Ph.D. / Molecular Microbiology and Immunology / Both poxviruses and γ2-herpesviruses share the K3-family of viral immune evasion proteins. These proteins are characterized by an amino-terminal RING-CH domain followed by two transmembrane domains. We analyzed several human homologues of the K3-family termed membrane-associated RING-CH (MARCH) proteins. All MARCH proteins localized to subcellular membranes while several reduced surface levels of known K3-family substrates. Thus, MARCH proteins appear to be structurally and functionally homologous to viral K3 proteins. One of the major challenges in determining the function of this family is the identification of their physiological substrates. To overcome this we created a quantitative proteomics approach which can be used to identify novel substrates for both the K3- and MARCH-families. Using stable isotope labeling by amino acids in cell culture, we compared the proteome of plasma membrane, golgi, and endoplasmic reticulum membranes in the presence and absence of K5 and MARCH-VIII. Quantitative mass spectrometric protein identification from these fractions revealed that CD316 (bone marrow stromal antigen 2), CD166 (activated leukocyte cell adhesion molecule) and syntaxin-4 were consistently underrepresented in the plasma membrane of K5 expressing cells, while CD44, CD81 (TAPA-1) and B-cell receptor-associated protein 31kDa (Bap31) were consistently underrepresented in the plasma membrane of MARCH-VIII expressing cells. Furthermore, downregulation of each of these proteins was independently confirmed. Our results both identify and characterize a novel family of human ubiquitin ligase enzymes and elucidate a novel technique which can analyze this family and be easily adapted to the analysis of other cellular enzymes viral immune modulators.

<p>Polyaniline nanocomposites doped with poly(vinylsulphonate) (PV-SO3 &minus / ) and nanostructured polystyrene (PSNP) latex beads functionalized with amine (PSNP-NH2) and sulphate (PSNP-OSO3 &minus / ) were prepared and characterised for use as nitrite electro-catalytic chemosensors and ochratoxin A immunosensors. The resultant polyaniline electrocatalytic chemosensors (PANI, PANI|PSNP-NH2 or PANI|PSNP-OSO3 &minus / ) were characterized by cyclic voltammetry (CV), ultraviolet-visible (UV-Vis) spectroscopy and scanning electron microscopy (SEM). Brown-Anson analysis of the multi-scan rate CV responses of the various PANI films gave surface concentrations in the order of 10&minus / 8 mol/cm. UV-vis spectra of the PANI films dissolved in dimethyl sulphoxide showed typical strong absorbance maxima at 480 and 740 nm associated with benzenoid p-p* transition and quinoid excitons of polyaniline, respectively. The SEM images of the PANI nanocomposite films showed cauliflower-like structures that were &lt / 100 nm in diameter. When applied as electrochemical nitrite sensors, sensitivity values of 60, 40 and 30 &mu / A/mM with corresponding limits of detection of 7.4, 9.2 and 38.2 &mu / M NO2 &minus / , were obtained for electrodes, PANI|PSNP-NH2, PANI and PANI|PSNP-SO3 &minus / , respectively. Immobilisation of ochratoxin A antibody onto PANI|PSNP-NH2, PANI and PANI|PSNPSO3 - resulted in the fabrication of immunosensors.</p>

Background: The secretory epithelial cells of the prostate gland use sophisticated vehicles named prostasomes to relay important information to sperm cells in semen. This prostasome-forming and secretory ability of the epithelial cells is also preserved in poorly differentiated prostate cancer cells. Aim: The aim of this thesis was to examine different characteristics of prostasomes, especially those derived from malignant prostate cells, linked to their potential role in diagnosis and prognostication of prostate cancer. Results: Serum samples of prostate cancer patients contained autoantibodies against seminal prostasomes in a higher concentration than did control sera. These autoantibodies were most frequently directed against 25 prostasome-associated proteins, but no one was prostate specific. Clusterin was one of the most frequently occurring prostasomal proteins. Elevated titers were however seen in both patients´ and control sera. Clusterin turned out to be a major antigen of seminal prostasomes. No prostate specific or prostate cancer specific protein was discovered upon proteomic analysis of prostasomes deriving from malignant cells of vertebral metastases of prostate cancer patients. Human chromosomal DNA was identified in both seminal prostasomes and PC-3 cell prostasomes and strong evidence existed that the DNA was localized inside the prostasomes. Four out of 13 DNA clones of seminal prostasomes featured gene sequences (31%). The corresponding figures for PC-3 cell prostasomes were 4 out of 16 clones (25%). Conclusions: Prostasomes are immunogenic and give rise to serum autoantibodies. The most frequently occurring autoantibodies were directed against 25 prostasomal proteins but none of these was exclusively prostate specific. Thirty different proteins were identified in prostate cancer metastasis-derived prostasomes but none of these proteins was prostate cancer specific. Human chromosomal DNA was identified in prostasomes of both normal and malignant cell origin.

