Ziel der vorliegenden Arbeit war die Identifizierung genetischer Faktoren, die das Plasmaproteom regulieren. Die Untersuchungen wurden im Modellsystem einer F2-Kreuzung zweier Inzucht-Mausstämme (FVB.LDLR-/-, C57BL/6.LDLR-/-) durchgeführt, die sich in ihrer Atheroskleroseausprägung unterscheiden. Von jedem der 453 Tiere der F2-Generation wurden Plasmaproteomprofile mittels Massenspektrometrie (MALDI-TOF) generiert. Diese Spektren wurden in zwei unabhängigen Datenanalysen ausgewertet und eine Kopplungsanalyse (QTL-Analyse, quantitative trait loci) der Phänotypen mit jeweils 192 genetischen Markern in jedem der F2-Tiere durchgeführt. So wurden die Datensätze von Proteom und Genom miteinander kombiniert, um Genorte, die mit unterschiedlich regulierten Proteinen in Verbindung stehen, zu identifizieren. Dieser Ansatz ist bisher in der Literatur nicht beschrieben worden. In der vorliegenden Arbeit wird sowohl die Methodik der statistischen Auswertung als auch die weitere Analyse der generierten Daten beschrieben. Es wurden zahlreiche hochsignifikante Kopplungssignale gefunden, von denen zwei durch die Identifizierung von Proteinen verifiziert werden konnten. Es handelt sich hierbei um das Apo-A2 des HDL auf Chromosom 1 und Hämoglobin subunit alpha auf Chromosom 11. Eine Kolokalisation der gefundenen Proteine mit Loci der Atherosklerosedisposition konnte nicht identifiziert werden. Dieser Ansatz zeigt erstmals, dass eine hypothesenfreie Verbindung proteomischer und genomischer Daten möglich ist und zur Identifizierung genetisch regulierter Plasmaproteine beitragen kann.

Introduktion: Sepsis är utan behandling ett livshotande tillstånd, en korrekt behandling behöver en snabb och tillförlitlig artidentifiering. Olika prepareringsmetoder av positiva blododlingar inför direkt identifiering med MALDI-TOF finns. MBT Sepsityper® IVD Kit är en CE-märkt metod. För att följa IVDR-direktivet behöver Sepsityper jämföras med den nuvarande in-house-metoden. Dessa två metoder jämfördes utifrån förmåga att ge ett tillförlitligt, snabbt resultat där även den praktiska metoden samt ekonomiska aspekten undersöktes Material och metod: Alla positiva blododlingar som undersöktes preparerades med in- house-metoden och Sepsityper innan analys med MALDI-TOF MS. Med in-house-metoden användes saponin för att lysera de humana cellerna medans Sepsityper använde lyseringsbuffert. Resultatets tillförlitlighet presenteras som scorevärde där >2 är tillförlitligt till speciesnivå, 1,7–1,99 till genusnivå och <1,7 är ej tillförlitligt. Resultat: 135 positiva blododlingar undersöktes där in-house-metoden gav 115 med ett scorevärde över 1,7 medans Sepsityper® gav 100 prover med ett scorevärde över 1,7. Bland dessa prover var det 62 gramnegativa bakterier och 53 grampositiva. Slutsats: En skillnad mellan antalet identifieringar med scorevärde över 1,7 sågs men var ej signifikant enligt CHI2 test där antalet var högre för house metoden. Den data som samlats ger ej inte tillräckligt med stöd för att inte avvika från IVDR och fortsätta med in-house- metoden. / Background: Sepsis without treatment is a life-threatening condition, a rapid as well as reliable identification of the bacteria is needed. Different preparation methods of positive blood cultures for rapid identification are available. MBT Sepsityper® IVD Kit is one of them and is a CE-marked method. To comply with the IVDR directive, Sepsityper® needs to be tested and compared with the current in-house method. These two methods were compared based on the ability to provide fast and reliable results. Material and method: All the positive blood samples that were examined were prepared by the two methods then analysed with MALDI-TOF MS. The in-house-method used saponin to lyse the blood cells, Sepsityper used a lysisbuffert. How reliable the results are presented as score value, >2 means that the result is reliable to species identification, between 1.7-1.99 to genus identification and <1.7 is not reliable. Results: 135 positive blood cultures were examined and the in-house-method gave 115 with a score value above 1.7 while Sepsityper® gave 100 bottles a score value over 1.7. Among the bottles there were 62 gram-negative bacteria and 53 gram-positive bacteria. Conclusion: A difference between the number of identifications with a score value above 1.7 were seen where the number was higher for the in-house method, but the difference was not significant according to the Chi2 test. The data collected do not provide sufficient support for not following IVDR and not switch to Sepsityper®.