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Joyner, Jeffrey Clark. "The Use of 2D-LC-MS/MS in disease characterization and global proteomics." Connect to resource, 2006. http://hdl.handle.net/1811/6604.
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Thesis (Honors)--Ohio State University, 2006.Title from first page of PDF file. Document formatted into pages: contains 46 p.; also includes graphics. Includes bibliographical references (p. 46). Available online via Ohio State University's Knowledge Bank.
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Vieira, José Cavalcante Souza. "Investigação de metalotioneínas em peixes da região de Jirau - bacia do Rio Madeira - Rondônia." Botucatu, 2017. http://hdl.handle.net/11449/150736.
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Orientador: Pedro de Magalhães PadilhaResumo: Devido a sua grande concentração de nutrientes, tais como proteínas, vitaminas e minerais, o peixe é considerado um dos alimentos mais saudáveis que se pode encontrar na natureza. No entanto, a ingestão de peixes é considerada a forma predominante de via de exposição do ser humano ao mercúrio (Hg), principalmente para as populações que vivem às margens dos rios, onde o peixe constitui a principal fonte de proteína. Na tentativa de elucidar os mecanismos de toxicidade das espécies mercuriais, o teor desse metal tem sido estudado intensamente pela comunidade científica nas últimas décadas em amostras de solo, sedimentos, humanos e peixes na Amazônia brasileira. Sabe-se que as espécies mercuriais bioacumuladas nos tecidos dos seres vivos ligam-se a metaloproteínas, e quando há uma concentração alta de metal tóxico nos organismos, esses passam a expressar proteínas de defesa, denominadas metalotioneínas (MTs) responsáveis pelo transporte e eliminação de metais tóxicos. Apesar de estudos mostrarem o aumento das metalotioneínas em animais expostos a metais potencialmente tóxicos, essas proteínas não foram caracterizadas para confirmação de sua veridicidade, são analisadas por métodos indiretos, esse fato leva a necessidade de técnicas mais precisas na identificação de metalotioneínas. Levando em consideração o exposto esse estudo teve como objetivo otimizar métodos de quantificação de mercúrio e técnica de eletroforese para identificação de possíveis metalotioneínas biomarcadoras d... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Due to its high concentration of nutrients, such as proteins, vitamins and minerals, fish is considered one of the healthiest foods that one can find in nature. However, fish intake is considered to be the predominant human exposure pathway to mercury (Hg), especially for populations living along riverbanks where fish are the main source of protein. In the attempt to elucidate the toxicity mechanisms of mercurial species, the content of this metal has been intensively studied by the scientific community in recent decades in soil, sediment, human and fish samples in the Brazilian Amazon. It is known that mercurial species bioaccumulated in the tissues of living beings bind to metalloproteins, and when there is a high concentration of toxic metal in organisms, they begin to express defense proteins, called metallothioneins (MTs) responsible for the transport and elimination of Toxic metals. Although studies have shown the increase of metallothioneins in animals exposed to potentially toxic metals, these proteins have not been characterized to confirm their veridicity, are analyzed by indirect methods, this fact leads to the need for more precise techniques in the identification of metallothioneins. Taking into account the above, this study aimed to optimize mercury quantification methods and electrophoresis technique for identification of possible mercury biomarkers metallothionein in muscular and hepatic tissue of fish of economic interest, Tucunaré (Cichla spp.), Filhote (Bra... (Complete abstract click electronic access below)
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Bittarello, Alis Correia. "Estudo de biomarcadores de mercúrio em peixes da amazônia por meio da metalômica e análise do estresse oxidativo." Botucatu, 2017. http://hdl.handle.net/11449/151174.
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Orientador: Pedro de Magalhães PadilhaResumo: O mercúrio é um metal tóxico, de distribuição ubíqua, com capacidade para bioacumulação e biomagnificação, que provoca alterações em biomoléculas importantes no metabolismo e contribui para o estabelecimento do estresse oxidativo em organismos aquáticos. Logo, o presente estudo teve por objetivo identificar e avaliar possíveis biomarcadores proteicos e/ou enzimáticos da toxicidade do mercúrio em peixes da região amazônica, por meio do estudo metaloproteômico e avaliação do estresse oxidativo. Foram utilizadas metodologias de fracionamento e identificação de proteínas por eletroforese bidimensional (2D PAGE) associada à espectrometria de massas (MS), mapeamento do mercúrio, em spots proteicos, por espectrometria de absorção atômica em forno de grafite (GFAAS) e avaliação de marcadores de estresse oxidativo. As espécies utilizadas foram o Plagioscion squamosissimus (corvina) e Colossoma macropomum (tambaqui), coletados na área da Usina Hidrelétrica de Jirau (rio Madeira-RO), que foram selecionadas em função da abundância populacional, interesse para a pesca e posição diferente na cadeia trófica (carnívoro e onívoro, respectivamente). Os tecidos amostrados foram o hepático, renal e muscular. Os resultados obtidos demonstraram maior concentração de mercúrio total no P. squamosissimus, espécie carnívora, e padrão de distribuição deste elemento igual para ambas as espécies (fígado>rim>músculo). Há tendência para maior atividade enzimática nos tecidos hepático e renal da espécie com... (Resumo completo, clicar acesso eletrônico abaixo)
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Nakata, Michael Takeshi. "Simulating the FTICR-MS Signal of a Decaying Beryllium-7 Ion Plasma in a 2D Electrostatic PIC Code." Diss., CLICK HERE for online access, 2010. http://contentdm.lib.byu.edu/ETD/image/etd3370.pdf.
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Eckberg, Melanie N. "Forensic Toxicological Screening and Confirmation of 800+ Novel Psychoactive Substances by LC-QTOF-MS and 2D-LC Analysis." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3923.
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Novel psychoactive substances (NPS) represent a great challenge to toxicologists due to the ability of illicit drug manufacturers to alter NPS chemical structures quickly and with ease to circumvent legislation regulating their use. Each time a new structure is introduced, there is a possibility that it has not been previously recorded in law enforcement or scientific databases. Many toxicology laboratories use targeted analytical methods that rely on libraries of known compounds to identify drugs in samples. However, these libraries do not include large numbers of NPS which could result in non-identification or detection.
High-resolution mass spectrometry (HRMS) has been suggested as a method for screening a wide variety of analytes due to its higher sensitivity and mass accuracy as compared to some other forms of mass spectrometry. This technique can generate characteristic MS/MS spectral data for use in compound identification. The main goal of this research was to create a high-resolution mass spectrometry (HRMS) library of NPS and metabolites, as well as validate a method for screening and confirmation of these substances. The study consisted of three main tasks which included; the development of a large high-resolution MS/MS spectral library and database, validation of a method for screening and confirmation of over 800 NPS and metabolites, and screening of blind-spiked and authentic urine specimens to determine real-world applicability of the HRMS library and method.
During validation, several isomeric and structurally related NPS were observed which could not be adequately separated using traditional LC methods. A fourth task was therefore added to investigate improved separation using two-dimensional liquid chromatography (2D-LC). Increased resolving power is achieved in 2D-LC through the coupling of multiple orthogonal separation systems. Ultimately, an on-line, comprehensive method was developed using orthogonal reversed-phase columns in each dimension (RP x RP) for improved separation of co-eluting and isomeric synthetic cannabinoids.
This work can aid laboratories in the identification of NPS through the use of a validated LC-QTOF-MS method for screening and confirmation and HRMS spectral library. In instances where isomeric and structurally related NPS are not sufficiently separated, RP x RP methods can be explored.
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Niranjane, Ajay Pundaiikrao, and ajay niranjane@gmail com. "Screening diverse cellulase enzymes from the white rot fungus Phlebia gigantea for high activity and large scale applications." RMIT University. Applied Sciences, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20080513.150257.
