Objective: The human immunodeficiency virus type 1 (HIV-1) currently infects over 30 million people worldwide. It uses one of two main co-receptors to infect cells. The primary objective of this thesis is to evaluate genotypic and phenotypic assays for co-receptor usage in the clinical setting and investigate approaches for improvement of these assays. Methods: The concordance of recombinant co-receptor phenotyping assays and the predictive ability of genotype-based methods including the ‘11/25’ rule, position specific scoring matrices (PSSMs), and support vector machines (SVMs) were evaluated in the clinical setting using patient-derived plasma samples. Samples and patient data were evaluated in cross-sectional analyses from a retrospective population-based cohort of HIV-infected individuals enrolled in the HIV/AIDS Drug Treatment Program in British Columbia, Canada. Results: Current implementations of HIV V3 region-based predictors for HIV co-receptor usage tested on patient derived samples are inadequate in the clinical setting, primarily due to low sensitivities as a result of difficult to detect minority species. Recombinant phenotype assays also show discordances when tested against each other on the same set of patient derived samples, raising doubts if any of these assays can truly be considered a ‘gold standard’. Significant associations between clinical progression, viral sequence-based predictors of co-receptor usage and the output of recombinant assays are observed, suggesting that sensitivity can be improved by incorporating CD4% into genotype-based predictors. This is verified with a SVM model which showed a 17% increase in sensitivity when CD4% was incorporated into training and testing. Conclusion: This work in this thesis has exposed the difficulty in determining the co-receptor phenotype in the clinical setting, primarily due to minority species. Although genotypic methods of screening for HIV co-receptor usage prior to the administration of CCR5 antagonists may reduce costs and increase turn-around time over phenotypic methods, they are currently inadequate for use in the clinical setting due to low sensitivities. Although the addition of clinical parameters such as CD4 count significantly increases the predictive ability of genotypic methods, the presence of low-levels of X4 virus continues to reduce the sensitivity of both genotypic and phenotypic methods.

An extract of the tuber of Callilepis laureola is regarded as the source of a powerful therapeutic agent, known as Impila. Its use is associated with fatal hepatic and renal necrosis, the renal toxin being atractyloside (ATR). The aims of this study were threefold. Firstly, to generate a model set of biological specimens (urine, serum, liver and kidney) from rats dosed with 5-25 mg ATR/kg bwt. Secondly, to develop a competitive ELISA and HPLC method for the diagnosis of ATR poisoning employing the model specimens as test samples. Thirdly, to localise the target organs, cells and organelles of ATR, in vivo. The HPLC method necessitated the systematic development of the derivatisation of ATR with 9-anthryldiazomethane, sample clean up employing hexane, methanolic hydrochloric acid and a silica minicolumn, as well as the chromatographic conditions. Optimal resolution was obtained with a 3.9 x 150 mm NovaPak reverse phase column, fluorescence detection (excitation = 365 nm, emission = 425 nm) and a solvent system of MeOH:1M ammonium acetate:1M glacial acetic acid:water (38:2:2:58). This method has a detection limit of 0.001 ng ATR, shows a mean recovery of 89% and detected approximately 6.7 ug ATR/g wet weight of tuber tissue. The toxin was also detected in some of the urine samples at levels of about 200 pg/ml, but not in the serum. The production of antibodies to ATR for use in the ELISA and immunocytochemical investigations required the investigation of the conjugation procedure, carrier type, host species and immunization protocol. Optimal antibody yield, specificity and affinity was obtained with an acid-treated Salmonella minnesota bacterial carrier conjugated to ATR by carbodiimide, although there were indications of class switch inhibition and Tlymphocyte suppression by ATR. The development of the ELISA yielded a protocol involving the coating with a bovine serum albumin-ATR conjugate, blocking with bovine serum albumin, incubating the primary antibody at 4°C and detection with a secondary antibody-alkaline phosphate conjugate. This method detected ATR in both urine and serum from ATR-dosed rats and shows a detection limit of 10 ng. Since the less sensitive ELISA detected ATR in samples where the HPLC did not, this suggested that ATR is biotransformed in vivo, such that its retention time on a reverse phase column is affected, but not its epitope determinants. The results of the organ function assays demonstrated that, when administered intra-peritoneally, ATR is not hepatotoxic, but is a powerful nephrotoxin, targeting for the microvilli of the brush border of the proximal tubules, and compromising glomerular permselectivity and distal tubular function. In addition, this toxin inhibits proline transport in the proximal tubule, and therefore probably affects protein biosynthesis. Renal regeneration is noted 3 days post-dosing, as demonstrated by calcium excretion. Immunocytochemistry was optimised on tuber tissue and necessitated the intracellular fixation of the toxin, using carbodiimide, to prevent leaching out of the ATR. The toxin was encapsulated in vesicles in the tuber tissue. Atractyloside was also located in the kidney of ATR-treated rats, up to 72 hours after exposure, targeting the microvilli of the proximal tubule brush border, the mitochondrial cristae and specific sites on the Golgi apparatus membrane. Microvilli disruption and mitochondrial swelling was noted within 24 hours after exposure to the toxin while after 72 hours, loss of mitochondrial integrity was observed. The development of these diagnostic assays for ATR have provided the means to monitor the levels of this toxin in plant extracts and mammalian body fluids. Future work should include the identification of the hepatotoxin associated with Impila, the effects of the route of administration on the toxicity of this remedy and furthermore, the identification of a suitable antidote, which could include the use of duramycin and stevioside. The association between compounds blocking the ADP/ATP antiporter in the c-state and Reye's syndrome should also provide an interesting area of research. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1991.

