Metabolomics approaches have recently been used to understand the complex molecular interactions of biological systems. One popular area in which these methods are being developed is to understand the biochemical changes during abiotic and biotic stresses; for example, how a cell may respond to a drug. Since metabolites are the end products of gene expression, these can be used to indicate the result of the activities and interaction of the cell or organism with its environment. The investigation of the level and compositional changes of metabolites against metabolic stresses such as chemotherapeutic treatment (drug exposure) are required to understand more fully abiotic perturbation to biological systems. The aim of this project was to understand the metabolic effect that the anti-viral drugs indinavir and lopinavir (currently used by HIV patients) have on HPV-related cervical cancer cell lines by measuring changes in metabolism using a wide range of analytical techniques; including Fourier transform infrared (FT-IR) and Raman spectroscopies, and gas and liquid chromatography-mass spectrometry (GC and LC-MS). The analyses and interpretation of the large volumes of complex multidimensional data generated by metabolomics approaches were performed with a combination of multivariate data analysis techniques such as principal components analysis (PCA) and canonical variates analysis (CVA), as well as univariate approaches such as N-Way analysis of variance (ANOVA). By combining biochemical imaging, metabolite fingerprinting and footprinting, and metabolite profiling, with multi- and uni-variate analyses, the actions and effects of the anti-viral drugs were investigated. FT-IR spectroscopy was initially used to generate global biochemical finger- and foot-prints, and Raman spectroscopy was employed to investigate intracellular distribution of metabolites, and other cellular species, as well as the localisation of drug molecules within cells. FT-IR spectroscopy ascertained that the intra- and extra-cellular metabolomes were being directly influenced in a fashion that correlated with increasing anti-viral dosing; these effects were phenotypic rather than measurements of the drug level. Raman imaging spectroscopy indicated that the indinavir but not lopinavir was being compartmentalised within the cell nucleus, but only in HPV early protein 6 (E6) expressing cells. This observation was further confirmed by fractionation of cell samples into nuclear and cytoplasmic fractions and assessing the indinavir concentrations via LC-MS. Finally, LC-MS and GC-MS metabolite profiling were employed to investigate changes in the intracellular metabolome in response to the anti-viral compounds across a range of physiologically relevant concentrations and in the presence and absence of the E6 oncoprotein. General effects of both anti-viral compounds included the regulation of metabolites such as glutathione, octenedionoic and octadecenoic acids, which may be involved in stress related responses, reduced levels of sugars and sugar-phosphates indicating a potential arrest of glycolysis, and reduced levels of malic acid indicating potential decreased flux into the TCA cycle; all indicating that central metabolism was being reduced. Finally, LC-MS based quantification indicated that in the presence of E6, lopinavir was actively removed from the cell, whereas the indinavir intracellular concentration increased concomitantly with the level of dosing. These investigations have revealed that metabolomics approaches are an apt tool for the study of anti-viral effects within cell cultures, but improvements need to be made with respect to the major limitation of metabolite identification.

A comprehensive investigation of sensitive ecosystems in South Florida with the main goal of determining the identity, spatial distribution, and sources of both organic biocides and trace elements in different environmental compartments is reported. This study presents the development and validation of a fractionation and isolation method of twelve polar acidic herbicides commonly applied in the vicinity of the study areas, including e.g. 2,4-D, MCPA, dichlorprop, mecroprop, picloram in surface water. Solid phase extraction (SPE) was used to isolate the analytes from abiotic matrices containing large amounts of dissolved organic material. Atmospheric-pressure ionization (API) with electrospray ionization in negative mode (ESP-) in a Quadrupole Ion Trap mass spectrometer was used to perform the characterization of the herbicides of interest. The application of Laser Ablation-ICP-MS methodology in the analysis of soils and sediments is reported in this study. The analytical performance of the method was evaluated on certified standards and real soil and sediment samples. Residential soils were analyzed to evaluate feasibility of using the powerful technique as a routine and rapid method to monitor potential contaminated sites. Forty eight sediments were also collected from semi pristine areas in South Florida to conduct screening of baseline levels of bioavailable elements in support of risk evaluation. The LA-ICP-MS data were used to perform a statistical evaluation of the elemental composition as a tool for environmental forensics. A LA-ICP-MS protocol was also developed and optimized for the elemental analysis of a wide range of elements in polymeric filters containing atmospheric dust. A quantitative strategy based on internal and external standards allowed for a rapid determination of airborne trace elements in filters containing both contemporary African dust and local dust emissions. These distributions were used to qualitative and quantitative assess differences of composition and to establish provenance and fluxes to protected regional ecosystems such as coral reefs and national parks.