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) är en viktig metod för artidentifiering av mikroorganismer på kliniska mikrobiologiska laboratorier. Enligt rekommendationer från Bruker Daltonics skall matrixapplicering ske relativt omedelbart efter att mikroorganismer har applicerats. Syftet med studien var att utvärdera effekter på artidentifiering vid förlängda tidsintervall mellan applicering av mikroorganismer och matrix med MALDI-TOF MS. Målet var att optimera arbetsflödet på mikrobiologilaboratoriet, laboratoriemedicin, Region Jönköping län (RJL). I studien undersöktes hur identifieringen av mikroorganismer påverkades av applicering avbakterie- och jästsvampstammar (n = 267) och α-Cyano-4-hydroxycinnaminsyra (HCCA)-matrix på en MALDI-provplatta vid varierande tidsintervall upp till tre timmar. Analys med MALDI-TOF MS genomfördes med masspektrometrarna MALDI Biotyper Sirius IVD System och Bruker MicroFlex LT. Resultaten visade att förlängda tidsintervall mellan applicering av mikroorganismer och matrix upp till tre timmar inte hade någon signifikant effekt på scorevärden vid artidentifiering, vilket innebar att tidsintervallen är acceptabla för artidentifiering med MALDI-TOF MS. Detta ger värdefull information för att optimera arbetsflödet och öka effektiviteten på mikrobiologilaboratoriet. / Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an important method for species level identification in clinical microbiology laboratories. According to recommendations from Bruker Daltonics matrix application should occur relatively immediately after microorganisms have been applied. The aim of the study was to evaluate the effects on microbial identification at extended time intervals between microbial and matrix application using MALDI-TOF MS. The objective was to optimize the workflow at the microbiology laboratory, laboratory medicine, Region Jönköping län (RJL). The study investigated the impact on identification of microorganisms between the application of bacterial and yeast strains (n = 267) and α-Cyano-4-hydroxycinnamic acid (HCCA) matrix on a MALDI target plate of various time intervals up to three hours. MALDI-TOF MS was performed using MALDI Biotyper Sirius IVD System and Bruker MicroFlex LT mass spectrometers.The results showed that a delay of matrix application up to three hours had no significant effect on score values, indicating that time did not affect the accuracy of microbial identification using MALDI-TOF MS. Consequently, the study provided valuable information for optimizing the workflow and increasing the efficiency of the microbiology laboratory.

Vanliga fenoliska antioxidanter som används i polymerer orsakar färgändringar i polymeren. Detta arbete berör antioxidanter med jämförelsevis begränsad färgändring, med fokus på att utveckla metoder för analys av dessa. UV-stabilisatorerna UV2, UV5, UV1, UV4, UV3 och UV6 är också inkluderade i detta arbete. Metodutvecklingen involverade både kapillärelektrofores och ”matrix assisted laser desorption ionization-time of flight mass spectrometry” (MALDI-TOF). Den bästa metoden för analys av de flesta av additiven inkluderade MALDI-TOF med 2’,6’-dihydroxyacetophenon (10 mg/ml) i TA50 som matris och hexafluoroisopropanol som lösningsmedel. När en metod för detektion av analyterna hade tagits fram, så inleddes utveckling av en metod för extraktion av additiv från polymera material. Extraktion av UV5 var framgångsrik vid användning av toluen vid 80 °C i ultraljudsbad i tre timmar. Det extraherade UV5 detekterades sedan med metoden som hade utvecklats för det rena additivet. / Ordinary phenolic antioxidants used in polymers give rise to color formations. This work concerns antioxidants with limited color-formations in comparison, with the focus being development of methods for analysis of these. Also included in this work are the high molecular weight UV-stabilizers UV2, UV5, UV1, UV4, UV3 and UV6. The method development involved both capillary electrophoresis and matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF). The best method for analysis of most additives involved using MALDI-TOF with a matrix consisting of 2’,6’-dihydroxyacetophenone (10 mg/ml) in TA50 and with hexafluoro isopropanol as the solvent. When a method for detection of the analytes had been obtained, a method for extraction of the additives from polymers was developed. UV5 was successfully extracted using toluene as the extracting solvent at 80 °C under sonication for three hours. The extracted UV5 was then detected using the method developed for the pure additive.

No description available.

