Intergenic Consensus-Pcr (Eric-Pcr) Analysis Among Raw Vegetables Isolates Of Campylobacter Jejuni., Tuan Suraya Tuan Soh

Student Works (2010-2019)

A total of 20 (n=20) raw vegetable isolates of Campylobacter jejuni were examined for the presence of virulence genes and genetic diversity using enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) analysis. All C. jejuni isolates were obtained from the laboratory of Food Science and Biotechnology, University Putra Malaysia, Serdang, Selangor. When specific PCR amplification were determined, all raw vegetables isolates of Campylobacter jejuni contained cadF and ceuE genes. Whereas, 12 (12/20) isolates were positive cdtB and 6 (6/20) were positive cdtC. None of the C. jejuni isolates was cdtA positive. Using ERIC-PCR analysis, all 20 isolates of C. jejuni were …

Antimicrobial Potential Of Selected Actinomycetes Isolated From The Marine Ecosystem., Nur Rahimatul Hayati Abdul Rahman

Student Works (2010-2019)

Actinomycetes are widespread in marine ecosystem. They are of interest in research field as they are capable to produce bioactive secondary metabolites which can be developed into useful pharmaceutical products. An example of the product is antibiotics which can be used to treat infectious diseases. The potential of antibacterial and antifungal activity of eleven marine derived actinomycetes from the genus Streptomyces were studied. They were tested against bacteria Enterobacter faecalis, Staphylococcus aureus, Bacillus subtilis, Pleisiomonas shigelloides and Pseudomonas aeruginosa and fungi Candida parapsilosis and Candida albicans. Primary screening by the cross streak method and secondary screening by diffusion using paper …

Study Of Bacterial Diversity In The Oral Cavity Of Malaysian Subjects., Teoh Wuen Yew

Student Works (2010-2019)

About 700 species of bacteria can inhabit the human oral cavity. This project initially investigated the bacterial diversity within the oral cavity of Malaysian subjects by using culture-dependent techniques and 16S rDNA sequence analysis. The second part of the research profiled the antibiotic resistance of the identified oral bacteria by the Etest method. Three sampling sites of the oral cavity from nine healthy subjects were analyzed: the tooth surface, gingival crevice, and dorsum of the tongue. The tooth surface was shown to harbor 41 species, gingival crevice harbored 51 species and tongue dorsum 41 species. On average, each subject carried …

Application Of Pcr-Based Serogrouping Of Salmonella Enterica., Mohammed Elbagir Mohammed Elhassan Nori

Student Works (2010-2019)

Serotyping is the most fundamental approach in epidemiological surveillance and outbreak investigations for Salmonella. Many multiplex PCR assays have been reported for serotyping Salmonella based on O and H antigens. The aim of this study was to apply and improve the approach in differentiation and serotyping Salmonella enterica strains by combination of sequential multiplex PCRs targeting the O, H and Vi antigens of Salmonella, and this achieved by working on 126 strains. All the strains were purified on BSA and produced black colonies of Salmonella. The strains were confirmed by PCR amplification gene that targets the hilA. 122 of 126 …

Increased Perfusion And Angiogenesis In A Hindlimb Ischemia Model With Plasmid Fgf-2 Delivered By Noninvasive Electroporation, B. Ferraro, Y. L. Cruz, M. Baldwin, D. Coppola, R. Heller

Bioelectrics Publications

Gene therapy approaches delivering fibroblast growth factor-2 (FGF-2) have shown promise as a potential treatment for increasing blood flow to ischemic limbs. Currently, effective noninvasive techniques to deliver plasmids encoding genes of therapeutic interest, such as FGF-2, are limited. We sought to determine if intradermal injection of plasmid DNA encoding FGF-2 (pFGF) followed by noninvasive cutaneous electroporation (pFGFE+) could increase blood flow and angiogenesis in a rat model of hindlimb ischemia. pFGFE+ or control treatments were administered on postoperative day 0. Compared to injection of pFGF alone (pFGFE-), delivery of pFGFE+ significantly increased FGF-2 expression for 10 days. Further, the …

Yersinia Pestis Virulence Factor Yopm Undermines The Function Of Distinct Ccr2+Gr1+ Cells In Spleen And Liver During Systemic Plague, Zhan Ye