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Cellulosic biomass is the major organic matter produced in the biosphere. The biodegradation of this cellulosic material is achieved by enzymatic activities of the cellulose degrading microorganisms. These organisms usually express a complex extracellular or a membrane bound cellulolytic system comprising combination of several cellulase enzymes. Cellulases are the group of hydrolytic enzymes capable of hydrolysing insoluble cellulose to glucose. Phlebia gigantea is an aggressive white rot basidiomycete with ability to tolerate resinous extracts on freshly cut wood and higher growth rate. This helps the fungus to colonise the sapwood preventing other fungi from becoming established. Early research on the cellulase system of this organism reported the presence of a cellulase system composed of P-glucosidase, endoglucanase and a cellobiohydrolase. Based on these unpublished studies, our aim was to obtain a complete sequence of putative cellobiohydrolase I (CbhI) from this organism. Attempts to identify and isolate the cellulase gene resulted in an incomplete cDNA sequence of I 154 bp. To understand the cellulase system, expression and regulation of the cellulase enzymatic activity was examined for incubation of P. gigantea on substrates glucose, xylose, Avicel, carboxymethyl cellulose and cellobiose. The pH, total protein and biomass production results indicated that the capacity of P. gigantea to degrade cellulose is dependent upon the nature of the carbon source and the regulation of the cellulase synthesis is repressed in the presence of simple sugars like glucose and xylose. The study employed the highly effective method of purification by affinity adsorption and purified cellulase complex in large quantity. Characterisation of the kinetic properties of this cellulase complex revealed that the rate of cellulase catalysis were optimum at pH 5.0 and temperature 50GC. The purified complex was comprised of multiple proteins and demonstrated significant CMCase and CBHase activity on zymogram analysis. The purified cellulase complex was characterised by 2D gel electrophoresis and by peptide mass finger printing using MALDI-TOF massspectrometry analysis. The 2D gel analysis of the purified cellulase complex showed 15 spots within the range of pI 3.5 to pI 7 and the molecular weight between 20KDa to 100KDa. Three protein spots were selected based on the IEF and SDS zymogram and identified using MALDI-TOF MS analysis. These proteins were identified based on the peptide mass data belonging to the 6-phospho-a-glucosidase, p-glucosidase and glycosyl hydrolase family 13 a-amylase or pullulanases, suggesting the divergent evolution of specific cellulase proteins. This study showed P. gigantea as a potential cellulase source and the cellulase complex secreted by the induction of substrate, comprises a variety of enzymes related to hydrolysis of cellulose biomass. It is evident from this and previous studies that P. gigantea cellulase complex comprises of a specific set of enzymes that possess the ability to degrade crystalline cellulose and is one of the first organisms to colonise freshly cut wood. Further studies on the cellulase system of this primary colonist may open up the prospects to utilise this organism as the potential onsite bioreactor agent, pre-treating the biomass and increasing the economic feasibility of the industrial bioenergy processes.
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Halienová, Andrea. "Změny proteomu a metabolomu u vybraných organismů ve stresových podmínkách." Doctoral thesis, Vysoké učení technické v Brně. Fakulta chemická, 2010. http://www.nusl.cz/ntk/nusl-233313.
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Living conditions of every organism are influenced by various factors at this time. Some of them have positive effect on organism, some negative. Basic condition for surviving is the ability to resist and adapt to changing metabolic and living conditions. Every single stress effect can lead to changes in metabolism but organisms have ability to develope sufficient mechanisms for stress response. Some of them are similar for all living organisms (enzyme production, endogenous primary stress metabolites) some of them are specific for certain organism or stress type. Cell stress response can be observed on different levels (proteomic, genomic, metabolomic). In proper conditions it can be used indrustrially. In this work, influences of various stress factors were studied. These factors were applied on selected organisms – carotenogenic yeast and plant materials. Yeast stress response was induced by osmotic and oxidation stress factors. Changes on proteomic level and in production of selected secondary metabolites were observed. Proteome was analyzed by 1D and 2D electrophoresis with subsequent analysis of proteins by mass spectrometry. Yeast strain Rhodotorula glutinis CCY 20-2-26 showed the best adaptation to stress factors, which was moreover accompanied by overproduction of carotenoids. This finding can be premise for next industrial production of carotenoids. In plant samples predominantly enzymes and metabolites involved in antioxidant response were studied.
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Howard, James W. "The development of mass spectrometry-based methodologies for the high throughput quantitation of peptides in biological matrices." Thesis, Loughborough University, 2018. https://dspace.lboro.ac.uk/2134/32454.
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The aim of this research was the development of mass spectrometry-based methodologies for the high-throughput quantitation of peptides in biological matrices. Glucagon and GLP-1, which are of interest as biomarkers and in the development of therapeutics, were chosen as model peptides. Immunoassays that are traditionally used to quantify these often perform poorly; therefore, necessitating the development of alternative methodologies. Application of mass spectrometry-based methodologies to these analytes has, however, been limited, primarily due to sensitivity challenges, but also due to analytical challenges associated with their endogenous nature and instability in biological matrices. Chapter 2 describes the development and qualification of the first liquid-chromatography coupled tandem mass spectrometry (LC-MS/MS) method for the quantitation of endogenous glucagon from human plasma. A novel 2D extraction procedure was developed to ensure robustness and sensitivity, whilst a novel surrogate matrix quantitation strategy took into account the endogenous nature of the analyte. A lower limit of quantitation (LLOQ) of 25 pg/mL was qualified, which was a considerable improvement over that previously reported in the literature (250 pg/mL) for a LC-MS/MS method. Clinical samples were cross-validated against a conventional radioimmunoassay (RIA), and similar pharmacokinetic (PK) profiles resulted, demonstrating that the methods were complementary. In Chapter 2 glucagon instability in biological matrix was noted. To characterise this further, in Chapter 3 in vitro glucagon metabolites were identified using high-resolution mass spectrometry (HRMS). Metabolites observed by others (glucagon19-29, glucagon3 29 and [pGlu]3glucagon3 29) in alternative matrices were identified, alongside novel metabolites (glucagon20-29 and glucagon21-29). Cross-interference of these metabolites in immunoassays may help to explain their poor performance, whilst knowledge of metabolism may also aid the development of future stabilisation strategies. The method developed in Chapter 2 was refined in Chapter 4 to improve sensitivity, robustness and throughput, and to add GLP-1 as a secondary analyte. The sensitivity achieved (glucagon: 15 pg/mL LLOQ, GLP-1: 25 pg/mL LLOQ) is the highest reported for both peptides for an extraction avoiding immunoenrichment. Specificity of endogenous glucagon quantitation was assured using a novel approach with a supercharging mobile phase additive to access a sensitive qualifier transition. A cross-validation against established immunoassays using physiological study samples demonstrated some similarities between the methods. Differences between the immunoassay results exemplified the need to develop alternative methodologies. The resulting LC-MS/MS method is considered a viable alternative to immunoassays, for the quantitation of endogenous glucagon, dosed glucagon and/or dosed GLP-1 in human plasma.
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Anastacio, Amandine. "Etude du profil protéomique de follicules ovariens de souris à 3 différents stades de développement in vitro." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2014. http://tel.archives-ouvertes.fr/tel-00990894.