Routine monitoring of environmental pollution demands simplicity and speed without sacrificing sensitivity or accuracy. The development and application of sensitive, fast and easy to implement analytical methodologies for detecting emerging and traditional water and airborne contaminants in South Florida is presented. A novel method was developed for quantification of the herbicide glyphosate based on lyophilization followed by derivatization and simultaneous detection by fluorescence and mass spectrometry. Samples were analyzed from water canals that will hydrate estuarine wetlands of Biscayne National Park, detecting inputs of glyphosate from both aquatic usage and agricultural runoff from farms. A second study describes a set of fast, automated LC-MS/MS protocols for the analysis of dioctyl sulfosuccinate (DOSS) and 2-butoxyethanol, two components of Corexit®. Around 1.8 million gallons of those dispersant formulations were used in the response efforts for the Gulf of Mexico oil spill in 2010. The methods presented here allow the trace-level detection of these compounds in seawater, crude oil and commercial dispersants formulations. In addition, two methodologies were developed for the analysis of well-known pollutants, namely Polycyclic Aromatic Hydrocarbons (PAHs) and airborne particulate matter (APM). PAHs are ubiquitous environmental contaminants and some are potent carcinogens. Traditional GC-MS analysis is labor-intensive and consumes large amounts of toxic solvents. My study provides an alternative automated SPE-LC-APPI-MS/MS analysis with minimal sample preparation and a lower solvent consumption. The system can inject, extract, clean, separate and detect 28 PAHs and 15 families of alkylated PAHs in 28 minutes. The methodology was tested with environmental samples from Miami. Airborne Particulate Matter is a mixture of particles of chemical and biological origin. Assessment of its elemental composition is critical for the protection of sensitive ecosystems and public health. The APM collected from Port Everglades between 2005 and 2010 was analyzed by ICP-MS after acid digestion of filters. The most abundant elements were Fe and Al, followed by Cu, V and Zn. Enrichment factors show that hazardous elements (Cd, Pb, As, Co, Ni and Cr) are introduced by anthropogenic activities. Data suggest that the major sources of APM were an electricity plant, road dust, industrial emissions and marine vessels.

There is an alarming increase of explosions with devastating consequences, the ultimate being loss of life. Furthermore, these kinds of substances have a toxic effect on animals, nature and humans if they are incorrectly disposed. In order to counteract the rising trend and increase the feeling of security within the society, the Swedish Defense Research Agency (FOI) has started a new project which in the future might be used by the police in order to prevent possible terrorist attacks. The aim with this new project is to perform trace analysis of explosives in wastewater in order to receive an indication of where illegal production of explosives takes place. This method has the potential to be used for other matrixes, such as soil instead of wastewater or other water matrixes, thereby exposing possible harmful and contaminated places.   The aim with this thesis was to develop a method for an Ultra-High-Performance Liquid Chromatography (UHPLC) instrument in order to perform trace analysis of explosives in wastewater. Furthermore, the aim was also to develop a method for an automated solid phase extraction (SPE) instrument for sample clean-up. Lastly mass spectrometry was performed with a triple-quadrupole. A performance analysis was made for the developed UHPLC-method which resulted in a good repeatability. Furthermore, several experiments were conducted on the SPE-instrument in order to receive a yield close to 100%. The different experiments included comparison between the most beneficial eluent, volume of eluent and evaporation step. The highest yield was received with 3 ml acetonitrile without any evaporation step. A performance analysis was made of the developed method for the SPE-robot, which resulted in a good accuracy and precision. In hopes of lowering the detection limit, mass spectrometry was conducted by a preciously validated instrument based at FOI. A lower detection limit was received for all substances; R-salt 0,025 µg/ml, TNT 0,094 µg/ml and PETN 0,103 µg/ml.

Since their 'discovery' at the turn of the 21st century, giant viruses of the amoeba have captured the fascination of virologists. They have raised a plethora of questions regarding their evolution and ecological significance and have greatly defied a century's old definition of viruses. By now, it is understood that a handful of giant viruses enter the amoeba via the phagosomal pathway. This thesis chooses to focus on the giant Melbournevirus (MelV) regarding its entry and uncoating pathway. We now conclude that the initial attachment between MelV and amoeba cells is built upon glycan interactions based on evidence that mannose competitively inhibits MelV binding. This attachment likely entails an approximately 70 kDa mannose containing glycoprotein on the MelV. Mannose and other glycans induce secretion of proteins including phagosomal enzymes from amoeba. Based on these findings, it is hypothesised that the mannose-induced phagosomal enzymes could play a role in the uncoating of the MelV. The results further reveal isolated phagosomes, also to some extent the glycan-induced protein secretions, to have high levels of proteins involved in cell redox homeostasis. This implies that the highly oxidative environment of the phagosome may be an overlooked physiological factor when regarding the uncoating of the MelV. A deeper understanding of the physiological uncoating conditions can be used for studying internal structures of giant viruses, such as the enigmatic Large and Dense Body (LDB) of the MelV particle.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22015号 / 工博第4627号 / 新制||工||1721(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 浜地 格, 教授 梅田 眞郷, 教授 跡見 晴幸 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

