MSc (Med), Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwaterstrand / Emergence and spread of resistance to ciprofloxacin among Neisseria gonorrhoeae strains has reduced the options of effective treatment for gonococcal infections and has become a concern worldwide. Up until 2008, ciprofloxacin was recommended first-line therapy for treatment of presumptive N. gonorrhoeae infections in South Africa. At the time this MSc project was conceived, ciprofloxacin was still used as first-line therapy for presumptive gonococcal infections. A real-time polymerase chain reaction (PCR) assay was used to detect ciprofloxacin-resistant N. gonorrhoeae in DNA extracted from non-invasive urine samples collected as part of the national microbiological surveillance (NMS) programme during 2006-2007. The molecular epidemiology of ciprofloxacinresistant Neisseria gonorrhoeae was investigated by sequencing the quinolone resistance determining regions (QRDR) of the gyrA and parC genes of N. gonorrhoeae and performing N. gonorrhoeae multi-antigen sequence typing (NGMAST). As part of the NMS program for sexually transmitted infections (STIs) urine and urethral swabs were collected from men presenting with urethral discharge at primary health care clinics in Johannesburg (Gauteng), Cape Town (Western Cape) and Kimberley (Northern Cape). Urine samples and cultured N. gonorrhoeae isolates from 2006-2007 were stored at -700C and available for this study. Gonococci, previously isolated from urethral swabs, were subcultured directly onto New York City media. Isolate identity was re-confirmed by typical colony morphology and biochemical tests. Urine samples from Johannesburg were tested in order to develop the real-time PCR protocol. Subsequently, paired urethral swab DNA and N. gonorrhoeae cultures were tested from NMS patients recruited in Kimberley and Cape Town. Where possible, the PCR assay results were compared with paired antibiotic susceptibility data for ciprofloxacin. Quinolone resistance determining regions (QRDR) for gyrA and parC were screened for known point mutations associated with resistance to ciprofloxacin. Detection of mutations by the real-time PCR assay generally agreed with the phenotype of either decreased susceptibility or resistance to ciprofloxacin. All ciprofloxacin resistant gonococcal isolates had the same gyrA and parC mutations, which initially suggested that quinolone resistant N. gonorrhoeae (QRNG) in Kimberley, Cape Town and Johannesburg, may be attributed to the spread of a single clone. The use of a more discriminatory typing scheme, Neisseria gonorrhoeae Multi-Antigen Sequence Typing (NG-MAST) genotyping, revealed that ciprofloxacin resistant gonococcal isolates in Johannesburg and Cape Town were heterogeneous, with sequence type (ST) 217 being most prevalent in both cities (5/16, Johannesburg; 7/11, Cape Town). In contrast, all eight QRNG isolates from Kimberley were typed as ST 533. The use of molecular methods allowed ciprofloxacin antimicrobial susceptibility determination by PCR in non-invasive specimens. This is useful in situations where bacterial cultures are unavailable or die before antimicrobial susceptibility testing can be performed. Molecular assays to detect ciprofloxacin resistance may guide physicians as to the most ideal antimicrobial combinations for individual patient treatment. As a result of emerging widespread resistance gonococci to ciprofloxacin, in 2008, the Department of Health recommended that ciprofloxacin be removed as a first line therapy in the South African national sexually transmitted infections treatment guidelines for treatment of urethritis, cervicitis and their complications. Although ciprofloxacin is no longer used as a first-line therapy to treat gonorrhoea within our country, it may still be used in cases of severe penicillin allergy or as part of multi-drug therapy for gonococcal infections in the future. The ability to detect ciprofloxacin resistance by real-time PCR will be a useful technique in such situations.