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Alors que le protéome de l'ovocyte isolé, aux stades VG et MII a déjà été étudié, celui du follicule en croissance n'a jamais été décrit.Dans cette étude, nous avons cherché à identifier, comparer et caractériser les profils protéiques de follicules ovariens de souris à trois stades de leur développement in vitro distincts morphologiquement : follicules secondaires en début de culture - stade initial (IS), follicules avec une rupture complète de la membrane de Slavjanski (RMS) et follicules avec une cavité similaire à l'antrum (FA).Après un préfractionnement par IEF et une analyse LC-MS/MS en deux configurations (1D et 2D), 1403 protéines ont pu être identifiées dans le follicule ovarien de souris. 43,4 % (609) des protéines identifiées étaient communes aux trois stades et d'autres ont été identifiées uniquement à un stade : 71 au stade IS, 182 au stade RMS et 193 au stade FA. De plus, on a identifié 365 protéines qui n'avaient pas été décrites antérieurement dans le protéome de l'ovocyte ce qui pourrais indiquer qu'elles sont exprimées dans les cellules somatiques du follicule. Des analyses qualitatives et quantitatives complémentaires ont démontré une surreprésentation pour 44 fonctions biologiques par rapport aux fonctions biologiques des gènes constituant le génome de Mus musculus et mis en évidence des différences d'expression et d'abondance des protéines liées au cycle cellulaire, à la fixation des ions de calcium et à la glycolyse selon le stade de développement. Ces résultats représentent un point de départ pour beaucoup d'autres études de caractérisation moléculaire du développement folliculaire.
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Šopíková, Martina. "Změny proteinového profilu v průběhu sladování ječmene." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2008. http://www.nusl.cz/ntk/nusl-216437.
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This diploma thesis is focused on studies of changing of protein profile during barley malting. Substantial part of this work is devoted to the proteomics identification of barley proteins which change during malting and so become more stationary and they influence quality of beer (haze and foam in beer). For this experiment was used barley variety Jersey. In the theoretical part of this thesis there is information about beer, manufacturing of beer with description of important commodities for manufacturing of beer and information about barley malting and information about malting process. Next there is description of methods for separation of proteins (1D gel electrophoresis and 2D gel electrophoresis), MALDI TOF/TOF mass spectrometry and this use for the analysis and identification of proteins, the use of matrices and ways of the sample preparation. In the experimental part of this thesis there was carried out the optimisation of the dosage of sample for 1D gel electrophoresis and the optimisation of staining. The 15 % TRIS-HCl gel was the best, this gel was stained by Commassie Brilliant Blue G-250. For illustration of changes was made 2D gel electrophoresis. With help of method peptide mass fingerprinting and MS/MS protein of barley – protein Z, -amylase subtilisin inhibitor, -amylase a peroxidase were identificated. The analysis of barley extract intact proteins was carried out, this analysis was focused on changes of important barley protein LTP 1.
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Ngara, Rudo. "A proteomic analysis of drought and salt stress responsive proteins of different sorghum varieties." Thesis, University of the Western Cape, 2009. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_1434_1334579378.
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This study reports on a proteomic analysis of sorghum proteomes in response to salt and hyperosmotic stresses. Two-dimensional gel electrophoresis (2DE) in combination with mass spectrometry (MS) was used to separate, visualise and identify sorghum proteins using both sorghum cell suspension cultures and whole plants. The sorghum cell suspension culture system was used as a source of culture filtrate (CF) proteins. Of the 25 visualised CBB stained CF spots, 15 abundant and well-resolved spots were selected for identification using a combination of MALDI-TOF and MALDI-TOFTOF MS, and database searching. Of these spots, 14 were positively identified as peroxidases, germin proteins, oxalate oxidases and alpha-galactosidases with known functions in signalling processes, defense mechanisms and cell wall metabolism.
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Fertin, Marie. "Recherche de biomarqueurs circulants du remodelage ventriculaire gauche en post-infarctus du myocarde." Thesis, Lille 2, 2012. http://www.theses.fr/2012LIL2S025.
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Le remodelage ventriculaire gauche (VG) en post-infarctus du myocarde (IDM) est associé à une augmentation du risque d’insuffisance cardiaque et de décès, mais il demeure difficile à prédire en pratique clinique.L’objectif principal de ma thèse était la recherche de biomarqueurs circulants du remodelage VG par l’approche protéine candidate et par protéomique différentielle dans la population REVE-2.Par l’approche protéine candidate, nous avons confirmé que le peptide natriurétique detype B (BNP) était un puissant facteur prédictif du remodelage VG en post-IDM. La métalloprotéase matricielle-8 (MMP-8), la MMP-9, l’hepatocyte growth factor (HGF), la Créactive protéine (CRP), la troponine I ont également fait la preuve de leur association.Par l’approche protéomique différentielle, en électrophorèse 2D différentielle en fluorescence (2D-DIGE), la clusterine a été identifiée comme biomarqueur potentiel,positivement associée au remodelage VG, nécessitant toutefois des travaux de confirmation.Par SELDI TOF MS, nous avons sélectionné 26 pics définis par leur rapport m/z, commebiomarqueurs potentiels du remodelage VG, dont 12 ont pu être identifiés et devrontdésormais être validés : le pic de m/z 2777 a été identifié comme le peptide N-terminal issu del’albumine après clivage par la pepsine. Les autres pics correspondraient à des fragments protéolytiques de protéines que sont le fibrinogène, le complément C3, C4 et C1q.La découverte de nouveaux biomarqueurs du remodelage VG devrait permettre d’améliorer la stratification du risque en post-IDM afin d’identifier les patients devant bénéficier d’un suivi plus rapproché et peut-être d’une prise en charge thérapeutique plus agressiveLeft ventricular (LV) remodelling after myocardial infarction (MI) indicates a high risk of heart failure and death but remains difficult to predict in clinical practice. Biomarkers may help to refine risk stratification. The main purpose was to find circulating biomarkers of LV remodelling after MI, using two strategies : candidate protein approach and differential proteomic approach, working on a population with a clearly defined phenotype, the REVE-2 study, a prospective multicenter study including 246 patients with a first anterior Q-wave MI. Blood samples were obtained at hospital discharge, at 1 month, 3 months and 1 year. An echocardiography was performed at the same time except for the 1st month to assess LVR.By candidate protein approach, we confirmed that B-type natriuretic peptide (BNP) was a powerful predictor of LV remodelling after MI. Additional biomarkers, such as matrix metalloproteinase-8 (MMP-8), MMP-9, hepatocyte growth factor (HGF), C-reactive protein (CRP) and cardiac troponin I were found to be associated with LV remodelling, highlighting several pathways implicated in pathophysiology of LV remodelling. We have also shown that biomarkers in association (BNP and cardiac troponin I, BNP and MMP-8, BNP and MMP-9) could improve risk stratification in post-MI by selecting groups of patients at higher risk.As the ideal biomarker was still not identified, we applied a differential proteomic approach, with no a priori hypothesis, in order to characterize proteomic signature of LV remodelling. The use of a protein enrichment kit, consisting of a library of combinatorial hexapeptide ligands, compressed the protein concentration range of plasma and serum, through the simultaneous onestep dilution of high-abundance and concentration of lowabundance proteins. Protein enrichment kit prior to two-dimensional (2D) electrophoresis or SELDI TOF MS (surface-enhanced laser desorption–ionization time of flight) analysis enabled the detection of proteins that were not detected in native blood sample and the accessibility to proteolytic fragments obtained from major proteins. Clusterin (apolipoprotein J) was identified as a potential biomarker of LV remodelling by 2D-DIfferential Gel Electrophoresis (2D-DIGE). Clusterin was quantified by Western blot and ELISA and was found to be positively associated with LV remodelling. However, this association was not found with all LV remodelling parameters nor at each time during the year following MI, requiring further analysis. Differential proteomic approach by SELDI TOF MS selected 26 m/z peaks, as potential biomarkers of LV remodelling. Of them, 12 were identified by mass spectrometry. The 2777 m/z peak was identified directly from the ProteinChip array as being the N-terminal peptide (24–48 aa) generated from albumin by pepsin cleavage. Other peaks were identified after purification using chromatographic columns or liquid-phase isoelectric focusing : most of them were found to be proteolytic fragments of proteins like fibrinogen, C3, C4 and C1q complement. Identifications have now to be validated with specific techniques, usually by immmunoprecipitation and Western blot analysis.Finding new biomarkers of LV remodelling could help refine risk stratification and identify patients in whom more aggressive therapy and/or more frequent follow-up could be needed
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Magalhães, Ilídio Miguel Teixeira. "Proteome of biofilm produced by a S. pseudintermedius strain." Master's thesis, Universidade de Aveiro, 2014. http://hdl.handle.net/10773/14291.