The great variation displayed by nucleic acid molecules in human cells, and the continuous discovery of their impact on life, consequently require continuous refinements of molecular analysis techniques. Padlock probes and rolling circle amplification offer single nucleotide discrimination in situ, a high signal-to-noise ratio and localized detection within cells and tissues. In this thesis, in situ detection of nucleic acids with padlock probes and rolling circle amplification was applied for detection of DNA in the single cell gel electrophoresis assay to detect nuclear and mitochondrial DNA. This assay is used to measure DNA damage and repair.  The behaviour of mitochondrial DNA in the single cell gel electrophoresis assay has earlier been controversial, but it was shown herein that mitochondrial DNA diffuses away early in the assay. In contrast, Alu repeats remain associated with the nuclear matrix throughout the procedure. A new twelve gel approach was also developed with increased throughput of the single cell gel electrophoresis assay. DNA repair of three genes OGG1, XPD and HPRT and of Alu repeats after H2O2 induced damage was further monitored. All three genes and Alu repeats were repaired faster than total DNA. Finally, padlock probes and rolling circle amplification were applied for detection of the single stranded RNA virus Crimean Congo hemorrhagic fever virus. The virus was detected by first reverse transcribing RNA into cDNA.. The virus RNA together with its complementary RNA and the nucleocapsid protein were detected in cultured cells. The work presented here enables studies of gene specific damage and repair as well as viral infections in situ. Detection by ligation offers high specificity and makes it possible to discriminate even between closely related molecules. Therefore, these techniques will be useful for a wide range of applications within research and diagnostics.

Although inductively coupled plasma mass spectrometry (ICP-MS) is generally considered a reliable analytical technique, increasing demands on its capabilities require continued research and improvements. ICP-MS is susceptible to both matrix effects and drift, leading to a decline in accuracy and precision. A number of techniques are routinely used to compensate for these issues. Internal standardization is one such solution that requires relatively simple sample preparation and yet offers the possibility of improving both accuracy and precision. In order to be effective, an optimal analyte/internal standard pair must be chosen. Traditionally, analyte/internal standard pairs are chosen based on similarities in mass and/or ionization potential. The present studies sought to develop a program that determined standards based on the minimization of analytical error. 102 masses were monitored over 27 perturbations, i.e., changes to sample matrix and operating parameters. The standard deviations of the analyte/internal standard ratios were then used as a measure of internal standard performance. A thorough statistical analysis was conducted to determine trends between a good analyte/internal standard pair and similarities in chemical property. Similarities in mass offered the strongest relationship to a good internal standard choice, although many exceptions existed. The program was then tested over time and multiple instrument optimizations as well as on a completely different ICP-MS instrument. Results of these tests suggest that the data originally collected for the prediction program is not instrument-specific and thus provided a broader base of useful applications. Due to its unmatched sensitivity and multielement capabilities, ICP-MS is frequently utilized for biological samples. A more recent application, however, seeks to use ICPMS for the purpose of determining specific associations between metals and proteins. Such speciation requires a high resolution and reproducible separation prior to ICPMS analysis. Gel electrophoresis offers good separation and is well matched with the scanning properties of laser ablation sample introduction. The present study utilized native gel electrophoresis coupled with a uniquely modified electroblot system to improve sensitivity and to elucidate additional information. Chemically modified quartz fiber filters were successfully used as the transfer membrane to improve protein and metal capture efficiency. / text