by Lo Man-har. / Thesis (M.Sc.)--Chinese University of Hong Kong, 1994. / Includes bibliographical references (leaves 56-63). / LIST OF FIGURES --- p.5 / LIST OF TABLES --- p.6 / ACKNOWLEDGEMENTS --- p.8 / SUMMARY --- p.9 / Chapter 1. --- INTRODUCTION --- p.11 / Chapter 1.1 --- Lipid metabolism --- p.11 / Chapter 1.1.1 --- Chylomicron --- p.12 / Chapter 1.1.2 --- Very low density lipoprotein --- p.12 / Chapter 1.1.3 --- Low density lipoprotein --- p.13 / Chapter 1.1.4 --- High density lipoprotein --- p.14 / Chapter 1.2 --- Apolipoprotein B --- p.14 / Chapter 1.3 --- Apolipoprotein B gene --- p.15 / Chapter 1.4 --- Genetic variations in human apo B gene and their associations with abnormal lipid metabolism --- p.16 / Chapter 1.4.1 --- Abetalipoproteinemia --- p.16 / Chapter 1.4.2 --- Hypobetalipoproteinemia --- p.17 / Chapter 1.4.3 --- Familial hypercholesterolemia (FH) --- p.17 / Chapter 1.5 --- Polymorphisms of apo B gene --- p.17 / Chapter 1.6 --- Methods for detection of polymorphisms --- p.19 / Chapter 2. --- OBJECTIVES --- p.20 / Chapter 3. --- MATERIALS AND METHODS --- p.21 / Chapter 3.1 --- Materials and equipments --- p.21 / Chapter 3.1.1 --- Enzymes --- p.21 / Chapter 3.1.2 --- DNA markers --- p.21 / Chapter 3.1.3 --- General reagents --- p.21 / Chapter 3.1.4 --- Equipments --- p.22 / Chapter 3.2 --- Buffers --- p.22 / Chapter 3.3 --- Agarose gel electrophoresis --- p.22 / Chapter 3.4 --- Study subjects --- p.23 / Chapter 3.4.1 --- Cord blood samples --- p.23 / Chapter 3.4.2 --- Geriatric subjects --- p.23 / Chapter - --- Cases --- p.23 / Chapter - --- Controls --- p.24 / Chapter 3.5 --- Clinical Data --- p.24 / Chapter 3.6 --- Blood collection --- p.24 / Chapter 3.7 --- Biochemical analysis --- p.25 / Chapter 3.8 --- DNA extractions --- p.25 / Chapter 3.9 --- Polymerase chain reaction (PCR) --- p.26 / Chapter - --- Oligonucleotide primers --- p.26 / Chapter - --- Signal peptide insertion/deletion polymorphism --- p.26 / Chapter - --- Xba I polymorphism --- p.27 / Chapter - --- Eco RI polymorphism --- p.28 / Chapter 3.10 --- Data analysis --- p.29 / Chapter 4. --- RESULTS --- p.30 / Chapter 4.1 --- Optimization of PCR --- p.30 / Chapter 4.2 --- Clinical features of the case and control subjects --- p.30 / Chapter 4.3 --- Genotyping --- p.31 / Chapter 5. --- DISCUSSION --- p.33 / Chapter 5.1 --- Optimization of PCR protocols --- p.33 / Chapter 5.2 --- Clinical data --- p.34 / Chapter 5.3 --- Allelic frequencies of the three polymorphisms of apo B gene --- p.35 / Chapter 5.4 --- Association of polymorphisms of apo B gene with the case group --- p.36 / Chapter 5.5 --- Association of polymorphisms of apo B gene with hyperlipidaemia --- p.36 / Chapter - --- Signal peptide insertion/deletion polymorphism --- p.36 / Chapter - --- Xba I polymorphism --- p.38 / Chapter - --- Eco RI polymorphism --- p.38 / Chapter 5.6 --- Conclusion --- p.39 / APPENDIX I --- p.53 / APPENDIX II --- p.54 / Chapter 6. --- REFERENCES --- p.56

by Lai, Shiu Hong. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1993. / Includes bibliographical references (leaves 129-147). / TITLE PAGE --- p.I / THESIS COMMITTEE --- p.II / ABSTRACT --- p.III / ACKNOWLEDGMENTS --- p.V / ABBREVIATIONS --- p.VI / TABLE OF CONTENTS --- p.VII / LIST OF TABLES --- p.XI / LIST OF FIGURES --- p.XII / Chapter Chapter 1. --- Arbitrarily Primed Polymerase Chain Reaction (AP-PCR) Analysis of Lent inula edodes / Chapter 1. --- Introduction / Chapter 1.1 --- General Introduction --- p.1 / Chapter 1.2 --- Purpose of Study --- p.4 / Chapter 2. --- Literature Review / Chapter 2.1 --- Biology of Lentinula edodes / Chapter 2.1.1 --- "Overview," --- p.6 / Chapter 2.1.2 --- Life Cycle of Lentinula edodes --- p.6 / Chapter 2.1.3 --- Dedikaryotization (Monokaryotization) --- p.12 / Chapter 