This diploma thesis focuses on polar pesticides and their analysis in agricultural commodities. One of the aims was establishing of the method for quantitative determination of diquat and paraquat using liquid chromatography with tandem mass spectrometry. Optimization parameters based on the European reference laboratories recommendations, availability of laboratory equipment and method suitability for routine analyses were taken into account. Extraction of analytes was based on shaking with acidified methanol with formic or hydrochloric acid. Considering the matrix complexity, purification with sorbents and/or acetonitrile precipitation were applied. Method validation was carried out on several levels for selected representative agricultural commodities. Part of the thesis is a field experiment where potatoes plants were sprayed with the diquat active substance. Samples of treated plants and tubers were analyzed for diquat residues. The validated method was also used for screening of diquat and paraquat residues in feed samples collected within official controls of the Central Institute for Supervising and Testing in Agriculture in 2020. The final method enables to analyze diquat and paraquat with sensitivity suitable for the maximal residue limit controls.

Background: Paediatric poisoning is a common presentation to emergency departments worldwide. There is a paucity of data on the role of liquid chromatography-tandem mass spectrometry (LC-MS/MS), in the management of paediatric poisoning in low-and middle-income countries (LMICs). In high-income countries, most studies are retrospective, and few include children. Objective: The study describes the prevalence of liquid chromatography-tandem mass spectrometry confirmed paediatric poisoning at Red Cross War Memorial Children's Hospital, Cape Town, South Africa. Methods Children admitted with suspected poisoning between 1 January 2017 and 31 December 2017, were recruited. All patients had a urine and/or blood sample sent for LC-MS/MS toxicology. Data collected included demographic data, clinical features, investigations, management, outcome and social interventions. Results 152 children, with median age of 39 (IQR 25 -61) months were enrolled of which 128 (84%) were poisoning cases. Of the 128 poisoning cases, 88 (69%) presented with a history of ingesting a known substance, 16(12%) an unknown substance and 24(19%) were cases of occult poisoning. LC-MS/MS was able to identify a substance in 92% of the cases of occult poisoning. In those who had presented with a seemingly known substance, LC-MS/MS found a different substance in 15 cases. LC-MS/MS was also able to detect multiple drugs in 40 patients. Of the poisoning cases, six (5%) cases were attempted homicide cases and 5 (4%) cases were attempted suicide cases. No children died. Individualized social interventions were instituted in poisoning cases. Emergency placement safety reasons was required in 6 children. Conclusion: When the limitations are known, LC-MS/MS is useful in identifying cases of occult poisoning; identifying patients who have ingested multiple substances and/or an unknown substance and when targeted towards child protection. As LC-MS/MS is an expensive test, it should be used judiciously in LMICs.

ASTM D3241 (Standard Test Method for Thermal Oxidation Stability of Aviation Turbine Fuels) measures the thermal oxidative stability of jet fuels under elevated temperature and pressure conditions. When jet fuels fail ASTM D3241, either at the refinery or in the distribution system, there can be supply disruptions and financial losses. Understanding the causes of poor thermal oxidative stability in jet fuels could help prevent or mitigate issues. In order to develop a deeper understanding of the molecular precursors that lead to ASTM D3241 failures, a number of analytical methodologies and data treatment techniques have been developed, applied, and reported here. Statistical analysis of LC/MS ESI data from jet fuels with varying thermal oxidative stabilities allows for the identification of molecules that are significant to ASTM D3241 failures. Differential statistical analysis of LC/MS ESI data from jet fuels before and after thermal oxidative stressing in a QCM reactor elucidates which significant molecules are being consumed during oxidation and which molecules are increasing in abundance. The analysis of thermal oxidative deposits that form during thermal oxidative stressing in the QCM reactor allows for the insight into the molecular components of the deposits. Attapulgus clay removes the polar molecules that lead to thermal oxidative stability issues in the refinery. Extraction of Attapulgus clay that has been used in a refinery to filter jet fuel with a series of solvents removes the polar molecules into a series of fractions. The subsequent analysis of the fractions by comprehensive GCxGC/MS leads to the identification of the different homologous series of molecules that are removed by the clay. The analyses developed and employed here are shown to be particularly useful for the analysis of trace polar nitrogen and oxygen containing molecules. Similar homologous series of molecules are identified across all of the different analyses. It is also clear from some of the analyses, along with previously reported data in the literature, that reactive sulfur-containing molecules are significant to poor thermal oxidative stability as measured by ASTM D3241 and to the formation of thermal oxidative deposits. There is still an opportunity to find methodologies to better characterize the sulfur species present and correlate them to the data that is reported here.

In this diploma thesis I dealt with developing of separation technique LC-MS for determination of thaumatin. I dealt with isolation and determination of thaumatin in model food sample.