University of Kentucky Doctoral Dissertations

Yersinia pestis, the infective agent of bubonic and pneumonic plague, is classified as a category A agent of bioterrorism. YopM, a protein toxin of Y. pestis, is necessary for full virulence in a systemic plague mouse model with ambient-temperature grown bacteria. We used this model to identify the cells undermined by YopM. Natural killer (NK) cells were previously reported to be lost in spleen and blood in a YopM-associated way; however, NK cell depletion was found not to occur in liver, and ablation of NK cells had no effect on bacterial growth, indicating that NK cells are redundant …

Thermocrinis Minervae Sp. Nov., A Hydrogen And Sulfur-Oxidizing, Thermophilic Member Of The Aquificales From A Costa Rican Terrestrial Hot Spring, Sara L. Caldwell, Yitai Liu, Isabel Ferrera, Terry Beveridge, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

A thermophilic bacterium, designated strain CR11T , was isolated from a filamentous sample collected from a terrestrial hot spring on the south-western foothills of the Rincón volcano in Costa Rica. The Gram-negative cells are approximately 2.4–3.9 mm long and 0.5–0.6 mm wide and are motile rods with polar flagella. Strain CR11T grows between 65 and 85 6C (optimum 75 6C, doubling time 4.5 h) and between pH 4.8 and 7.8 (optimum pH 5.9–6.5). The isolate grows chemolithotrophically with S0 , S2O2{ 3 or H2 as the electron donor and with O2 (up to 16 %, v/v) as the sole electron …

Phage Lysins - Structure, Genetics And Applications, Jennifer Garry

Theses

Antibiotics are of the utmost importance in the fight against pathogenic bacteria, however, in recent years there has been a continual increase in the development of antibiotic resistance among bacteria. As a result it has become essential to develop new technologies to combat these pathogens. One such technology is the application of phage lysins as antimicrobial agents against pathogenic infections. A promising phage lysin is LysK, a 495 amino-acid protein derived from Staphylococcal Phage K. LysK can lyse a wide range of staphylococcal species including MRSA. It is also capable of killing both live and dead cells increasing its potential …

Biosynthesis Of Exopolysaccharides From Lactic Acid Bacteria And Evaluation Of Their Prebiotic Potential, Colette Ann Forde

Theses

In this study, two strains of lactic acid bacteria (LAB) namely Weissella kimchii F28 and W. confusa MGl were used for the production of exopolysaccharides (EPS) from sucrose. Both strains produced glucan polysaccharides. In the case of W. kimchii F28, the EPS isolation procedure was performed six times, making modifications in order to optimize the yield of EPS. The maximum yield of EPS for this strain was 16 g per litre of culture. In the case of W. confusa MGl, the EPS isolation procedure was followed five times, resulting in a maximum yield of EPS for this strain of 34.4 …

Detection And Molecular Characterization Of Canine Enteric Viruses In Southern Ireland., Susan Mcelligott

Theses

Enteric viruses, such as canine parvovirus (CPV) and canine coronavirus (CCoV), are a major cause of gastroenteritis in dogs. More serious clinical symptoms occur in young pups, or when both of these viruses infect an animal simultaneously. Caliciviruses and rotaviruses can also cause gastroenteritis in dogs, but these viruses, while causing significant problems in other animal species and humans, are considered to be less significant pathogens of canines. However, on occasion, these viruses have been reported to produce severe clinical symptoms such as vomiting, haemorrhagic enteritis and severe dehydration.