2.2 --- Genome Analysis of the Mushroom --- p.13 / Chapter 2.3 --- Genetic Markers of Lentinula edodes / Chapter 2.3.1 --- Overview --- p.15 / Chapter 2.3.2 --- Auxotrophic Markers --- p.16 / Chapter 2.3.3 --- Biochemical Markers --- p.17 / Chapter 2.3.4 --- Molecular Markers / Chapter 2.3.4.1 --- RFLPs --- p.19 / Chapter 2.3.4.2 --- PCR-Based Markers --- p.20 / Chapter 2.4 --- Polymerase Chain Reaction (PCR) / Chapter 2.4.1 --- The principle of PCR --- p.22 / Chapter 2.4.2 --- Applications of PCR on Mushroom Studies --- p.26 / Chapter 2.5 --- Arbitrarily Primed Polymerase Chain Reaction / Chapter 2.5.1 --- Principle of AP-PCR --- p.27 / Chapter 2.5.2 --- Applications of AP-PCR on Mushroom Studies --- p.29 / Chapter 2.6 --- Genetic Linkage Analysis / Chapter 2.6.1 --- Overview --- p.31 / Chapter 2.6.2 --- The LOD Score Method --- p.34 / Chapter 3. --- Materials and Methods / Chapter 3.1 --- Mushroom Strains and Culture Media --- p.36 / Chapter 3.2 --- Culture Method --- p.36 / Chapter 3.3 --- Solutions --- p.36 / Chapter 3.4 --- Primers --- p.38 / Chapter 3.5 --- Isolation of DNA from Lentinula edodes / Chapter 3.5.1 --- Mini-Preparation of Fungal DNA from L. edodes for PCR amplification --- p.42 / Chapter 3.5.2 --- Cesium Chloride Method: Mini-Preparation of Fungal DNA for PCR amplification --- p.43 / Chapter 3.6 --- Quantitative Measurements of DNA --- p.44 / Chapter 3.7 --- Arbitrarily Primed Polymerase Chain Reaction (AP-PCR) for the Amplification of Genomic DNA of L. edodes --- p.45 / Chapter 3.8 --- Analysis of DNA Samples with Agarose Gel Electrophoresis --- p.46 / Chapter 3.9 --- Analysis of DNA Samples with Polyacrylamide Gel Electrophoresis (PAGE) --- p.47 / Chapter 3.10 --- Silver Staining --- p.48 / Chapter 3.11 --- Single Stranded Conformation Polymorphism (SSCP) Analysis of Polymorphic DNA Fragments / Chapter 3.11.1 --- Elution and Amplification of DNA --- p.49 / Chapter 3.11.2 --- PCR-SSCP --- p.50 / Chapter 3.12 --- Segregation and Linkage Analysis / Chapter 3.12.1 --- Chi-Square Test --- p.51 / Chapter 3.12.2 --- The LOD Score Method --- p.52 / Chapter 4. --- Results / Chapter 4.1 --- DNA Extraction --- p.54 / Chapter 4.2 --- AP-PCR Amplified Fragments and Fragment Number --- p.58 / Chapter 4.3 --- Dedikaryotization Demonstration --- p.60 / Chapter 4.4 --- Identification of Polymorphic Genetic Markers --- p.64 / Chapter 4.4.1 --- AP-PCR Fingerprints from Single Primer --- p.66 / Chapter 4.4.2 --- AP-PCR Fingerprints Using Two Primers --- p.76 / Chapter 4.5 --- Segregation of Polymorphic Markers in Single Spore Isolates (SSIs) --- p.81 / Chapter 4.6 --- Single Stranded Conformation Polymorphism (SSCP) of Identified Polymorphic DNA Fragments --- p.86 / Chapter 4.7 --- Linkage Analysis of the Identified AP-PCR Markers --- p.89 / Chapter 5. --- Discussions / Chapter 5.1 --- DNA Extraction --- p.92 / Chapter 5.2 --- Arbitrary Primers --- p.93 / Chapter 5.3 --- Dedikaryotization Demonstration --- p.95 / Chapter 5.4 --- Identification of Polymorphic Genetic Markers --- p.96 / Chapter 5.5 --- AP-PCR Analysis of a Mushroom --- p.97 / Chapter 5.6 --- Mendelian Segregation Pattern of the Polymorphic Markers --- p.99 / Chapter 6. --- Conclusion and Further Studies --- p.101 / Chapter 2. Electrophoretic Karyotype Analysis of Lentinula edodes / Chapter 7. --- Introduction --- p.106 / Chapter 8. --- Literature Review / Chapter 8.1 --- Overview --- p.108 / Chapter 8.2 --- Protoplasts --- p.109 / Chapter 8.3 --- Pulsed Field Gel Electrophoresis (PFGE) / Chapter 8.3.1 --- Principle --- p.110 / Chapter 8.3.2 --- Applications of PFGE in Studies of Fungi --- p.112 / Chapter 9. --- Materials and Methods / Chapter 9.1 --- Strains and Culture Media --- p.114 / Chapter 9.2 --- Solutions --- p.114 / Chapter 9.3 --- Production of Lentinula edodes