Thesis (MScMedSc (Pathology. Medical Microbiology))--Stellenbosch University, 2008. / The genus Mycobacterium is a group of acid–fast, aerobic, slow- growing organisms which include more than 90 different species. A member of this genus, Mycobacterium tuberculosis, belonging to the Mycobacterium tuberculosis complex (MTB), is the causative agent of tuberculosis (TB). This disease is currently considered a global emergency, with more than 2 million deaths and over 8 million new cases annually. TB is the world’s second most common cause of death after HIV/AIDS. About one-third of the world’s population is estimated to be infected with TB. This catastrophic situation is further compounded by the emergence of Multi Drug Resistant tuberculosis (MDR-TB) and in more recent times, Extensive Drug Resistant tuberculosis (XDR-TB). Early diagnosis is critical to the successful management of patients as it allows informed use of chemotherapy. Also, early diagnosis is also of great importance if the menace of MDR-TB and XDR-TB is to be curbed and controlled. As MTB is highly infectious for humans, it is of paramount importance that TB be diagnosed as early as possible to stop the spread of the disease. Traditional conventional laboratory procedures involving microscopy, culture and sensitivity tests may require turnaround times of 3-4 weeks or longer. Tremendous technological advancement over the years such as the advent of automated liquid culture systems like the BACTEC® 960 and the MGITTM Tube system, and the development of a myriad of molecular techniques most of which involves nucleic acid amplification (NAA) for the rapid identification of mycobacterial isolates from cultures or even directly from clinical specimens have contributed immensely to the early diagnosis of tuberculosis. Most of these NAA tests are nevertheless fraught with various limitations, thus the search for a rapid, sensitive and specific way of diagnosing tuberculosis is still an active area of research. The search has expanded to areas that would otherwise not have been considered ‘conventional’ in diagnostic mycobacteriology. One of such areas is mass spectrometry. This study joins the relatively few studies of its kind encountered in available literature to establish the ground work for the application of mass spectrometry, specifically Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-ToF MS) in the field of diagnostic mycobacteriology. This is an area which is in need of the speed, sensitivity and specificity that MALDI-ToF technique promises to offer. Since this technology is still in its infancy, the use of utmost care in the preparation of reagents, and the handling and storage of the organisms used to generate reference mass spectra for the database cannot be overemphasized. Similarly, the optimization of certain crucial experimental factors such as inactivating method and choice of matrix is of paramount importance. The main aim of this thesis was to generate a database of reference mass spectra fingerprints of selected (repository) Mycobacterium species. This necessitated the standardization of an experimental protocol which ensured that experimental factors and the various instrument parameters were optimized for maximum spectra generation and reproducibility. A standard operating procedure (SOP) for generating the database of reference mass spectra finger print of selected Mycobacterium species was developed and used to investigate the ability of the database to differentiate between species belonging to the same clinical disease complex as well as the nontuberculosis complex. The findings of this study imply that if the defined protocol is followed, the database generated has the potential to routinely identify and differentiate (under experimental conditions) more species of Mycobacterium than is currently practical using PCR and its related techniques. It is therefore a realistic expectation that when the database is clinically validated and tested in the next phase of the study, it will contribute immensely to the diagnosis of tuberculosis and other mycobacterioses. It will also aid in the identification of emerging pathogens particularly amongst the non-tuberculous mycobacteria.

This diploma thesis is focused on species identification of sand flies belonging to two genera of the subfamily Phlebotominae, genus Phlebotomus and Sergentomyia. Genus Phlebotomus together with the genus Lutzomyia of New World include the only proven vectors of Leishmania parasites and they are also carriers of viral and bacterial infections. Species of the genus Sergentomyia are proven vectors of sister genus Sauroleishmania that infects reptiles, but for several decades there have been speculations about their possible involvement in the transmission of mammalian Leishmania species. These suspicions arise mainly from repeated findings of mammalian Leishmania parasites in their digestive system. Correct species determination of medically significant hematophagous arthropods is very important especially for purposes of epidemiological studies so that efficient vector control may be correctly set. Routine identification of sand flies is based on morphological characters located mainly on their heads and genitalia. However, these characters may be variable within a species, they require certain expertise and in the field samples they may be damaged, making proper species identification impossible. This thesis therefore presents two alternatives of sand fly identification based on molecular...