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Mestrado em BioquímicaStaphylococcus pseudintermedius is an opportunistic pathogenic bacterium responsible for most skin and post-surgical infections in dogs. The number of bacterial strains resistant to β-lactam antibiotics is increasing and are the major challenges now faced by veterinary medicine. Bacteria that produce biofilm are more resistant to treatment and thus, the production of this structure is already considered a virulence factor. In a biofilm, bacteria are embedded in a matrix of extracellular polymeric substances (EPS) some of which are proteins. With the objective to know more of this array element, the characterization of the biofilm matrix proteome (BMP) from a highly virulent S. pseudintermedius strain isolated from a dog with severe pyoderma was performed. Biofilm was developed by culturing the S. pseudintermedius strain 5819/10 in specific media. The biofilm matrix was then be separated from bacterial cells and evaluated for their protein content and complexity. Finally, the proteome was separated by 1D electrophoresis and characterized by nanoLC-ESI-Q-TOF and analysed using bioinformatics tools. The BMP of strain S. pseudintermedius 5819/10 consisted in a diverse group of proteins, where 63% of the proteins could be related to either the extracellular region or the plasma membrane, as protein complexes, and most of them had functions essential to cell survival. However, it was not possible to establish a clear relation between them and biofilm formation. Proteins known to be involved in biofilm formation consisted mostly of regulator factors of biofilm formation as well as virulence factors of-mainly-bacterial cell adhesion and host colonization. The prevalence of adhesins and the almost total absence of proteins involved in EPS synthesis pointed to a biofilm matrix where cells are directly or indirectly closely glued together to each other.
Staphylococcus pseudintermedius (S.pseudintermedius) é uma bactéria patogénica oportunista, responsável pela maioria das infeções cutâneas e pós-cirúrgicas em cães. O número de estirpes resistentes a antibióticos β-lactâmicos está a aumentar constituindo actualmente um dos grandes desafios enfrentados pela medicina veterinária. As bactérias mais resistentes ao tratamento são aquelas que produzem biofilme sendo esta capacidade considerada um fator de virulência. Num biofilme, as bactérias estão envoltas numa matriz de substâncias poliméricas extracelulares (SPE), algumas das quais são proteínas. Tendo por objectivo obter mais informação acerca do biofilme, foi caracterizado o proteoma da matriz do biofilme de uma estirpe bastante virulenta de S. pseudintermedius isolada de um cão com piodermite profunda. Para tal cultivaram-se biofilmes da estirpe de S. pseudintermedius 5819/10 em meio apropriado, separou-se a matriz das suas células bacterianas e avaliou-se as proteínas presentes quanto ao seu conteúdo e complexidade. Posteriormente o proteoma foi separado por electroforese 1D, caracterizado por nanoLC-ESI-Q-TOF e analisado usando ferramentas bioinformáticas Constatou-se que o proteoma da matriz do biofilme da estirpe 5819/10 de S. pseudintermedius é muito diverso e que 63% das proteinas podem estar relacionadas com a região extracelular do biofilme ou da membrana plasmática na forma de complexos proteicos. Verificou-se também que a maioria das proteínas identificadas possui funções essenciais para a sobrevivência da bactéria mas não foi possível estabelecer uma relação clara entre elas e a formação de biofilmes. Algumas proteínas que se sabe estarem envolvidas na formação de biofilmes foram identificadas, tratam-se principalmente de factores reguladores da formação de biofilme e outros factores de virulência relacionados com a colonização de um hospedeiro a adesão bacteriana a uma superfície. A prevalência de adesinas e a ausência quase total de proteínas envolvidas na síntese de SPEs, forneceu dados que apoiam a hipótese que a matriz do biofilme do S. pseudintermedius 5819/10 seja constituída por células directamente ou indirectamente unidas entre si.
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Kouloura, Eirini. "Phytochemical investigation of Acronychia species using NMR and LC-MS based dereplication and metabolomics approaches." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05P636/document.
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Les plantes médicinales constituent une source inexhaustible de composés (des produits naturels - PN) utilisé en médecine pour la prévention et le traitement de diverses maladies. L'introduction de nouvelles technologies et méthodes dans le domaine de la chimie des produits naturels a permis le développement de méthodes ‘high throughput’ pour la détermination de la composition chimique des extraits de plantes, l'évaluation de leurs propriétés et l'exploration de leur potentiel en tant que candidats médicaments. Dernièrement, la métabolomique, une approche intégrée incorporant les avantages des technologies d'analyse moderne et la puissance de la bioinformatique s’est révélé un outil efficace dans la biologie des systèmes. En particulier, l'application de la métabolomique pour la découverte de nouveaux composés bioactifs constitue un domaine émergent dans la chimie des produits naturels. Dans ce contexte, le genre Acronychia de la famille des Rutaceae a été choisi sur la base de son usage en médecine traditionnelle pour ses propriétés antimicrobienne, antipyrétique, antispasmodique et anti-inflammatoire. Nombre de méthodes chromatographiques modernes, spectrométriques et spectroscopiques sont utilisées pour l'exploration de leur contenu en métabolites suivant trois axes principaux constituant les trois chapitres de cette thèse. En bref, le premier chapitre décrit l’étude phytochimique d’Acronychia pedunculata, l’identification des métabolites secondaires contenus dans cette espèce et l'évaluation de leurs propriétés biologiques. Le deuxième chapitre vise au développement de méthodes analytiques pour l'identification des dimères d’acétophénones (marqueurs chimiotaxonomiques du genre) et aux stratégies utilisées pour la déréplication de ces différents extraits et la caractérisation chimique des composés par UHPLC-HRMSn. Le troisième chapitre se concentre sur l'application de méthodologies métabolomique (RMN et LC-MS) pour l'analyse comparative (entre les différentes espèces, origines, organes), pour des études chimiotaxonomiques (entre les espèces) et pour la corrélation des composés contenus avec une activité pharmacologiqueMedicinal plants constitute an unfailing source of compounds (natural products – NPs) utilised in medicine for the prevention and treatment of various deceases. The introduction of new technologies and methods in the field of natural products chemistry enabled the development of high throughput methodologies for the chemical composition determination of plant extracts, evaluation of their properties and the exploration of their potentials as drug candidates. Lately, metabolomics, an integrated approach incorporating the advantages of modern analytical technologies and the power of bioinformatics has been proven an efficient tool in systems biology. In particular, the application of metabolomics for the discovery of new bioactive compounds constitutes an emerging field in natural products chemistry. In this context, Acronychia genus of Rutaceae family was selected based on its well-known traditional use as antimicrobial, antipyretic, antispasmodic and anti-inflammatory therapeutic agent. Modern chromatographic, spectrometric and spectroscopic methods were utilised for the exploration of their metabolite content following three basic axes constituting the three chapters of this thesis. Briefly, the first chapter describes the phytochemical investigation of Acronychia pedunculata, the identification of secondary metabolites contained in this species and evaluation of their biological properties. The second chapter refers to the development of analytical methods for the identification of acetophenones (chemotaxonomic markers of the genus) and to the dereplication strategies for the chemical characterisation of extracts by UHPLC-HRMSn. The third chapter focuses on the application of metabolomic methodologies (LC-MS & NMR) for comparative analysis (between different species, origins, organs), chemotaxonomic studies (between species) and compound-activity correlations
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Miranda, Helder. "Stress response in the cyanobacterium Synechocystis sp. PCC 6803." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-43086.