Protoplast --- p.115 / Chapter 9.4 --- Electrophoretic Conditions --- p.116 / Chapter 9.4.1 --- Condition for Saccharomyces cerevisiae chromosomes --- p.117 / Chapter 9.4.2 --- Condition for Candida albicans chromosomes --- p.117 / Chapter 9.4.3 --- Condition for Schizosaccharomyces pombe chromosomes --- p.118 / Chapter 10. --- Results / Chapter 10.1 --- Protoplast Production of Lentinula edodes / Chapter 10.1.1 --- Effects of Age of Mycelium on Protoplast Yield --- p.119 / Chapter 10.1.2 --- Effects of Various Osmotic Stabilizers on Protoplast Yield --- p.121 / Chapter 10.1.3 --- Effects of Two Lytic Enzymes on Protoplast Yield --- p.123 / Chapter 10.1.4 --- The Optimal Condition --- p.123 / Chapter 10.2 --- Electrophoretic Karyotype of L. edodes --- p.124 / Chapter 11. --- Discussions / Chapter 11.1 --- Protoplast Production of Lentinula edodes --- p.126 / Chapter 11.2 --- Electrophoretic Karyotype --- p.127 / REFERENCES

Resumo: Um total de 196 amostras fecais de bezerros leiteiros mestiços, de 7 a 30 dias de idade de ambos o sexos foram colhidas em 31 propriedades com o objetivo de determinar a ocorrência de Cryptosporidium na região Noroeste do Estado de São Paulo, assim como caracterizar molecularmente as espécies envolvidas nesta parasitose. Realizou-se a análise microscópica pela técnica de coloração negativa com verde malaquita em todas as amostras de fezes. Para identificação molecular de Cryptosporidium, utilizou-se a reação de nested PCR, utilizando primers específicos para amplificação de fragmentos do gene codificador da subunidade 18S do RNA ribossômico e do gene da glicoproteína GP 60, submetendo o produto da PCR a sequenciamento e análise filogenética. Por meio de exame de fezes, foi observada positividade de 2% (4/196), por meio de microscopia, e de 10,7% (21/196) pela nested PCR. Como resultado do sequenciamento, foram identificadas quatro espécies de Cryptosporidium: C. parvum (subtipo IIa15G2R1) C. ryanae, C. bovis e C. andersoni. Esta descoberta de C. parvum subtipo IIaA15G2R1 na região estudada ilustra a utilidade da subtipagem. Embora estes resultados iniciais baseados em subtipos com GP60 sejam úteis para compreender a dinâmica de transmissão das espécies de Cryptosporidium, o número de amostras analisadas é relativamente pequeno e muito mais ainda pode ser pesquisado. É interessante notar que as informações de tipagem molecular com o gene 18S rRNA e a subtipagem com o gene GP60, permitem que os epidemiologistas possam rastrear as fontes de surtos das diferentes espécies de Cryptosporidium. / Abstract: A total of 196 fecal samples from crossbred calves, 7-30 days old of both sexes were collected in 31 properties with the objective of determining the prevalence of Cryptosporidium in the northwestern region of São Paulo, as well as characterizing the molecular species involved in this parasite. We performed microscopic analysis by the technique of negative staining with malachite green in all stool samples. For molecular identification of Cryptosporidium, we used the reaction of nested PCR using specific primers for amplification of gene fragments coding for the 18S subunit ribosomal RNA gene and the glycoprotein GP 60 by subjecting the PCR product sequencing and phylogenetic analysis. By stool examination, positivity was observed 2% (4 / 196) by means of microscopy, and 10.7% (21/196) by nested PCR. As a result of sequencing, we identified four species of Cryptosporidium: C. parvum (subtype IIa15G2R1) C. Ryanair, C. bovis and C. andersoni. This discovery of C. IIaA15G2R1 parvum subtype in the studied region illustrates the usefulness of subtyping. Although based on these initial results with GP60 subtypes are useful for understanding the transmission dynamics of the species of Cryptosporidium, the number of samples is relatively small and much more can still be searched. It is interesting to note that the information of molecular typing with 18S rRNA gene and subtyping with the GP60 gene, allow epidemiologists can track sources of outbreaks of different species of Cryptosporidium. / Orientador: Luiz Claudio Nogueira Mendes / Coorientador: Marcelo Vasconcelos Meireles / Banca: Ricardo Velludo Gomes de Soutello / Banca: Katia Denise Saraiva Bresciani / Mestre