Proteomics is the global analysis of proteins that covers a broad range of technologies aimed at determining the identity and quantity of proteins expressed in the cell, their three-dimensional structure and interaction partners. In contrast to genome, proteome reflects more accurately on the dynamic state of the cell, tissue, or an organism. Therefore much is expected from proteomics to yield better disease markers for early diagnosis and therapy monitoring, as well as biomarkers that would indicate environmental exposure or provide prediction of biological age. In this thesis, I have developed and applied robust and sensitive subproteomic approaches to study the effect of aging as well as and environmental pollution using different animal models. In the first part, a high-throughput proteomic method based on liquid chromatography coupled to 2-dimensional gel electrophoresis (LC/2-DE) was developed. The usefulness of this method has been demonstrated by applying it to the assessment of marine pollution in a field experiment. Next, I have utilized this subproteomic approach to study the effect of aging in mouse kidney of both genders. As a result, a protein expression signature of aging kidney was obtained, revealing gender-dependent alterations in proteome profiles of aging mouse kidney. In order to further reduce the dynamic range of protein expression and increase the sensitivity of proteomic analysis, I have applied a shotgun mass spectrometry-based proteomic approach using isobaric tags for relative and absolute quantification (iTRAQ) coupled to liquid chromatography and tandem mass spectrometry (LC-MS/MS) to study age-related differences in peroxisome-enriched fractions from mouse liver. Only eight proteins showed statistically significant difference in expression (p&lt;0.05) with moderate folds. This study indicates that age-depended changes in the liver proteome are minimal, suggesting that its proteome is efficiently maintained until certain age. Finally, in the context of aging studies and the role of peroxisomes in aging, I have tested the utility of cell-penetrating peptides (CPPs) as agents for protein delivery into acatalasemic peroxisomes using yeast as a model. The results obtained suggest that CPPs may be suitable for the delivery of antioxidants to peroxisomes and in future could provide a tool for the protein therapy of age-related diseases. / At the time of the doctoral defense, the following publications were unpublished and had a status as follows: Paper 3: Submitted, Paper 4: Submitted.

Die Demenz mit Lewy-Körperchen (DLB) ist eine progrediente neurodegenerative Erkrankung und stellt nach der Alzheimer-Erkrankung eine der häufigsten Ursachen einer Demenz dar. Betroffene leiden neben dem zentralen Merkmal Demenz an Fluktuationen der Kognition, Parkinsonismus und visuellen Halluzinationen. Charakteristische neuropatholgische Kennzeichen der DLB sind α-Synuklein-enthaltende Lewy-Körperchen und -Neuriten, die sich in kortikalen und subkortikalen Hirnregionen finden. Bei der klinischen Diagnostik dieser Erkrankung sind neben der Beurteilung klinischer Befunde laborchemische, psychometrische, apparative und bildgebende Verfahren von Bedeutung, jedoch ist eine sichere Diagnose nur bioptisch zu stellen. Gegenstand dieser Arbeit war die Untersuchung des Liquorproteomprofils von DLB-Patienten im Vergleich zu neurologisch gesunden Kontrollen und die Identifikation von regulierten Proteinen im Liquor bei der DLB durch Verwendung klassischer Methoden der Proteomik. Nach initialer Depletion von zwölf häufigen Proteinen wurden die Liquorproben mittels zweidimensionaler Gelektrophorese aufgetrennt, die Proteinexpressionsmuster quantitativ verglichen und anschließend insgesamt 23 verschiedene Proteine aus 44 regulierten Gelspots massenspektrometrisch identifiziert. Es fanden sich Proteine involviert in die Immunantwort, den Lipidstoffwechsel, den Glukosestoffwechsel, die Signaltransduktion und die Zellstruktur sowie einige, die sich keiner dieser funktionellen Gruppen zuordnen ließen. Von vier ausgewählten Proteinen - Complement C4a, Transthyretin, Contactin-1 und Chromogranin A - wurden Western Blots angefertigt, wofür Liquor sowohl von DLB-Patienten und gesunden Kontrollen als auch zum weiterführenden Vergleich von Parkinson- und Alzheimer-Patienten verwendet wurde. Die Ergebnisse dieser Arbeit zeigen auf Proteinebene die Vielfalt der biologischen Prozesse, die bei der DLB gestört ist. Zum Teil lassen sich Parallelen zu anderen neurogenerativen Erkrankungen erkennen, einige Proteine konnten jedoch erstmalig und einzig als bei der DLB reguliert nachgewiesen werden.