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Adaptation to environmental changes is important for the survival of living organisms. Under extreme abiotic conditions, organic molecules (such as lipids, proteins and nucleic acids) are prone to damage. Under these conditions stress response mechanisms are activated, either to prevent the source of damage or to promote the rapid turnover of damaged molecules. Like all photoautotrophic organisms, cyanobacteria are sensitive to high light intensity and oxidative stress, which induces damage to the photosynthetic apparatus. My thesis is divided in two subjects related to particular stress responses in the cyanobacterium Synechocystis sp. PCC 6803: 1) the role of Deg/HtrA proteases and 2) investigations on the small CAB-like proteins. Deg/HtrA proteases are ATP-independent serine endopeptidases with a characteristic C-terminal PDZ domain. These proteases are largely dispersed among living organisms, with many different functions, mostly involved in protein quality control. The genome of Synechocystis sp. PCC 6803 contains three genes coding for Deg/HtrA proteases: HtrA, HhoA and HhoB. These proteases are essential for survival under high light and heat stress, and may overlap in their functions. During my Ph.D. studies I focused on the identification of the precise localization of the Deg/HtrA proteases in the cyanobacterial cell, analyzed the biochemical properties of recombinant Synechocystis Deg/HtrA proteases in vitro and adopted proteomic and metabolomic approaches to study the physiological importance of these proteases. My data show that Deg/HtrA proteases are not only important in stress response mechanisms under adverse conditions, but are also involved in the stabilization of important physiological processes, such as polysaccharides biosynthesis and peptidoglycan turnover. The small CAB-like proteins (SCPs) belong to the light harvesting-like family of stress induced proteins and are thought to be involved in the photoprotection of the photosynthetic apparatus. Five small CAB-like proteins where identified in Synechocystis sp. PCC 6803 (ScpA-E). In my studies I identified another relative to the SCPs, LilA, which I found to be co-transcribed with ScpD. I also focused on the subcellular localization and identification of potential interaction partners of the SCPs.
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Harju, Mikael. "Analysis of PCBs with special emphasis on comprehensive two-dimensional gas chromatography of atropisomers." Doctoral thesis, Umeå universitet, Kemi, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-54.
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There are 209 PCB congeners, 136 of which have been found in technical PCB mixtures and hence may be found in the environment as a result of either intentional or unintentional release. The identification and quantification of the congeners are difficult due to analytical bias from coeluting PCBs and other persistent organic pollutants. Among the 209 possible PCB congeners, 19 tri- and tetra-ortho chlorinated congeners exist in stable atropisomeric conformations. The racemization barrier were determined for twelve of the nineteen atropisomers and was found to be between 176-185 kJ × mol-1 and ca. 250 kJ × mol-1 for tri- and tetra-ortho PCB, respectively. Further, a buttressing effect of 6.4 kJ × mol-1 was observed for congeners with vicinal ortho-meta chlorines. Comprehensive two-dimensional gas chromatography (GC×GC) was used to analyze the atropisomers and other PCBs. A Longitudinally Modulated Cryogenic System (LMCS) was used with liquid CO2 as cryogen. The LMCS was optimized for semi-volatile organic substances, primarily PCBs. The trap temperature was shown to be an important factor for the trapping and desorption efficiency, as was the thermal mass of the column used in the modulator region. A number of column sets were tested and the separation efficiency, congener resolution and analysis time was evaluated. Good separation of non- and mono-ortho PCBs and “bulk” PCBs (in a technical PCB) was obtained within 8 min using a smectic liquid crystal column (LC50) as the first and a nonpolar column as the second dimension column. Using a second column, an efficient nonpolar (DB-XLB) column, which separates many PCB congeners, were combined with a polar (cyanopropyl) or shape selective (LC50) second dimension column. As a maximum, 181 of the 209 congeners and 126 of the 136 Aroclor PCBs were resolved. The seven frequently measured PCBs (PCBs 28, 52, 101, 118, 138, 153 and 180) and all WHO-PCBs were separated from all other Aroclor PCBs. Chiral PCBs are released into the environment as racemic mixtures. However, organisms have been shown to enantiomerically enrich many of the atropisomers, suggesting that enantioselective biotransformations occur. Non-racemic PCB enrichment has also been seen in mammalians including humans, which is of particular concern because of the potential health risk. An analytical procedure were therefore developed and used to determine the levels of atropisomeric PCBs, planar-PCBs (WHO-PCBs) and total PCBs in seals with different health status. GC×GC was used to separate the target PCBs from other PCBs and potential interferences. A chiral column (permethylated â-cyclodextrin) was used in combination with a polar or shape selective column and enantiomeric fractions (EFs) were determined for five atropisomeric PCBs, i.e. CBs 91, 95, 132, 149 and 174. Some atropisomers had EF that deviated largely from racemic. The deviation was larger in liver than blubber, indicating enantioselective metabolism. However, there was no selective passage of the studied atropisomeric PCBs across placenta and no selective blood-brain barrier. Similarly, no correlation between EFs and health status was observed, although there was a correlation between total PCBs and health status.
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Shiryaeva, Liudmila. "Proteomics and metabolomics in biological and medical applications." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-43520.
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Biological processes in living organisms consist of a vast number of different molecular networks and interactions, which are complex and often hidden from our understanding. This work is focused on recovery of such details for two quite distant examples: acclimation to extreme freezing tolerance in Siberian spruce (Picea obovata) and detection of proteins associated with prostate cancer. The first biological system in the study, upon P. obovata, is interesting by this species ability to adapt and sustain extremely low temperatures, such as -60⁰C or below. Despite decades of investigations, the essential features and mechanisms of the amazing ability of this species still remains unclear. To enhance knowledge about extreme freezing tolerance, the metabolome and proteome of P. obovata’s needles were collected during the tree’s acclimation period, ranging from mid August to January, and have been analyzed. The second system within this study is the plasma proteome analysis of high risk prostate cancer (PCa) patients, with and without bone metastases. PCa is one of the most common cancers among Swedish men, which can abruptly develop into an aggressive, lethal disease. The diagnostic tools, including PSA-tests, are insufficient in predicting the disease’s aggressiveness and novel prognostic markers are urgently required. Both biological systems have been analyzed following similar steps: by two-dimensional difference gel electrophoresis (2D-DIGE) techniques, followed by protein identification using mass spectrometry (MS) analysis and multivariate methods. Data processing has been utilized for searching for proteins that serve as unique indicators for characterizing the status of the systems. In addition, the gas chromatography-mass spectrometry (GC-MS) study of the metabolic content of P.obovata’s needles, from the extended observation period, has been performed. The studies of both systems, combined with thorough statistical analysis of experimental outcomes, have resulted in novel insights and features for both P. obovata and prostate cancer. In particular, it has been shown that dehydrins, Hsp70s, AAA+ ATPases, lipocalin and several proteins involved in cellular metabolism etc., can be uniquely associated with acclimation to extreme freezing in conifers. Metabolomic analysis of P. obovata needles has revealed systematic metabolic changes in carbohydrate and lipid metabolism. Substantial increase of raffinose, accumulation of desaturated fatty acids, sugar acids, sugar alcohols, amino acids and polyamines that may act as compatible solutes or cryoprotectants have all been observed during the acclimation process. Relevant proteins for prostate cancer progression and aggressiveness have been identified in the plasma proteome study, for patients with and without bone metastasis. Proteins associated with lipid transport, coagulation, inflammation and immune response have been found among them.