Every year, more than a million people are diagnosed with colorectal cancer (CRC) that develops in the large intestine. It is one of the most studied cancers in the world but still more knowledge about how this cancer develops and acts is needed in order to use more effective ways to treat CRC. Autophagy is a vital mechanism in cells that is also suggested to maintain cancer cell survival. In normal cells, it plays an important role by removing damaged cells and organelles as well as eliminating pathogens. Under metabolic stress this mechanism is induced to provide enough nutrients and energy for the cell to survive. Cancer cells are exposed to greater environmental stress than normal cells and therefore, cancer cells exhibit higher levels of autophagy suggesting it to be a crucial mechanism for their survival. Gaining a deeper understanding of this essential mechanism and its activation might provide new insights and improved treatments for the fight against colorectal cancer. In situ Proximity Ligation Assay (PLA) is a protein detection method that enables sensitive and specific detection of proteins and protein-protein interactions (PPIs) in cell lines and tissue samples. The method uses simultaneous recognition of two independent antigens on a protein or protein complex together with a rolling circle amplification (RCA) to form a rolling circle product (RCP) on top of the target. By using fluorescent oligonucleotides, RCP can be visualized and is seen as a bright spot that enables sensitive detection of the target at single-molecule resolution. The aim of this study was to develop assays to detect endogenous molecular events known to be biomarkers of autophagy in situ in order to study autophagy mechanism in CRC patient samples. We focused our research on two PPIs that were known to interact when autophagy is induced. The first investigated interaction was between microtubule-associated protein 1A/1B- light chain 3 (LC3) and sequestome-1 (SQSTM1), an interaction that occurs during autophagy initiation. The second interaction was between B-cell lymphoma 2 (Bcl-2) and Bcl-2/adenovirus E1B 19-kDa interacting protein 3 (BNIP3) that takes place during hypoxia-induced autophagy. To study whether these PPIs can be used as a detection method to monitor autophagy, we used a well- established cell model based on serum starvation and CoCl2 - an hypoxic mimetic- treatment of the intestinal cancer cell line Caco-2 in comparison to normal culture condition. According to isPLA quantification, detection of both PPIs was distinctly higher in treated cells compared to untreated cells giving promising results and suggesting that they can be potentially used as suitable assays to monitor these biomarkers of autophagy. For development of an improved protein detection method that enables the study of several PPIs simultaneously in a tissue sample (In situ Multiplexing), we conjugated directly a short oligonucleotide strand to the primary antibodies. These formed proximity probes could later be used in in situ for multiplexing.

