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<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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In human microbiome analysis, sequencing of bacterial 16S rRNA genes has revealed a role for the gut microbiota in maintaining health and contributing to various pathologies. Novel community analysis techniques must be evaluated in terms of bias, sensitivity, and reproducibility and compared to existing techniques to be effectively implemented. Next- generation sequencing technologies offer many advantages over traditional fingerprinting methods, but this extensive evaluation required for the most efficacious use of data has not been performed previously. Illumina libraries were generated from the V3 region of the 16S rRNA gene of samples taken from 12 unique sites within the gastrointestinal tract for each of 4 individuals. Fingerprint data were generated from these samples and prominent bands were sequenced. Sequenced bands were matched with OTUs within their respective libraries. The results demonstrate that denaturing gradient gel electrophoresis (DGGE) represents relatively abundant bacterial taxa (>0.1%) beta-diversity of all samples was compared using Principal Coordinates Analysis (PCoA) of UniFrac distances and Multi-Response Permutation Procedure (MRPP) was applied to measure sample cluster strength and significance; indicator species analysis of fingerprint bands and Illumina OTUs were also compared. The results demonstrate overall similarities between community profiling methods but also indicate that sequence data were not subject to the same limitations observed with the DGGE method (i.e., only abundant taxa bands are resolved, unable to distinguish disparate samples). In addition, the effect of stochastic fluctuations in ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? differ for DGGE and next-generation sequencing. I compared pooled and individual reactions for samples of high and low template concentration for both Illumina and DGGE using the combined V3-V4 region of the 16S rRNA gene, and demonstrated that template concentration has a greater impact on reproducibility than pooling. This research shows congruity between two disparate molecular methods, identifies sources of bias, and establishes new guidelines for minimizing bias in microbial community analyses.

Thesis by publication. / "August 2006" / Thesis (PhD)--Macquarie University, Division of Environmental & Life Sciences, Dept. of Biological Sciences & Dept. of Chemistry & Biomolecular Sciences), 2007. / Bibliography: leaves 157-183. / 1. Introduction -- 1.1. Proteomics and two-dimensional electrophoresis -- 1.2. A proteomic approach to study the filamentous fungus Trichoderma -- 1.3. Aims of the thesis -- 2. Materials and methods -- 3. Results and discussion -- 3.1. Method development for the display and identification of fungal proteins by 2DE and mass spectrometry -- 3.2. Discovery of novel determinants in the biological control of phytopathogens by Trichoderma atroviride -- 3.3. Summary and concluding remarks. / Trichoderma harzianum and T. atroviride are filamentous fungi commonly found in soil. Both display biocontrol capabilities against a range of phytopathogenic fungi including Rhizoctonia solani and Botrytis cinerea which are known pests of hundreds of commercially important crops including tomatoes, potatoes, beans, cucumber, strawberries, cotton and grapes. These Trichoderma species secrete a combination of enzymes degrading cell walls and antibiotics to overgrow and kill fungal phytopathogens. They are seen as an environmentally friendly alternative to chemical fungicides currengly used on crops. / A proteomic approach was taken to separate and identify proteins from a strain of T. harzianum with well established biocontrol properties. Several methods were developed in this thesis to display the whole proteome content and several subcellular proteome fractions from T. harzianum. Proteins were separated by two-dimensional electrophoresis and identified by mass spectrometric methods. The resulting proteomic maps represent the first extensive array of cellular and sub-cellular proteomes for T. harzianum. / Cellular protein patterns of T. atroviride (T. harzianum P1) grown on media containing either glucose or R. solani cell walls were compared by differential gel electrophoresis to identify a suite of new proteins involved in the biological control response. Twenty four T. atroviride protein spots up-regulated in the presence of the R. solani cell walls were identified by mass spectrometry and N-terminal sequencing. Proteins identified from this study included previously implicated enzymes degrading cell walls and three novel proteases, vacuolar serine protease, vacuolar protease A and trypsin-like protease. The genes encoding two of these proteases, vacuolar protease A and vacuolar serine protease have been cloned by degenerate primer PCR and genomic walking PCR and sequenced. The gene sequences and protein sequences derived from these genes have been partially characterised. / Mode of access: World Wide Web. / 194 leaves ill

\kur{Beauveria bassiana} is a entomopathogenic polyphagous fungus commonly found in soil and it is parasite of soil insects, mainly of the stages of insect that occur in soil. At the present time it is used in plant protection against more than 70 species of insects. In the Czech Republic \kur{Beauveria bassiana} has the greatest importance in the fight against bark beetle \kur{Ips typographus} in the NP Šumava in these days. This study was focused on the evaluation of genetic variability \kur{Beauveria bassiana} strains on the basis of microsatellite analysis and the comparison of four separation methods: electrophoresis in 2% agarose gel, electrophoresis in 3% synergel, chip electrophoresis and fluorescent capillary electrophoresis in term of the most precise separation of PCR products. We used 41 strains which were collected in the NP Šumava and 20 strains from long-term collection determined as an exotic in this study. This large geographical scale group contains the strains from whole world and in addition it was upgraded by the strains collected from the NP Krkonoše and South Moravia. For the microsatellite analysis there were used 11 pairs of primers but for inter-comparison of separative methods were chosen only 4 pairs of primers. The population of \kur{Beauveria bassiana} strains collected from the NP Šumava were evaluated by analysis of microsatellites as a conservative and fully closed regardless of the source and the location. The strains from the large geographical scale group showed the great genetic variability. In terms of separation, the best and most suitable separation method was proved, the fluorescent capillary electrophoresis. Despite of its difficult financial aspect, this method was evaluated as the most precise and the most sensitive. Its advantage is in possibility to detect the smallest differences in the length of single allele in the range 1-2 bp, which is for the gel electrophoresis impossible.