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Samuel, Jacob Matthew. "Development of methods for the analysis of human protamine via 2D LC-MS/MS." Thesis, 2018. https://hdl.handle.net/2144/33039.
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Protamine, a set of small basic proteins (P1 and P2), play a key role in compacting and protecting the DNA in sperm. As such, the structure of how P1 and P2 bind to DNA and potentially themselves and each other is of interest to several fields including forensics. In forensic DNA analysis, protamine binding of DNA is taken advantage of in the “differential extraction” procedure in which a sample that contains sperm and non-sperm cells can have DNA from the two different cell types separated and extracted at different points thus preventing a mixture of DNA. A key component of this greater structure and what makes the differential extraction functional are the disulfide bonds formed by protamine. So as a first step to elucidating the protamine-DNA complex, methods to analyze human protamine via 2D-Liquid Chromatography-Mass Spectrometry (2D-LC-MS) were developed in the hopes they could be used for disulfide bond mapping. Methods and multiple strategies for digestion, 2D-LC-MS were investigated and developed using chum salmon protamine. Digestion strategies were developed for Chymotrypsin and Lys-C, Trypsin or Arg-C with incubation times and substrate:enzyme mass ratios optimized. Various “trap and elute” 2D-chromatography configuration were tested for analysis intact and digested protein. Using H2O with 2% NH4OH as the loading mobile phase and H2O and Acetonitrile both with 0.5% formic acid as the eluting mobile phases with the first dimension column being an HLB (Hydrophilic Lipophilic Balance) 2.1 x 30 mm column and the second dimension being an C18 2.1 x 100 mm was found to produce the highest signal.
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Kuo, Yung-Yu, and 郭永宇. "Profiling novel urinary markers for prostate cancer by 2D HPLC-ESI-MS." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/01842560567854299065.
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碩士臺灣大學
化學研究所
98
Prostate cancer ranks the seventh cause of cancer-related death in Taiwan and the second in United States. The incidence and mortality rates of prostate cancer have been rising rapidly in the past decades. Currently, there are no accurate and specific biomarkers which could discriminate clinically relevant from clinically benign disease. The better indicators and progression are needed to avoid unnecessary treatment. Clinically, prostate-specific antigen (PSA) screening still seems the only way to diagnose the carcinoma of prostate, but lately researches showed that PSA is not prostate cancer specific. Finding novel biomarkers that are sensitive, specific and can be examined by non-invasive means are imperative. In this thesis, the on-line 2D LC-MS and off-line 2D LC-MS methods are the main approaches to unravel the protein profiling information from urine samples. In order to acquire the moderate experimental results and establish the complete urine sample analysis for identifying prostate cancer, we use these two approaches and tested the effects of modifying several parameters (oven temperature, mobile phase gradient, salt concentration and so on). In online cases, though it can be automatically operated, the information obtained turned out to be unsatisfactory. In offline cases, it demanded much manpower for sample preparation and operating the LC-MS system. The results in offline cases not only show higher intensity and sensitivity than online cases, but provide more useful information.
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Lee, Wei-Han, and 李威漢. "The Development of On-line Single / Staggered Multi-Step Elution SPE-CE-MS and Heart-cut 2D–CE-MS." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/36753382916516650744.
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博士臺灣大學
化學研究所
98
A PDMS based two-leveled two cross design interface was proposed for on-line coupling SPE-CE-MS. In this interface, the SPE column and the CE separation column were positioned orthogonally and two crosses were fabricated on the interface. With the two cross design, the operation of SPE could be performed independently without unexpected flow through leakage into the separation column. The performance of the interface was optimized using a peptide mixture. The position of the SPE column related to the CE separation channel was found to be critical to the performance of the system. Under the optimal position, the separation efficiency was similar to a CE-MS experiment without SPE. The peptide signals were enhanced 50 to 100-fold and the repeatability was within 4% RSD for migration time and 10% RSD for peak area. A tryptic digest of cytochrome C was used to demonstrate the feasibility of the interface in protein identification at a level of 1 ng/mL. In a protein mixture analysis, the identification of proteins usually suffers in low sequence coverage in the single run CZE-ESI-MS/MS. An original concept of on-line coupling multistep elution solid phase extraction (SPE) to CZE-MS/MS was proposed to increase sequence coverage of protein mixture analysis. The multistep elution SPE (the first dimension) provides an additional dimension of separation prior to CZE (the second dimension) and extends the separation capacity for protein mixture analysis. Furthermore, a staggered CZE method was described to increase the throughput of each CZE runs in the second dimension separation and thus to reduce entire analysis time. In this study for protein mixture standards, more than 60% of additional peptides were discovered , and more than 50% was improved in sequence coverage by using multistep elution SPE-CE-MS/MS. By using staggered CZE method, half of the entire analysis time could be saved (54%) in comparison with the sequential CZE method used in multistep elution SPE-CE-MS/MS and thus avoiding the time-consuming analytical procedure in comprehensive 2D separation. An interface for heart-cut 2D CE-MS was proposed to increase separation selectivity in mixture analysis. Several concepts were adapted to overcome the limitations of heart-cut 2D-CE designed in the present studies. First, the manipulation of chip-based interface provides an isolated buffer system to connect two sets of capillary electrophoresis. Second, the parallel separation of the two dimensional capillary electrophoresis was detected simultaneously by a pulsed electrospray-based duel-channel CE-MS system. In this study, the system was demonstrated by using capillary zone electrophoresis- micellar electrokinetic chromatography (CZE-MEKC) system to analyze sulfonamide mixtures. Under the consideration of correspondence in EOF for fused silica capillary the PDMS based chip channel, 8 sulfonamide standards can be transferred successfully without loss and peak broadening during the heart-cutting operation. The preliminary feasibility of heart-cut CZE-MEKC with dual-channel CE-MS was studied in sulfonamides analysis. Four sulfonamides(SDZ、SMR、STZ、SMM) were transferred into the MEKC channel by the heart-cut interface after separation in the first dimension of CZE. The migration order of four heart-cut sulfonamides was found similar order in the single-run MEKC.
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Mella, Malorie Ann. "Detection of cocaine and its major metabolites in bone following outdoor decomposition after chronic cocaine administration using 2D-LC/MS/MS." Thesis, 2017. https://hdl.handle.net/2144/20788.
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In the field of forensic toxicology, several challenges exist with quantification analysis of cocaine and metabolites in post mortem samples. Cocaine can prove difficult to detect and quantify in blood, urine, and soft tissues following extensive decomposition. Alternative matrices, such as hair, nails, and bone could prove useful in detecting chronic drug use in post-mortem toxicology cases. Detection and quantification of drugs in complex matrices is difficult to accomplish due to time-consuming extraction processes, and inability to detect an analyte at trace levels. Further, analysis of drugs in hard tissues, such as hair and bone, has only been attempted in recent years. Even fewer studies have investigated detection of drugs following decomposition of remains, specifically outdoor decomposition. The objective of this study was to develop a robust extraction and clean up methodology, in which a homogenization step precedes, to efficiently extract drugs from complex matrices, reach a target limit of detection (LOD) and to maintain instrument performance using multidimensional chromatography. Multi-dimension chromatography platform such as two dimensional liquid chromatography tandem mass spectrometry ( 2D-LC/MS/MS,) offers options not compatible with single dimension
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units. With large volume injection capabilities of aqueous and organic extracts, the analytical process be reduced from multiple hours to minutes.