Shiu Ka Man. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (leaves 176-182). / Abstract also in Chinese. / Acknowledgments --- p.i / Presentations Derived from the Present Thesis Work --- p.ii / Chinese Abstract --- p.iii / English Abstract --- p.iv / List of Abbreviations --- p.v / Abbreviation for Amino Acids and Nucleotides --- p.vii / List of Figures --- p.viii / List of Tables --- p.vi / Contents / Chapter Chapter.1 --- Literature Review --- p.1 / Chapter 1.1 --- Transcriptional Regulation of Gene Expression --- p.1 / Chapter 1.2 --- MT: A Brief Review --- p.4 / Chapter 1.3 --- Transcriptional Regulation of MT --- p.15 / Chapter 1.4 --- MT Promoter Organization and Function --- p.18 / Chapter 1.5 --- Fish MT Genes --- p.29 / Chapter 1.6 --- Aim and Rationale of Present Studies --- p.32 / Chapter Chapter 2 --- PCR Cloning of Common Carp MT Gene --- p.34 / Chapter 2.1 --- Introduction --- p.34 / Chapter 2.1.1 --- The Biology of Common Carp --- p.34 / Chapter 2.1.2 --- The Study of Common Carp MT --- p.35 / Chapter 2.2 --- Materials and Methods --- p.39 / Chapter 2.2.1 --- Materials --- p.39 / Chapter 2.2.1.1 --- Polymerase Chain Reaction (PCR) --- p.39 / Chapter 2.2.1.2 --- Agarose Gel Electrophoresis --- p.39 / Chapter 2.2.1.3 --- Gene Clean by Sephaglas´ёØ BandPrep Kit (Pharmacia) --- p.40 / Chapter 2.2.1.4 --- TA Cloning --- p.40 / Chapter 2.2.1.5 --- Transformation of Plasmid Vector into Competent Cell (Heat Shock Method) --- p.41 / Chapter 2.2.1.6 --- Preparation of Plasmid DNA --- p.41 / Chapter 2.2.1.7 --- DNA Sequencing --- p.42 / Chapter 2.2.1.7.1 --- Template Denaturation and Primer Annealing --- p.42 / Chapter 2.2.1.7.2 --- Labeling and Termination Reaction --- p.42 / Chapter 2.2.1.7.3 --- DNA Sequencing Electrophoresis --- p.43 / Chapter 2.2.1.8 --- Total RNA Extraction --- p.43 / Chapter 2.2.1.9 --- PolyA RNA Extraction --- p.44 / Chapter 2.2.1.10 --- Micro Bio-Spin Chromatography --- p.44 / Chapter 2.2.1.11 --- Analysis of the Transcription Start Site --- p.45 / Chapter 2.2.2 --- Methods --- p.46 / Chapter 2.2.2.1 --- Polymerase Chain Reaction (PCR) --- p.46 / Chapter 2.2.2.2 --- Gene Clean by Sephaglas ´ёØ BandPrep Kit (Pharmacia) --- p.46 / Chapter 2.2.2.3 --- TA Cloning --- p.47 / Chapter 2.2.2.4 --- Transformation of Plasmid Vector into Competent Cell (Heat Shock Method) --- p.47 / Chapter 2.2.2.5 --- Transformation of Plasmid Vector into Competent Cell (Heat Shock Method) --- p.48 / Chapter 2.2.2.6 --- Preparation of Plasmid DNA --- p.48 / Chapter 2.2.2.6.1 --- Small Scale Alkali Preparation of Plasmid DNA --- p.48 / Chapter 2.2.2.6.2 --- Large Scale Preparation of Plasmid DNA using Wizard Maxiprep Kit (Promega) --- p.49 / Chapter 2.2.7 --- DNA Sequencing --- p.50 / Chapter 2.2.2.7.1 --- Template Denaturation and Primer Annealing --- p.50 / Chapter 2.2.2.7.2 --- Labeling and Termination Reaction --- p.51 / Chapter 2.2.2.7.3 --- DNA Sequencing Electrophoresis --- p.51 / Chapter 2.2.2.8 --- Total RNA Extraction --- p.52 / Chapter 2.2.2.9 --- PolyA RNA Extraction --- p.53 / Chapter 2.2.2.10 --- Analysis of the Transcription Start Site --- p.55 / Chapter 2.3 --- Results --- p.56 / Chapter 2.3.1 --- PCR Cloning of the MT Gene --- p.56 / Chapter 2.3.2 --- Identification of the Transcriptional Start Site --- p.57 / Chapter 2.4 --- Discussion --- p.60 / Chapter 