Many viral vaccines for canines are formulated using old vaccine viral …

Electric Pulses To Prepare Feeder Cells For Sustaining And Culturing Of Undifferentiated Embryonic Stem Cells, Lauren M. Browning, Tao Huang, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Current challenges in embryonic-stem-cell (ESC) research include inability of sustaining and culturing of undifferentiated ESCs over time. Growth-arrested feeder cells are essential to the culture and sustaining of undifferentiated ESCs, and they are currently prepared using gammaradiation and chemical inactivation. Both techniques have severe limitations. In this study, we developed a new, simple and effective technique (pulsed-electric-fields, PEFs) to produce viable growth-arrested cells (RTS34st) and used them as high-quality feeder cells to culture and sustain undifferentiated zebrafish ESCs over time. The cells were exposed to 25 sequential 10- nanosecond-electric-pulses (10nsEPs) of 25, 40 and 150 kV/cm with 1s pulse interval, …

Chloroquine Susceptibility And Reversibility In A Plasmodium Falciparum Genetic Cross, Jigar J. Patel, Drew Thacker, John C. Tan, Perri Pleeter, Lisa Checkley, Joseph M. Gonzales, Bingbing Deng, Paul D. Roepe, Roland A. Cooper, Michael T. Ferdig

Biological Sciences Faculty Publications

Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT) are major determinants of verapamil (VP)-reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 x Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the South-East Asia-derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute …

Copper Isotope Fractionation During Surface Adsorption And Intracellular Incorporation By Bacteria, Jesica Urbina Navarrete

Open Access Theses & Dissertations

Copper isotopes may prove to be a useful tool for investigating bacteria-metal interactions recorded in natural waters, soils, and rocks. However, experimental data that constrain Cu isotope fractionation in biologic systems are limited and unclear. In this study we utilized Cu isotopes (65Cu) as a tool to investigate Cu-bacteria interactions, including surface adsorption and intracellular incorporation. Experiments were conducted with individual Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) bacterial species as well as with bacterial consortia from several natural environments. Adsorption experiments were conducted with live or dead cells over the pH range 2.5 to 6. Surface adsorption of Cu …

The Role Of Sumoylation Of Ledgf/P75 In Hiv-1 Infection, Murilo Tadeu Domingues Bueno

Open Access Theses & Dissertations

The lens epithelium-derived growth factor (LEDGF) proteins p75 and p52 are transcriptional co-activators that protect cells from stresses through modulation of stress and heat shock-related genes. Besides regulating such genes, LEDGF/p75 is also important in the process of HOX gene expression and leukemia transformation driven by the MLL histone methyl transferase complex. By exploiting a similar mechanism of interaction between LEDGF/p75 and MLL, the HIV-1 viral protein Integrase (IN) associates with LEDGF/p75 in order to execute efficient viral DNA integration. This present work has identified that LEDGF proteins are posttranslationally modified by SUMO-1 and -3. SUMOylation was found to target …

Pattern Recognition In Cytopathology For Papanicolaou Screening, Jonathan Blackledge, Dmitriy Dubovitskiy

Conference papers

A unique space oriented filer is presented in order to detect and isolate the cell of a nucleus for applications in cytopathology. A classification method for nuclei is then considered based on the application of a set of features which includes certain fractal parameters. Segmentation algorithms are considered in which a self-adjustable sharpening filter is designed to enhance object location. Although the methods discussed and the algorithms developed have a range of applications, in this work we focus the engineering of a system for automating a Papanicolaou screening test using standard optical images

Analysing The Effects Of Loss Of Sin3 In Drosophila Melanogaster, Aishwarya Swaminathan

Wayne State University Dissertations

Sin3A has been previously shown to be an essential gene for Drosophila viability and is implicated in the regulation of cell cycle. In this study, we show that SIN3 is not only required for embryonic viability but also for post-embryonic development. Genetic analysis suggests that the different isoforms of SIN3 may regulate unique sets of genes during development. The developmental lethality occurring due to ubiquitous knock down of SIN3 is hypothesized to be to the result of defects in cell proliferation. Conditional knock down of SIN3 in the wing discs results in a curly wing phenotype in the adult fly. …

Immunomodulatory Effect Of Host And Fungal Eicosanoids During Host-Pathogen Interactions With Candida Albicans, Gitanjali Kundu

Wayne State University Dissertations

Candida albicans, an opportunistic fungal pathogen, poses a significant clinical threat to immunocompromised patients. Diseases associated with this fungus ranges from superficial mucosal infection to life-threatening systemic candidiasis. The mechanisms by which Candida persists at mucosal surfaces in the face of an adaptive response are unclear. Candida produces immunomodulatory oxylipins that cross-react functionally with host eicosanoids, which are considered to play important role in regulating innate and adaptive immune responses. Our objective was to characterize the role of prostaglandins produced by the host and this fungus during host pathogen interactions, both in vitro with dendritic cells (DCs) and macrophages, and …