All rat specimens used for this study fell under an Institutional Animal Care and Use Committee (IACUC) protocol. The rodents underwent a 10-12 weeks chronic intravenous self-administration of cocaine. This was followed by a six-week period of abstinence, followed again by a three-week period of cocaine self-administration before being euthanized. Average daily dosages for each rat fell within a range of 13-19 mg/kg. A total of 14 cocaine positive rats were placed outside and above ground in the Boston University Forensic Anthropology Outdoor Research Facility (Holliston, MA, U.S.A) for a period of 12 months. All recoverable skeletal samples were collected for testing. Drug free control rat bones were also acquired by placing drug-free rats outdoors, above ground, until full decomposition occurred. In this study, a method analyzing cocaine and its major metabolites benzoylecgonine and ecgonine methyl ester was developed.
After homogenization of whole bones, the extraction process was performed using a mixed mode reversed-phase/ion exchange sorbent. The use of a 2D LC/MS/MS technology eliminates the need for a lengthy evaporation step in the extraction method. The chosen 2D LC/MS/MS used in this application was identified using a 6x6 automated method development protocol. The manual extraction of the bone samples was completed in less than an hour. The analysis was performed using 100μL of the final organic solvent (MeOH) extracts.
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The limit of quantitation (LOQ) for cocaine and benzoylecgonine was measured at 0.05ng/g (0.05ng/mL or 50pg/g) of sample material and the LOQ for ecgonine methyl ester was measured at 0.1ng/g (0.1 ng/mL or 100pg/g). The extraction method for cocaine proved to give a linear dynamic range of 2.5 orders of magnitude (0.05 ng/g to 10ng/g with an R2 = 0.998.
The micro extraction protocol combined with a multi-dimension chromatography used in this study decreased sample preparation time without sacrificing the quality seen with current single dimension chromatography techniques. The procedure developed in this study can be utilized on bone and completed in less than an hour before injection into the 2D-LC/MS/MS system.
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Forest, Anik. "Évaluation de différentes composantes chromatographiques d'un système nano-LC-MS pour des applications protéomiques." Thèse, 2006. http://hdl.handle.net/1866/17985.
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-Ju, Chun, and 陳君茹. "1.Post-translational modification on protein by glyoxal and methylglyoxal2.Characterization contain 3-nitrotyrine protein in human urine by 2D-PAGE and LC/NSI/MS/MS." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/55606096158017229679.
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碩士國立中正大學
化學所
95
1. The non-enzymatic conjugated addition product of glucose or aldehyde derivatives and glycation reaction of protein are the main cause of vascular complications of diabetes. If the concentration of glucose remains at high level in the body, the amount of ?dicarbonyl compounds, such as glyoxal and methylglyoxal, also increases. Glyoxal is obtained from glucose and amino acid oxidation, lipid peroxidation; methylglyoxal is mainly from glucose degradation intermediate product: G-3-P self-decompose. These reactive ?dicarbonyl compounds react with protein, lipids and amino acids to form saccharides as the final product. This study makes use of LC/NSI/MS to investigate the reaction of glyoxal and methylglyoxal with the amino acids on protein. First, we use LC/NSI/MS to confirm that glyoxal and methylglyoxal react with N?acetyl-cysteine and N?acetyl-L-lysine to form cross-linked products. Next, we use somatostain, which contains 14 amino acids and disulfide bond to react with glyoxal and methylglyoxal respectively and we have detected their addition and cross-linked products. Finally, we investigated the selectivity of glyoxal and methylglyoxal with human hemoglobin. We found that there was a single glyoxal addition on at Lys-11 of ?globin, and Lys-16, Lys-144 and Cys-93 of β-globin:, whereas methylglyoxal were found to add ?globin at Arg-31and β-globin at Lys-144 and Arg-104. We also confirm that glyoxal forms hydroimidazolone with ?globin at Arg-92. Similar hydroimidazolone also occurs with methylglyoxal and ?globin at Arg-31and Arg-92. However, the cross-linked products of glyoxal or methylglyoxal with human hemoglobin have not been identified. 2. In cancer research, inflammation is a very crucial and dangerous factor. During infection and inflammation, the activated macrophages and neutrophils will produce excess superoxide anion and NO which will react rapidly to produce peroxynitrite. Peroxynitrite could lead to breakage and mutation of DNA, and it also reacts with protein to form 3-nitrotyrosine. Many inflammation and neural degradation diseases are related to 3-nitrotyrosine, including eye inflammation, retinal ischemia, and cancer. In 2000, a report showed that using anti-3-nitrotyrosine together with Western blotting and mass spectromety effectively identified proteins containing 3-nitrotyrosine in mouse’s retinal. This study tried to determine proteins that contain 3-nitrotyrosine in human urine using 2D-PAGE and mass spectrometry. First, we eliminated most salts in our urine sample using acetone precipitation and centrifugal device, then separated the proteins by 2D-PAGE. Next, we used anti-3-nitrotyrosine antibody-base Western blotting to locate the nitrated protein. Before identifying the proteins in 2D-PAGE, the gel was digested. Hence, different gel microwave digestion conditions were carried out to find the best conditions. The urine samples were then analyzed using this condition. Currently, we successfully identified 3 kinds proteins containing 3-nitrotyrosine, including, protein complex 4, epsilon 1 subunit; adaptor related; LIM domain only 6[Homo sapiens] and Hypothetical protein FLJ32940 isoform 1. We also found a protein, transmembrane protein 16 F[Homo sapiens], containing nitrotryptothan.
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吳秀珠. "Characterization of Cu, Zn, Cd, Co-containing Biomolecules in Rabbit Serum and Supplement by 2D SEC/RPLC Chromatographic Techniques coupled with ICP-MS and ESI-MS Detection." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/11640354438277429767.
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Erickson, Alison Russell. "Characterization of the Human Host Gut Microbiome with an Integrated Genomics / Proteomics Approach." 2011. http://trace.tennessee.edu/utk_graddiss/1180.
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The new field of ‘omics’ has spawned the development of metaproteomics, an approach that has the ability to identify and decipher the metabolic functions of a proteome derived from a microbial community that is largely uncultivable. With the development and availabilities of high throughput proteomics, high performance liquid chromatography coupled to mass spectrometry (MS) has been leading the field for metaproteomics. MS-based metaproteomics has been successful in its’ investigations of complex microbial communities from soils to the human body.
Like the environment, the human body is host to a multitude of microorganisms that reside within the skin, oral cavity, vagina, and gastrointestinal tract, referred to as the human microbiome. The human microbiome is made up of trillions of bacteria that outnumber human genes by several orders of magnitude. These microbes are essential for human survival with a significant dependence on the microbes to encode and carryout metabolic functions that humans have not evolved on their own. Recently, metaproteomics has emerged as the primary technology to understand the metabolic functional signature of the human microbiome.
Using a newly developed integrated approach that combines metagenomics and metaproteomics, we attempted to address the following questions: i) do humans share a core functional microbiome and ii) how do microbial communities change in response to disease. This resulted in a comprehensive identification and characterization of the metaproteome from two healthy human gut microbiomes. These analyses have resulted in an extended application to characterize how Crohn’s disease affects the functional signature of the microbiota.
Contrary to measuring highly complex and representative gut metaproteomes is a less complex, controlled human-derived microbial community present in the gut of gnotobiotic mice. This human gut model system enhanced the capability to directly monitor fundamental interactions between two dominant phyla, Bacteroides and Firmicutes, in gut microbiomes colonized with two or more phylotypes. These analyses revealed membership abundance and functional differences between phylotypes when present in either a binary or 12-member consortia. This dissertation aims to characterize host microbial interactions and develop MS-based methods that can provide a better understanding of the human gut microbiota composition and function using both approaches.