En contrôlant le passage para- et transcellulaire des composés du sang vers le cerveau (et inversement), la barrière hémato-encéphalique (BHE) constitue la « gardienne » du compartiment cérébral. Bien que relativement connu dans son aspect physiologique, le phénotype BHE des cellules endothéliales des capillaires cérébraux (BCECs) reste mal compris au regard des mécanismes moléculaires qui gouvernent son établissement et son maintien. Dans cette optique, à l’aide du modèle in vitro de BHE développé au laboratoire (co-culture de BCECs bovines et de cellules gliales de rats), nous avons réalisé deux études protéomiques comparatives afin d’identifier les protéines cytoplasmiques potentiellement impliquées dans l’induction et le maintien de ce phénotype: d’une part une approche qualitative sans marquage (label free) et d’autre part une approche quantitative grâce à un marquage isotopique préalable des protéines (isotope-coded protein label, ICPL). Les deux approches, label free et ICPL se sont révélées complémentaires et ont permis, respectivement, l’identification de 447 et de 412 protéines (dont 290 quantifiées). Quatre protéines d’un intérêt particulier dans le domaine de la BHE (phosphatase alcaline tissu-non spécifique, TNAP ; protéine 1 possédant un domaine d’homologie à Eps15, EHD1 ; superoxyde dismutase, SODC et homologue 7 de la protéine de la maladie de Parkinson PARK7, DJ-1) ont fait l’objet de caractérisations biochimiques approfondies et ouvrent des pistes d’investigation sur des potentielles voies cellulaires induites par les cellules gliales et impliquées dans le phénotype BHE. / The blood-brain barrier (BBB) controls the para- and transcellular crossing of compounds from blood to brain (and inversely) and establishes the “gatekeepers” of the brain. The major part of therapeutic drugs developed to fight the brain diseases is deemed inefficient in vivo due to the presence of the BBB that they are unable to cross. Although relatively well known in its physiological aspect, the BBB phenotype of brain capillary endothelial cells (BCECs) remains largely under known and misunderstood in regards of the molecular mechanisms that govern its establishment and its maintenance. To this goal, using the in vitro BBB model developed in the laboratory (co-culture of bovine BCECs with rat glial cells), we performed two differential proteomic studies to identify the main cytoplasmic proteins involved in the establishment and maintenance of this phenotype: a qualitative label free approach and a quantitative isotope-coded protein labeling (ICPL) approach.The two different approaches, label free and ICPL, are complementary and led to the identification of 447 and 412 proteins, respectively. Four proteins of particular interest for BBB (tissue-non specific alkaline phosphatase, TNAP; Eps15 homology domain containing protein 1, EHD1; superoxide dismutase, SODC and Parkinson disease protein 7 homolog PARK7, DJ-1) have been more deeply studied and they open new discovery prospects related to cellular pathways induced by glial cells and involved in the BBB phenotype.

As mudanças climáticas associadas às atividades humana são devidas principalmente às emissões de CO2 na atmosfera provenientes da queima de combustíveis de origem fóssil. Desta forma, faz-se necessária a substituição dessas fontes fósseis de geração de energia, por fontes renováveis. Dentre as alternativas de fontes renováveis, podemos destacar os biocombustíveis produzidos a partir de microalgas, as quais apresentam composição rica em óleos e proteínas. Um dos grandes desafios encontrados na conversão de biomassa em biocombustíveis é a caracterização detalhada das microalgas. A identificação de espécies através da espectrometria de massas com Ionização/Dessorção à Laser Assistida por Matriz acoplada a analisador por tempo de vôo (MALDI-TOF-MS) utilizada na análise de perfil de proteínas de micro-organismos, e posterior rápida identificação por comparação com os padrões armazenados em bancos de dados (fingerprint) tem se sobressaído. Existem poucos trabalhos na literatura abordando a identificação de espécies de microalgas utilizando a técnica de MALDI-TOF-MS e nenhum trabalho abordando a análise a partir do uso de células de microalgas liofilizadas. Desta forma, nesse trabalho foi estudada a influência de diversos parâmetros tais como placa, modo de análise, valor de PIE, valor de IS2, matriz e solvente de matriz e amostra nos espectros de massas do tipo MALDI-TOF-MS para análise do perfil proteico de células liofilizadas das espécies de microalgas Chlorella vulgaris, Chlorella sp., Desmodesmus sp., Monoraphidium sp. e Oocystis sp. Primeiramente, os cultivos foram realizados em um sistema de agitador orbital otimizado de tal maneira que todas as posições apresentassem as mesmas condições. Após os cultivos, as células foram secas para posterior análise de espectrometria de massas. Para determinação da metodologia que fornecesse os melhores espectros de massas, foram avaliados, aleatoriamente, 3 parâmetros: número de íons (P1), relação sinal/ruído do pico base (P2) e intensidade do pico base (P3). Foi observado que para a