Antagonistic Activity Of Selected Marine-Derived Streptomyces Spp. Against Plesiomonas Shigelloides., Angelyn Melaya Kloni

Student Works (2010-2019)

In this study, primary and secondary screenings were conducted to evaluate the antibacterial and anti-yeast potential of the eleven selected marine-derived Streptomyces spp., particularly against P. shigelloides. The strains were categorized into three colour groups for morphological grouping according to the colour of aerial mycelium; namely grey, yellow green, and white colour groups. Diffusible pigments were produced by eight of the strains tested. Strain(s) from grey and white with red diffusible pigments colour groups displayed strong antibacterial activity. The yeasts tested were resistant to the bioactive metabolite(s) produced by some of the Streptomyces spp. which had shown high activity against …

Soil Organic Matter Fractions And Aggregate Distribution In Response To Tall Fescue Stands, I. P. Handayani, Mark S. Coyne, R. S. Tokosh

Plant and Soil Sciences Faculty Publications

The study was conducted to evaluate the influences of tall fescue management on soil organic matter fractions and macro- and microaggregate distribution. Soil samples were collected from four paired adjacent fields consisting of five years of tall fescue mono and poly stands in Western Kentucky. Soil samples from 0 to 15 cm and 15 to 30 cm soil depths were analyzed for soil organic C and N, particulate organic matter C (POM-C) and N (POM-N), macro- and micro aggregate distribution and C-associated with macro- and micro- aggregates. Significant effects were observed between stands for all the properties, except total C, …

Bryostatins: Biological Context And Biotechnological Prospects, Amaro E. Trindade-Silva, Grace E. Lim-Fong, Koty H. Sharp

Arts & Sciences Faculty Publications

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and Bryostatins are a family of protein kinase C modulators that have potential applications in biomedicine. Found in miniscule quantities in a small marine invertebrate, lack of supply has hampered their development. In recent years, bryostatins have been shown to have potent bioactivity in the central nervous system, an uncultivated marine bacterial symbiont has been shown to be the likely natural source of the bryostatins, the bryostatin biosynthetic genes have been identified and characterized, and bryostatin analogues with promising biological activity have been developed and tested. Challenges in …

The Im-9 Cell Line: A Model For Evaluating Tcdd-Induced Modulation Of The Polymorphic Human Hs1,2 Enhancer Within The 3' Immunoglobulin Heavy Chain Regulatory Region, Ruth C. Chambers-Turner

Browse all Theses and Dissertations

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a disrupter, of B-cell differentiation, induces binding of the aryl hydrocarbon receptor (AhR) nuclear complex to dioxin responsive elements (DRE) within the mouse immunoglobulin heavy chain regulatory region (3'IgHRR), and produces a marked inhibition of 3'IgHRR activation, IgH expression, and antibody secretion in a well-characterized mouse B-cell line (CH12.LX). The mouse 3'IgHRR consists of at least four enhancers (hs3a; hs1,2; hs3b; hs4), and is highly homologous with the three enhancers (hs3; hs1,2; hs4) of the human 3'IgHRR. A polymorphism of the human hs1,2 enhancer (resulting in varying numbers of tandem repeats containing a DRE and κB site) has …

Rev Interacts With Tubulin Heterodimers To Cause Cell Cycle Defects, Poornima Kotha Lakshmi Narayan

Browse all Theses and Dissertations

Rev is a regulatory protein that plays an important role in the replication of HIV virus by post-transcriptionally promoting expression of viral proteins late in infection. Rev expression also slows cell growth, leads to an accumulation of cells in G2/M specifically before the spindle checkpoint, and can produce changes in ploidy. Because Rev is capable of depolymerizing microtubules (MTs) in vitro, possibly by a mechanism shared with Kinesin-13 proteins, themselves potent cellular MT depolymerases, I tested the hypothesis that these cellular defects were due to an interaction between Rev and tubulin.