<p>The translational potential of diagnostic and prognostic platforms developed using expression microarray technology is evident. However, the majority of array-based diagnostics have yet to make their way into the clinical laboratory. Current approaches tend to focus on development of multi-gene classifiers of disease subtypes, but very few studies evaluate the translational potential of these assays. Likewise, only a handful of studies focus on development of approaches to optimize array-based tests for the ultimate goal of clinical utility. Prior to translation into the clinical setting, molecular diagnostic platforms should demonstrate a number of characteristics to ensure optimal and efficient testing and patient care. Assays should be accurate and precise, technically and biologically robust, and should take into account normal sources of biological variance that could ultimately affect test results. The overarching goal of the research presented in this dissertation is to develop methods for evaluating and optimizing the translational potential of molecular diagnostics developed using expression microarray technology.</p><p> </p><p>The first research section of this dissertation is focused on our evaluation of the impact of intratumor heterogeneity on precision in microarray-based assays in breast cancer. We conducted genome-wide expression profiling on 50 needle core biopsies from 18 breast cancer patients. Global profiles of expression were characterized using unsupervised clustering methods and variance components models. Array-based measures of estrogen (ER) and progesterone receptor (PR) status were compared to immunohistochemistry. The precision of genomic predictors of ER pathway status, recurrence risk, and sensitivity to chemotherapeutics were evaluated by interclass correlation. Results demonstrated that intratumor variation was substantially less than the total variation observed across the patient population. Nevertheless, a fraction of genes exhibited significant intratumor heterogeneity in expression. A high degree of reproducibility was observed in single gene predictors of ER (intraclass correlation coefficient (ICC)=0.94) and PR expression (ICC=0.90), and in a multi-gene predictor of ER pathway activation (ICC=0.98) with high concordance with immunohistochemistry. Substantial agreement was also observed for multi-gene signatures of cancer recurrence (ICC=0.71), and chemotherapeutic sensitivity (ICC=0.72 and 0.64). Together, these results demonstrated that intratumor heterogeneity, although present at the level of individual gene expression, does not preclude precise micro-array based predictions of tumor behavior or clinical outcome in breast cancer patients.</p><p> </p><p>Leading into the second research section, we observed that in some cancer types, certain genes behave as molecular switches and have either an "on" or "off" expression state. Specifically, we observed these molecular switch genes exist in breast cancer as robust diagnostic and prognostic markers, including ER, PR, and HER2, and define tumor subtypes associated with different treatment and patient survival. We hypothesized that clinically relevant molecular switch (bimodal) genes exist in epithelial ovarian cancer, a type of cancer with no established molecular subgroups. To test this hypothesis, we applied a bimodal discovery algorithm to a publically available ovarian cancer expression microarray dataset (GSE9891:285 tumors; 246 malignant serous (MS), 20 endometrioid (EM), 18 low malignant potential (LMP) ovarian carcinomas). Genes with robust bimodal expression were identified across all ovarian tumor types and within selected subtypes. Of these bimodal genes, 73 demonstrated differential expression between LMP vs. MS and EM, and 22 genes distinguished MS from EM. Fourteen bimodal genes had significant association with survival among MS tumors. When these genes were combined into a single survival score, the median survival for patients with a favorable versus unfavorable score was 65 versus 29 months (p<0.0001, HR=0.4221). Two independent datasets (n=53 high grade, advanced stage serous and n=119 advanced stage ovarian tumors) validated the survival score performance. Taken together, the results of this study revealed that genes with bimodal expression patterns not only define clinically relevant molecular subtypes of ovarian carcinoma, but also provide ideal targets for translation into the clinical laboratory.</p><p> </p><p>Finally, the third research section of this dissertation focuses on development of robust blood-based molecular markers of decompression stress (DS). DS is defined as the pathophysiological response to inert gas coming out of solution in the blood and tissues when a body experiences a reduction in ambient pressure. To date, there are no established molecular markers of DS. We hypothesized that comparing gene expression before and after human decompression exposures by genome-wide expression profiling would identify candidate molecular markers of DS. Peripheral blood was collected 1hr before and 2hr after 93 hyperoxic, heliox experimental dives (n=54). Control arms included samples collected 1 hour before and 2 hours after high pressure oxygen breathing (n= 9) and surface exercise (n=9), and samples collected at 7am and 5pm for time of day (n=11). Pre and post-dive expression data collected from normoxic nitrox experimental dives were utilized for independent validation. Blood samples were collected into PaxGene RNA tubes. RNA was extracted and processed for globin reduction prior to cDNA synthesis and Affymetrix U133A GeneChip hybridization. 746 genes were differentially expressed following hyperoxic, heliox decompression exposures (permutation adjusted p-value cutoff 1.0E-4). After filtering control significant genes, 726 genes remained. Pathway analysis demonstrated a significant portion of genes were associated with innate immune response (p<0.0001). A 362 multi-gene signature of significant, covariant genes was then applied to the independent dataset and demonstrated differentiation between pre and post-dive samples (p=0.0058). There was no significant correlation between signature and venous bubble grade or bottom time in the validation study. Our results showed that expression profiling of peripheral blood following decompression exposures, while controlling for experimental and normal sources of biological variance, identifies a reproducible multi-gene signature of differentially expressed genes, primarily comprising genes associated with innate immune response and independent of venous bubble grade or dive profile. </p><p> </p><p>Taken together, the research and results presented in this dissertation represent considerable advances in the development of approaches to guide microarray-based diagnostics towards the ultimate goal of clinical translation.</p> / Dissertation