2.4.1 --- PCR Cloning of the MT Gene --- p.60 / Chapter 2.4.2 --- Comparison of Common Carp MT Promoter with Other --- p.60 / Chapter 2.4.3 --- Identification of the Transcriptional Start Site --- p.62 / Chapter 2.5 --- Conclusion --- p.63 / Chapter Chapter 3. --- Functional Assay of Common Carp MT Promoter --- p.64 / Chapter 3.1 --- Introduction --- p.64 / Chapter 3.1.1 --- Fish MT Promoters --- p.64 / Chapter 3.2 --- Materials and Methods --- p.68 / Chapter 3.2.1 --- Materials --- p.68 / Chapter 3.2.1.2 --- Micro Bio-Spin Chromatography --- p.68 / Chapter 3.2.1.3 --- Construction of Deletion Mutants --- p.68 / Chapter 3.2.1.4 --- Isolation of Hepatocytes --- p.69 / Chapter 3.2.1.5 --- Determination of LC50 Values for Common Carp Hepatocytes --- p.69 / Chapter 3.2.1.6 --- Transfection by LipofectAMINE´ёØ (Gibco) --- p.70 / Chapter 3.2.1.9 --- Determination of the Amount of Protein by BCA Protein Assay --- p.70 / Chapter 3.2.1.10 --- β-galactosidase Analysis --- p.71 / Chapter 3.2.2 --- Methods --- p.72 / Chapter 3.2.2.1 --- Subcloning of 5' Flanking Region of Common Carp MT Gene into Reporter Gene --- p.72 / Chapter 3.2.2.2 --- Micro Bio-Spin Chromatography (Bio-rad) --- p.72 / Chapter 3.2.2.3 --- Creating Deletion Mutants --- p.73 / Chapter 3.2.2.4 --- Isolation of Hepatocytes --- p.73 / Chapter 3.2.2.5 --- Determination ofLC50 Values for Common Carp Hepatocytes --- p.74 / Chapter 3.2.2.6 --- Transfection with LipofectAMINE´ёØ (Gibco BRL) --- p.75 / Chapter 3.2.2.7 --- Optimization of Incubation Time of Cells with LipofectAMINE´ёØ --- p.75 / Chapter 3.2.2.8 --- Optimization of Amount of DNA for Transfection --- p.76 / Chapter 3.2.2.9 --- Determination of Protein Concentration by --- p.76 / Chapter 3 2.2.10 --- β-galactosidase Analysis --- p.77 / Chapter 3.2.2.11 --- Fluorescence Measurement --- p.77 / Chapter 3.2.2.12 --- Dose-Response Curve of Different Metals on Transfected Cells --- p.77 / Chapter 3.2.2.13 --- "Fold-Induction of Different Metals, LPS and H202" --- p.78 / Chapter 3.3. --- Result --- p.79 / Chapter 3.3.1 --- Deletion Mutants --- p.79 / Chapter 3.3.2 --- LC50 of Common Carp Hepatocytes --- p.80 / Chapter 3.3.3 --- Optimization of Transfection --- p.81 / Chapter 3.3.4 --- Dose Response Curve --- p.85 / Chapter 3.3.5 --- Deletion Mutants with Different Treatments --- p.95 / Chapter 3.4 --- Discussion --- p.109 / Chapter 3.4.1 --- LC50 Values of Metal Toxicity in Different in vitro Fish Cells Studies --- p.109 / Chapter 3.4.2 --- Dose Response Curve (Figure 3.9 to 3.16) --- p.110 / Chapter 3.4.3 --- Fold Induction in Deletion Mutants --- p.111 / Chapter 3.5 --- Conclusion --- p.128 / Chapter Chapter 4. --- MRE-Binding Proteins --- p.129 / Chapter 4.1 --- Introduction --- p.129 / Chapter 4.1.1 --- MTF-1 --- p.129 / Chapter 4.1.1.1 --- Structure of MTF-1 --- p.129 / Chapter 4.1.1.2 --- MTF-1 is a Zinc Dependent Factor --- p.130 / Chapter 4.1.1.3 --- Band-shift Assay of MTF-1 --- p.132 / Chapter 4.1.1.4 --- MTF-1 is Essential for Both Basal and Metal-Induced MT Transcription --- p.133 / Chapter 4.1.2 --- MBP-l --- p.134 / Chapter 4.1.3 --- MBF-l l --- p.35 / Chapter 4.1.4 --- Rat Zinc Activated Protein --- p.135 / Chapter 4.1.5 --- MREBF-1 and MREBF-2 --- p.136 / Chapter 4.1.6 --- Human Zinc Regulatory Factor --- p.136 / Chapter 4.1.7 --- MREBP --- p.137 / Chapter 4.1.8 --- Aim of This Chapter --- p.138 / Chapter 4.2 --- Materials and Methods --- p.139 / Chapter 4.2.1 --- Materials --- p.139 / Chapter 4.2.1.1 --- Preparation of Nuclear Extract from Common Carp Liver Tissue --- p.139 / Chapter 4.2.1.2 --- Preparation of the Double-Stranded Oligonucleotides --- p.139 / Chapter 4.2.1.3 --- Binding Reaction of Protein and DNA --- p.141 / Chapter 4.2.1.4 --- Gel-Shift Mobility Electrophoresis --- p.142 / Chapter 4.2.1.5 --- Screening of Expression Library --- p.142 / Chapter 4.2.1.5.1 --- Preparation of Labeled DNA Probe --- p.142 / Chapter 4.2.1.5.2 --- Plating of the Library --- p.142 / Chapter 4.2.1.6. --- Isolation of Positive Clones In Vivo Excision --- p.143 / Chapter 4.2.2 --- Methods --- p.144 / Chapter 4.2.2.1 --- Gel Mobility-Shift Assays --- p.144 / Chapter 4.2.2.1.1 --- Preparation of Nuclear Extract from Common Carp Liver Tissue --- p.145 / Chapter 4.2.2.1.2 --- Preparation of the Double-Stranded Oligonucleotides --- p.145 / Chapter 4.2.2.1.3 --- Binding Reaction of Protein and DNA --- p.146 / Chapter 4.2.2.1.4 --- Gel-Shift Mobility Electrophoresis --- p.146 / Chapter 4.2.2.2 --- Screening of Expression Library --- p.146 / Chapter 4.2.2.2.1 --- Preparation of Labeled DNA Probe --- p.147 / Chapter 4.2.2.2.2 --- Plating of the Library --- p.148 / Chapter 4.2.2.2.3 --- Isolation of Positive Clones --- p.150 / Chapter 4.3 --- Results --- p.150 / Chapter 4.3.1 --- Gel Mobility-Shift Assays --- p.150 / Chapter 4.3.2 --- Expression Library Screening --- p.163 / Chapter 4.4 --- Discussion --- p.166 / Chapter 4.4.1 --- Gel Mobility-Shift Assays --- p.166 / Chapter 4.4.2 --- Expression Library Screening --- p.171 / Chapter 4.5 --- Conclusion --- p.172 / Chapter Chapter 5 --- Conclusion --- p.173 / Chapter 5.1 --- Conclusion --- p.173 / Chapter 5 2 --- Model of MT Gene Transcription --- p.174 / Chapter 5.3 --- Future Direction --- p.175 / references --- p.176

The small dinoflagellate Azadinium spinosum produces azaspiracid (AZA) toxins which can contaminate filter feeding shellfish to dangerous levels. Toxin-contaminated shellfish flesh, when consumed by humans, can cause acute intense illness and chronic health issues. Shellfish biotoxins are monitored in Scottish shellfish by Food Standards Scotland (FSS), and the concurrent monitoring of harmful phytoplankton in the water column acts as an important early warning system of future shellfish toxin contaminations. Since A. spinosum is very small (12-16 μm long) it is difficult to identify using a light microscope, therefore molecular techniques have been developed to detect species-specific environmental DNA from phytoplankton samples. In this thesis the application and verification of quantitative real time polymerase chain reaction (qPCR) is discussed in detail and documents its first use in Scottish waters to survey A. spinosum abundance and seasonality. The limit of detection of the method was found to be 2000 ±5600 cells L-1, however it is unclear whether this is adequate for regulatory monitoring because it is not yet understood how cell density in the water column relates to AZA shellfish toxicity. The qPCR probe and primer sequences were also found to be too specific to detect all strains of the A. spinosum species, as new strains have been isolated since their development. This is a significant hindrance to the application of the tool for monitoring which will need to be addressed in the future through the isolation of local A. spinosum strains. Over a year long sampling period, A. spinosum was detected only twice (maximum cell density of 2545 ±5600 cells L-1, August 2014) off the Shetland Islands. The seasonality of the species in Scottish waters could not be assessed with so little data, however other observed harmful species of importance to shellfish regulatory monitoring are discussed; of particular note an unusual bloom of Dinophysis acuta as its association with a temperature front at the mouth of Loch Fyne. This thesis critiques the use of this qPCR technique for A. spinosum detection at high-throughput. The issues which have been highlighted do not prevent its future use by FSS, but highlight specific areas of development which need addressed before national monitoring can occur.