To this end, Rev and select Rev mutants defective …

Short Communication: Antiretroviral Therapy Resistance Mutations Present In The Hiv Type 1 Subtype C Pol And Env Regions From Therapy-Naive Patients In Zambia, Sandra Gonzalez, Clement Gondwe, Damien C. Tully, Veenu Minhas, Danielle Shea, Chipepo Kankasa, Tendai M'Soka, Charles Wood

Nebraska Center for Virology: Faculty Publications

The prevalence of antiretroviral therapy (ART) resistance mutations present in HIV-1 subtype C pol and env regions of the proviral DNA was analyzed and compared from therapy-naive individuals before (Cohort A) and after (Cohort B) the availability of free ART in Zambia. Mutations present in sequences published in a previous study from Zambian ART-naive individuals infected with subtype C were analyzed using current parameters for the classification of ART drug resistance and compared with Cohorts A and B. No statistically significant differences were observed when comparing mutations present in the pol and env of these cohorts. However, an increase in …

Primary Gamma-Herpesviral Infection In Zambian Children, Veenu Minhas, Brad P. Brayfield, Kay L. Crabtree, Chipepo Kankasa, Charles D. Mitchell, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background: HHV-8 is closely related to Epstein-Barr virus (EBV), but the clinical presentations of these two infections in early childhood are not well understood. Also, it is not known whether infection by one virus correlates with another. Here, we compare the natural history of infection by these two viruses along with the clinical manifestations and risk factors that are associated with early childhood infection in Zambia, which is an endemic area for HHV-8.

Methods: This study was conducted in a cohort of 12 month old Zambian children (N = 677). Data on socio-economic status and a wide range …

Restricted Genetic Diversity Of Hiv-1 Subtype C Envelope Glycoprotein From Perinatally Infected Zambian Infants, Hong Zhang, Damien C. Tully, Federico G. Hoffmann, Jun He, Chipepo Kankasa, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background: Mother-to-child transmission of HIV-1 remains a significant problem in the resource-constrained settings where anti-retroviral therapy is still not widely available. Understanding the earliest events during HIV-1 transmission and characterizing the newly transmitted or founder virus is central to intervention efforts. In this study, we analyzed the viral env quasispecies of six mother-infant transmission pairs (MIPs) and characterized the genetic features of envelope glycoprotein that could influence HIV-1 subtype C perinatal transmission.

Methodology and Findings: The V1-V5 region of env was amplified from 6 MIPs baseline samples and 334 DNA sequences in total were analyzed. A comparison of …

Subtype-Associated Differences In Hiv-1 Reverse Transcription Affect The Viral Replication, Sergey Iordanskiy, Mackenzie Waltke, Yanjun Feng, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background: The impact of the products of the pol gene, specifically, reverse transcriptase (RT) on HIV-1 replication, evolution, and acquisition of drug resistance has been thoroughly characterized for subtype B. For subtype C, which accounts of almost 60% of HIV cases worldwide, much less is known. It has been reported that subtype C HIV-1 isolates have a lower replication capacity than B; however, the basis of these differences remains unclear.

Results: We analyzed the impact of the pol gene products from HIV-1 B and C subtypes on the maturation of HIV virions, accumulation of reverse transcription products, integration …

Topological Layers In The Hiv-1 Gp120 Inner Domain Regulate Gp41 Interaction And Cd4-Triggered Conformational Transitions, Andrés Finzi, Shi-Hua Xiang, Beatriz Pacheco, Dana-Farber Cancer Institute Wang, Jessica Haight, Aemro Kassa, Brenda Danek, Marie Pancera, Peter D. Kwong, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

The entry of human immunodeficiency virus (HIV-1) into cells is initiated by binding of the gp120 exterior envelope glycoprotein to the receptor, CD4. How does CD4 binding trigger conformational changes in gp120 that allow the gp41 transmembrane envelope glycoprotein to mediate viral-cell membrane fusion? The transition from the unliganded to the CD4-bound state is regulated by two potentially flexible topological layers (layers 1 and 2) in the gp120 inner domain. Both layers apparently contribute to the noncovalent association of unliganded gp120 with gp41. After CD4 makes initial contact with the gp120 outer domain, layer 1-layer 2 interactions strengthen gp120-CD4 binding …