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Bhandari, Devyani. "Application of solid phase extraction for storage and stability of drugs in biological fluids using 2D LC-MS technology." Thesis, 2019. https://hdl.handle.net/2144/38621.
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The issue with maintaining stability of compounds during storage and transportation has been universal across many fields such as clinical, pharmaceutical, food industry and especially in forensic laboratories where case backlogs hinder immediate analysis of samples upon collection. This study compares various storage conditions and analyzes changes in compound stability over 28 days. The various storage conditions compared in this study are temperature (+4 °C and -20 °C); water sample and urine sample and solid state (loading onto Solid Phase Extraction cartridges) and storing in its liquid state (present in the urine or water sample). 51 compounds were analyzed in this study belonging to pharmaceutical and hormone classes. Two Dimensional Liquid Chromatography was used for separation allowing the analysis of varied compounds in terms of chemistry. Mass Spectrometry was used for detection of these compounds. This study conclusively helped determine that there is no significant difference in stability of 42 out of 51 of these compounds on comparing them in solid versus liquid state over a period of 28 days. This helps determine that Solid Phase Extraction (SPE) cartridges can be used as an alternative for storage and transportation of these compounds. 46 compounds showed no significant difference in +4 and -20 °C temperature storage conditions as well. Despite not including a wash step during sample preparation between loading and elution, 11 out of 51 compounds did not show suppression or enhancement due to matrix effect. This study not only highlights the importance of sample preparation prior to analysis but also shows how SPE technique could help maintain stability of compounds during storage. In future studies, stability changes using SPE for long term storage could provide beneficial results to conclude if SPE techniques can provide an advantage over liquid state for a period longer than a month.
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Djukic, Michael. "Proteomic investigations and biomarker discovery in transient ischaemic attack." Thesis, 2017. http://hdl.handle.net/2440/112817.
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Between 15-26% of ischaemic strokes are preceded by transient ischaemic attack (TIA) making accurate and timely diagnosis of TIA important for stroke prevention. However, TIA diagnoses are highly reliant on subjective history gathering and clinical assessments to differentially diagnose true TIA conditions from mimic presentations. Unfortunately, the subjective nature of TIA diagnosis has created a surprisingly high amount of variability between diagnoses made by physicians and specialist neurologists. Use of biomarker tests could offer an objective quantitative measuring tool that reduces inter-observer variation through the establishment of standardised quantitative measures and improved reproducibility. When used in combination with comprehensive clinical assessments and neurological imaging, biomarkers may offer a useful adjunct to assist a treating clinician to accurately and reliably interpret the clinical finding and confidently diagnose and treat a TIA or mimic condition. This thesis proposes a framework for undertaking an exploration of the human plasma proteome, and performs the very first proteomic pilot study that identifies candidate plasma protein biomarkers associated with TIA, which could also be used to distinguish from mimic presentations.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, Adelaide Medical School, 2017.
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Ghitun, Mihaela. "Module microfluidique intégrant des séparations multidimensionnelles : applications d'analyses protéomiques sur des extraits cellulaires." Thèse, 2006. http://hdl.handle.net/1866/17982.
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Seibert, C., B. R. Davidson, B. J. Fuller, Laurence H. Patterson, W. J. Griffiths, and Y. Wang. "Multiple-approaches to the identification and quantification of cytochromes P450 in human liver tissue by mass spectrometry." 2009. http://hdl.handle.net/10454/6179.
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Here we report the identification and approximate quantification of cytochrome P450 (CYP) proteins in human liver microsomes as determined by nano-LC-MS/MS with application of the exponentially modified protein abundance index (emPAI) algorithm during database searching. Protocols based on 1D-gel protein separation and 2D-LC peptide separation gave comparable results. In total, 18 CYP isoforms were unambiguously identified based on unique peptide matches. Further, we have determined the absolute quantity of two CYP enzymes (2E1 and 1A2) in human liver microsomes using stable-isotope dilution mass spectrometry, where microsomal proteins were separated by 1D-gel electrophoresis, digested with trypsin in the presence of either a CYP2E1- or 1A2-specific stable-isotope labeled tryptic peptide and analyzed by LC-MS/MS. Using multiple reaction monitoring (MRM) for the isotope-labeled tryptic peptides and their natural unlabeled analogues quantification could be performed over the range of 0.1-1.5 pmol on column. Liver microsomes from four individuals were analyzed for CYP2E1 giving values of 88-200 pmol/mg microsomal protein. The CYP1A2 content of microsomes from a further three individuals ranged from 165 to 263 pmol/mg microsomal protein. Although, in this proof-of-concept study for CYP quantification, the two CYP isoforms were quantified from different samples, there are no practical reasons to prevent multiplexing the method to allow the quantification of multiple CYP isoforms in a single sample.
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King, Siang Goh, and 吳欽翔. "Comparison and Identification of venomous components between Eastern and Western Taiwan Cobra (Naja atra) by Two Dimensional High Performance Liquid Chromatography (2D-HPLC) and Electrospray Ionization Mass Spectrometry (ESI-MS)." Thesis, 2003. http://ndltd.ncl.edu.tw/handle/22065247906034960561.
Full textAbstract:
碩士國立清華大學
生命科學系
91
Eastern and western Taiwan Cobra (Naja atra) have been shown differences in morphology and toxicity, but the venomous components between them still remain obscure. Here we used two dimensional (Cation exchange and Reverse pharse) high performance liquid chromatography (2D-HPLC) and electrospray ionization mass spectrometry (ESI-MS) to identify and compare the venomous components between eastern and western Taiwan cobra. Molecular weight of 40 venomous proteins were determined, 12 of them were identified. A new cysteine-rich secretory protein (CRISP) with 24940 M.W. was first time found in this study. The N-terminal sequencing of this protein showed that it is highly homologous to ophanin, a CRISP isolated from king Cobra (Ophiophagus hannah) venom. Amount of this protein in crude venom is about 4-5% and showed constant expression in all Taiwan cobra. The proportions of cardiotoxin homologues were shown significantly different between eastern and western Taiwan cobra venoms. Analysis of eastern and western individual Taiwan cobra venomous components by high performance cation exchange liquid chromatography revealed cardiotoxin homologues A2 and A4 but not A6 are shown unique rich in western Taiwan cobra, the opposite result are observed in eastern Taiwan cobra. These results indicate that cardiotoxin homologues A2, A4 and A6 could become the key markers to distinguish eastern and western Taiwan cobra. In this study, we also found the northern Taiwan cobra whose morphology similar to eastern Taiwan cobra expressed both eastern and western Taiwan cobra cardiotoxin key markers. These results indicate the expression of unique cardiotoxin homologues in different geographical location might due to ecological causes.
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Gabuza, Kwazikwakhe. "Identification of differentially expressed proteins in obese rats fed different high fat diets using proteomics and bioinformatics approaches." 2013. http://hdl.handle.net/11394/3954.
Full textAbstract:
Philosophiae Doctor - PhDObesity is a medical condition in which an energy imbalance leads to excessive accumulation of body fat. Obesity leads to a reduction in life expectancy through its association with chronic diseases of lifestyle. The prevalence of obesity is rapidly increasing throughout the world. It is now accepted that most cases of obesity result from an interaction between genetic and environmental factors. This rapid increase in obesity generally leads to an increase in morbidity and mortality from chronic diseases such as cardiovascular disease, type 2 diabetes, osteoarthritis and cancer of which obesity is a risk factor. There is a lack of information in molecular research to explain how obesity predisposes individuals to these diseases. Proteomics is a molecular tool and a set of techniques used to identify changes at protein level from a diseased state. This study aims to identify differentially expressed proteins in serum of obese rats fed different isocaloric diets using proteomics.