maioria das amostras de microalgas, os parâmetros que mais influenciaram na obtenção de espectros de massas do tipo MALDI-TOF bem resolvidos foram a placa, o modo de análise, valor de PIE, valor de IS2 e a matriz. As variações obtidas nos espectros de massas, quando utilizados diferentes solventes tanto para a matriz quanto para a amostra, bem como a adição de isopropanol com o objetivo de melhorar a distribuição da matriz sDHB na placa de amostragem, não foram tão significativas como as observadas para os outros parâmetros avaliados nesse estudo. Como conclusão, o uso da matriz sDHB, solvente TA50 para amostra e matriz, análise na placa polished sob as condições de análise PIE 100ns, IS2 23kV mostraram-se muito mais efetivos para a análise de proteínas a partir de amostras de microalgas liofilizadas. A análise dos lipídios apresentou uma distribuição predominante dos ácidos graxos C16:0, C18:2 e C18:0 para os cultivos de 12 dias e C16:0, C18:2 e C22:6 para os cultivos de 8 dias. Entretanto, as proporções de C22:6 e C18:2 aumentaram para os cultivos de 8 dias. Dessa forma, as espécies de microalgas Chlorella vulgaris., Chlorella sp., Monoraphidium sp. e Oocystis sp. cultivadas por 8 dias podem ser convertidas em biocombustível por apresentarem ácidos graxos entre 14 e 18 carbonos e em sua composição. / Climate change associated to human activities are mainly due to CO&#8322 emissions from combustion of fossil fuels in the atmosphere. Thus, it is necessary to replace these fossil sources of energy generation for renewable sources. Among the alternative of renewable sources, biofuels derived from microalgae is am potential alternative, since microalgae present in their composition fatty acids and proteins. Characterization of microalgae is one of the challenges in the conversion of their biomass into biofuels. The microorganism species identification by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) thought the analysis of protein profile and subsequent fast identification by comparison with the standard protein profile (fingerprint) in the database has been outstanding. There are few studies in the literature about the identification of microalgae species using MALDI-TOF-MS technique and there is no one using cells of lyophilized microalgae. Thus, in this work was studied the influence of many parameters such as target, analysis mode, PIE, IS2 value, matrix, matrix solvent and sample solvent in the MALDI-TOF mass spectra for analysis of protein profile of lyophilized microalgae cells for the species Chlorella vulgaris cells, Chlorella sp., Desmodesmus sp., Monoraphidium sp. and Oocystis sp. Cultivations were carried out using an optimized shaker system, where all positions presented the same conditions. After the cultivation, the cells were dried for subsequent mass spectrometric analysis. To achieve the best mass spectra profile, 3 parameters were arbitrarily evaluated: number of ions (P1), base peak signal/noise ratio (P2) and base peak intensity (P3). It was observed for most microalgae samples, MALDI-TOF mass spectra profile were most influenced by target, analysis mode, PIE value, IS2 value and the matrix. Variations in the mass spectra obtained when different solvents were used (for matrix and sample) as well as the addition of isopropanol in order to improve the distribution of sDHB matrix on the spot, were not significant as that observed for the other parameters. In conclusion, the use of sDHB matrix, TA50 solvent for sample and matrix, analysis in polished target plate under the following analysis conditions: a PIE 100ns, a IS2 23kV, provided to be more effective for the analysis of protein from lyophilized microalgae cells. Lipid analysis of 12 days cultivated microalgae showed a predominant distribution of the C16:0, C18:2 and C18:0. The 8 days cultivation presented a distribution of C16:0, C18:2 and C22:6, but with C22:6 e C18:2 in a higher proportion. Since biofuel are produced by using the C14-C18 fatty acid contained in their composition, 8 days cultivation showed to be most effective for this purpose.

Effective analytical techniques need to be developed to characterize the products of lignin degradation experiments to be able to generate renewable products from lignin. Mass spectrometry is an valuable analytical approach for lignin characterizaion, but it is hindered by lignin’s poor ionization efficiency, especially in the positive ion mode. In this work, we attempt to improve lignin’s ionization by utilizing electrospray and laser desorption mass spectrometry coupled with the addition of cations and chemical derivatives. We confronted the ionization problem from both a top-down and bottom-up analytical approach by analyzing synthesized monomers, dimers, and polymers along with natural lignin extracts from switchgrass. We also utilized tandem mass spectrometry to sequence lignin dimers and determine their bonding motifs from their fragmentation patterns. We believe that resolving the ionization issues with lignin will open the door for easier and more efficient lignin break-down techniques and ultimately more accessible renewable products from lignin.