Abstract not available

Four main types of viruses capable of causing systemic and gastrointestinal infections, namely Coronavirus, Rotavirus, Parvovirus or Morbillivirus (Tennant et al, 1991) have been investigated in marsupials. A pilot study to develop and optimise the methodology was undertaken using Canine Coronavirus and the study was then extended to marsupials and other target viruses.In the marsupial portion of the study, a fragment of the correct size for the amplification of pol gene, 409 bp, was obtained from two different faecal samples from tammar wallaby (from Macquarie Fauna Park) and one western grey kangaroo (from Taronga Zoo). The results from tests are studied and compared. It is suggested that future further investigation should be directed at: 1/. Applying the protocols in this body of work to the testing of faecal samples from animals that have been diagnosed as positive with other diagnostic protocols. 2/. Examining more faecal samples from animals that present with active diarrhoea / Master of Science (Hons)

Twenty species and six subspecies of the genera Arcobacter and Campylobacter have been described to date. All are Gram-negative, microaerophilic, curved, spiral or S-shaped cells, and are members of the order Campylobacterales, class Epsilonproteobacteria phylum Proteobacteria. Though most members are pathogenic, C. jejuni, C. coli and A. butzleri are the most frequently isolated species from patients suffering from gastrointestinal illness. The current methods for their detection, identification, and differentiation are cumbersome, time consuming and lack specificity. DNA based molecular techniques including real-time Polymerase Chain Reaction (PCR) and Fingerprinting methods Terminal Restriction Fragments Length Polymorphism (T-RFLP) and Ligase Detection Reaction (LDR) have been used in this project to develop rapid detection and identification methods for Campylobacter and Arcobacter species. Five real-time PCR methods were developed which include: (a) rapid detection and identification of Campylobacter species using real-time PCR adjacent hybridisation probes, (b) rapid identification of C. jejuni using SYBR Green I, (c) rapid detection and differentiation of Arcobacter species using adjacent hybridisation probes, (d) rapid detection and differentiation of Arcobacter species and the Campylobacter group (C. coli, C. jejuni, C. lari, C. hyoilei, C. helviticus, C. hyointestinalis, C. insulaenigrae, C lanienae) using melting temperature (Tm) of adjacent hybridisation probes, and (e) a one tube real-time PCR multiplex for the rapid detection and identification of Campylobacter species, C. coli and C. jejuni using a TaqMan Probe, in an iCycler iQTM (BioRad, USA) and Light CyclerTM (Idaho Technology, USA). [Continued ...]

Polymerase chain reaction (PCR) sequencing of specific viral gene segments was used to investigate the phylogenetic relationships among the orbiviruses. Sequence comparisons of the bluetongue virus (BTV) RNA3 from different regions of the world (North America, South Africa, India, Indonesian, Malaysia, Australia and the Caribbean region) showed that geographic separation had resulted in significant divergence, consistent with the evolution of distinct viral populations. There were at least 3 topotypes (Gould, 1987); the Australasian, African - American and another topotype represented by BTV 15 isolated in Australia in 1986. The topotypes of BTV had RNA3 nucleotide sequences that differed by approximately 20 per cent. Analysis of BTV-specific gene segments from animal and insect specimens showed that bluetongue viruses had entered northern Australia from South East Asia, possibly by wind-borne vectors. Nucleotide sequence comparisons were used to show the close genetic relationship between BTV 2 (Ona-A strain) from Florida and BTV 12 from Jamaica, and to investigate the reassortment of BTV genome segments in nature. The mutation rates of the BTV RNA2 and RNA3 segments were estimated to be of the order of 10(-4) nucleotide changes/site/year, similar in magnitude to that reported for other RNA viruses.