This study investigated proteomic changes in bronchoalveolar lavage fluid (BALF) of beef calves to identify alterations related to development of naturally occurring bovine respiratory disease. BALF was collected from 162 healthy beef calves soon after weaning and transportation. Two-dimensional gel electrophoresis and mass spectrometric analysis revealed calves that later developed pneumonia had significantly lower levels of anti-inflammatory proteins including annexin A1, RAGE-binding protein, apolipoprotein-A, heat shock protein beta-1 and thioredoxin, but higher levels of antioxidant and pro-inflammatory proteins such as immunoglobulin light chain variable region, cyclophilin A, serum albumin precursor and glutathione S-transferase P. Difference in gel electrophoresis-based analysis further showed lower levels of annexin A1, annexin A2, peroxiredoxin I, calycyphosin, superoxide dismutase, macrophage capping protein and dihydrodiol dehydrogenase 3 in the calves that later developed pneumonia. Differences in annexin levels were partially confirmed by Western blot analysis. In healthy calves, immunohistochemistry revealed cytoplasmic expression of annexin A1 in surface epithelium of large airways, tracheobronchial submucosal glands, and goblet cells, and to a lesser degree in small airways but not in alveolar epithelium. Flow cytometry and immunocytochemistry labeled annexin A1 in blood and bronchoalveolar lavage neutrophils, monocytes, macrophages and lymphocytes. Annexin A2 expression was detected in surface epithelium of small airways, some mucosal lymphocytes, and endothelium, with weak expression in large airways, tracheobronchial submucosal glands and alveolar epithelium. For both proteins, the level of expression was similar in tissues collected 5 days after intrabronchial challenge with M. haemolytica compared to that from sham-inoculated calves. A sandwich ELISA for annexin A1 was developed. For use with BALF, the working range was 0.3-317 ng/ml and the sensitivity was 0.8 ng/ml. The coefficient of variation of intra-assay and the between assays was less than 20%. Together, these findings reveal annexins A1 and A2 as promising biomarkers of susceptibility to BRD in healthy at-risk calves. Further, the anti-inflammatory and pro-resolving functions of these proteins suggest roles in the pathogenesis of bacterial pneumonia of feedlot cattle. / Natural Sciences and Engineering Council (NSERC), Ontario Cattlemen’s Association, Ontario Ministry of Agriculture and Food and Ontario Veterinary College Fellowship Program

<p>Polyaniline nanocomposites doped with poly(vinylsulphonate) (PV-SO3 &minus / ) and nanostructured polystyrene (PSNP) latex beads functionalized with amine (PSNP-NH2) and sulphate (PSNP-OSO3 &minus / ) were prepared and characterised for use as nitrite electro-catalytic chemosensors and ochratoxin A immunosensors. The resultant polyaniline electrocatalytic chemosensors (PANI, PANI|PSNP-NH2 or PANI|PSNP-OSO3 &minus / ) were characterized by cyclic voltammetry (CV), ultraviolet-visible (UV-Vis) spectroscopy and scanning electron microscopy (SEM). Brown-Anson analysis of the multi-scan rate CV responses of the various PANI films gave surface concentrations in the order of 10&minus / 8 mol/cm. UV-vis spectra of the PANI films dissolved in dimethyl sulphoxide showed typical strong absorbance maxima at 480 and 740 nm associated with benzenoid p-p* transition and quinoid excitons of polyaniline, respectively. The SEM images of the PANI nanocomposite films showed cauliflower-like structures that were &lt / 100 nm in diameter. When applied as electrochemical nitrite sensors, sensitivity values of 60, 40 and 30 &mu / A/mM with corresponding limits of detection of 7.4, 9.2 and 38.2 &mu / M NO2 &minus / , were obtained for electrodes, PANI|PSNP-NH2, PANI and PANI|PSNP-SO3 &minus / , respectively. Immobilisation of ochratoxin A antibody onto PANI|PSNP-NH2, PANI and PANI|PSNPSO3 - resulted in the fabrication of immunosensors.</p>

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