The correlation between the chemical stability and the microbiological activity of polymyxin B in phosphate buffer pH 6.0 and in proprietary eye drops was evaluated. High Performance Liquid Chromatography (HPLC) was used to quantify the amount of the main components in samples stored at 43,50,55 and 60°C for a period of 500 h. The data indicated that there are significant differences in chemical stability among the different proprietary eye drops. The accurate decomposition rate constants and shelf-lives (~o) at 4°C of two of the six formulated eye drops and the standard polymyxin B solution stored in glass containers at pH 6.0 were established. It was concluded that microbiological assay by agar diffusion was unsuitable for determining the activity of control polymyxin B in phosphate buffer and polymyxin B in eye drops. Killing time determinations for polymyxin B against cell suspensions of P. aeruginosa NCTC 6750 were consequently used. Thioglycollate broth containingp- aminobenzoic acid (PABA) 0.16 %w/v and magnesium sulphate 1 %w/v was used as an inactivating recovery medium. The effect of preservatives and of second antibacterials contained in the eye drops were tested individually and combined with polymyxin B. Thiomersal 0.001 %w/v, trimethoprim 0.02 %w/v and thiomersal 0.001 %w/v plus trimethoprim 0.02 %w/v did not have an effect on the activity of polymyxin B 2000 U/ml. Neomycin was an exception and at the concentrations in the range 0.0192 to 0.16 %w/v exhibited an antagonistic effect. Chemical interaction between polymyxin B and neomycin could not be detected and it was considered that the inhibitory effect of neomycin may be the result of competition between polymyxin B and neomycin for the same binding sites on the cell surface. Gentamicin is active against P. aeruginosa NCTC 6750 and at concentrations of 0.075 and 0.036 %w/v it exhibited an additive effect with polymyxin B 2000 U/ml against the test organism. The results obtained with the samples stored at 55°C for a period of 500 h demonstrated the critical effect of pH. At a pH of 6.0 microbiological activity and chemical stability appeared optimal. The chemical stability data of five eye drop samples correlated with microbiological activity data. Exceptions were polymyxin B in one eye drop sample and control polymyxin B. These extensively decomposed samples showed good antibacterial activity which appeared to result from the activity of decomposition products. Chemical stability data for standard polymyxin B solution at pH 6.0 also correlated to microbiological activity data over the temperature range of 92 - 115°C. The polymyxin B retained detectable microbiological activity when the amount of PB1 was greater than 20%. It is suggested that the decomposition products which occurred at these higher temperatures did not possess antibacterial activity.

Thesis (M.S. - Hydrology and Water Resources)--University of Arizona, 1989. / Includes bibliographical references (leaves 147-156).

Thesis (M.S.)--Auburn University, 2007. / Abstract. Vita. Includes bibliographic references.

Universiẗat, Diss., 2006--Giessen.

Thesis (MSc (Microbiology))--University of Pretoria, 2008. / Summary in English. Includes bibliographical references.

Universiẗat-GH, Diss.--Paderborn, 1998.