Este estudo consistiu na investigação sobre a interação dos lubrificantes empregados na usinagem de metais com a matéria orgânica natural (substâncias húmicas), a sua mobilidade no solo, a degradação microbiológica e a remoção dos mesmos do solo. Realizou-se, também, um estudo sobre as mudanças nas características dos fluidos após a sua utilização. Para o processo de degradação das amostras de fluido, submetidos aos efeitos de diferentes fatores ambientais, foram utilizados quatro tratamentos : (i) microrganismos nativos, chamada amostra controle; (ii) amostra controle com matéria orgânica proveniente de turfa; (iii) amostra controle acrescida de microrganismos existentes nos efluentes de máquinas de corte; e (iv) amostra controle com adição de microrganismos de compostagem. Para a pesquisa da degradação sem o efeito dos parâmetros climáticos, foram utilizadas amostras de solo contaminadas mantendo-se em estufa, e a inoculação dos microrganismos em meios de cultura com e sem acréscimo de fonte alternativa de carbono. Como técnicas analíticas, foram utilizadas a CG-DIC e a CG-EM. Essas técnicas são indicadas tanto para estudar a composição dos fluidos quanto dos produtos de degradação microbiológica, tendo sido otimizados métodos analíticos para serem empregados no monitoramento ambiental e de estudos de degradação. As análises por IVTF e por EF também foram empregadas na identificação e quantificação dos fluidos. Observou-se uma considerável interação dos fluidos solúveis com a matéria orgânica do solo, embora tenham se apresentado com alta mobilidade para alguns constituintes, bem como um acelerado processo de degradação durante o uso. De outro modo, os fluidos insolúveis se apresentaram mais imóveis, ficando retidos na matéria orgânica do solo, entretanto, foram mais prontamente degradados no ambiente que os solúveis. A adição de matéria orgânica e de microrganismos de compostagem acelerou o processo de degradação para todos os fluidos de corte investigados. / This study is an investigation of the interaction of lubricants employed in metal machining and natural organic matter (humic substances), their mobility in soil, microbial degradation and their removal from the soil. Also, was performed study of changes in characteristic on fluids after their use. On degradation process from fluid samples, contaminated soils submitted to different environment factors, were used four treatments : (i) native microorganisms named control sample; (ii) control sample added by organic matter from peat; (iii) control sample added by microorganisms existing in flowing out from cutting machines; and (iv) control sample with addition of microorganisms from composting. For degradation research by no effect from climate parameters were used sample of contaminated soil been investigated in stove and microorganisms inoculation in culture mean with and without addition of alternative carbon source. As analytical techniques were used GC-FID and GG-MS. These techniques are both indicated for fluid composition studies and microbial degradation product. Analytic methods had been optimized to be employed on environmental monitoring and degradation studies. The FTIR and espectrofluorimetric methods were used for the fluid identification and quantification. Were observed a notable interaction between soluble fluids and soil organic matter, thought it had been verified high mobility for some compounds as well an accelerated process of degradation during their use. Otherwise, insoluble fluids were more immobile been restrained in soil organic matter, nevertheless, were readily degraded in environment than soluble ones. Organic matter and composting microorganisms\' addition accelerated the degradation process for all cutting fluids investigated.

Lysine methylation is a post-translational modification that regulates a large array of functionally diverse processes that are vital for cellular function. The role of methylation is best characterized on histone proteins due to their high concentration in the cell, but alongside histone modifications, lower abundance non-histone methylation is emerging as a prevalent and functionally diverse regulator of cellular processes. The direct biological impact of non-histone lysine methylation is less well understood because they are difficult to detect. The dynamic concentration range of the proteome masks their signal during proteomic analysis which impedes the detection of these low abundance methylated proteins. Increasing the concentration of proteins bearing methylation is required for improved discovery. This requires enriching the post-translational modification with a capturing reagent prior to analysis. This thesis details an optimized method for using the supramolecular host p-sulfonatocalix[4]arene as a stationary phase methyllysine enrichment reagent for real-life cell-extracted proteins. Prior to the optimizations described in this thesis, cell-derived peptide extracts were not retained within an early generation upper-rim modified calixarene column. But with the new protocols detailed in this thesis, proteins extracted from both cultured prostate cancer cells and industrially sourced brewer’s yeast were successfully retained by a lower-rim modified calixarene column. Thousands of methylated proteins with diverse functions and cellular localization were discovered using this method. Detection of low abundance methylated proteins will aid our discovery of all cellular methylation marks, which in turn, will help delineate their biological functions. / Graduate / 2020-11-30

Tissues are heterogeneous ecosystems comprised of various cell types. For example, in tumor tissues, malignant cancer cells are surround by various non-malignant stromal cells. Proteins, especially N-linked glycoproteins, are key players in tumor microenvironment and respond to many extracellular stimuli for involving and regulating intercellular signaling. Understanding the human proteome and glycoproteome in heterogeneous tissues with spatial resolution are meaningful for exploring intercellular signaling networks and discovering protein biomarkers for various diseases, such as cancer. In this study, we aimed to develop new liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based analytical methods for spatially-resolved proteome and glycoproteome profiling in tissue samples, and apply them for profiling potential biomarkers for pancreatic cancer. We first systematically and synchronously optimized the LC-MS parameters to increase peptide sequencing efficiency in data dependent proteomics. Taking advantage of its hybrid instrument design with various mass analyzer and fragmentation strageties, the Orbitrap Fusion mass spectrometer was used for systematically comparing the popular high-high approach by using orbitrap for both MS1 and MS2 scans and high-low approach by using orbitrap for MS1 scan and ion trap for MS2 scans. High-high approach outperformed high-low approach in terms of better saturation of the scan cycle and higher MS2 identification rate. We then systematically optimized various MS parameters for high-high approach. We investigated the influence of isolation window and injection time on scan speed and MS2 identification rate. We then explored how to properly set dynamic exclusion time according to the chromatography peak width. Furthermore, we found that the orbitrap analyzer, rather than the analytical column, was easily saturated with higher peptide loading amount, thus limited the dynamic range of MS1-based quantification. Finally, by using the optimized LC-MS parameters, more than 9000 proteins and 110,000 unique peptides were identified by using 10 hours of effective LC gradient time. The study therefore illustrated the importance of synchronizing LC-MS precursor targeting and high-resolution fragment detection for high-efficient data dependent proteomics. Understanding the tumor heterogeneity through spatially resolved proteome profiling is meaningful for biomedical research. Laser capture microdissection (LCM) is a powerful technology for exploring local cell populations without losing spatial information. Here, we designed an immunohistochemistry (IHC)-based workflow for cell type-resolved proteome analysis of tissue samples. Firstly, targeted cell type was stained by IHC using antibody targeting cell-type specific marker to improve accuracy and efficiency of LCM. Secondly, to increase protein recovery from chemically crosslinked IHC tissues, we optimized a decrosslinking procedure to seamlessly combine with the integrated spintip-based sample preparation technology SISPROT. This newly developed approach, termed IHC-SISPROT, has comparable performance with traditional H&E staining-based proteomic analysis. High sensitivity and reproducibility of IHC-SISPROT was achieved by combining with data independent proteomic analysis. This IHC-SISPROT workflow was successfully applied for identifying 6660 and 6052 protein groups from cancer cells and cancer- associated fibroblasts (CAFs) by using only 5 mm 2 and 12 μm thickness of hepatocellular carcinoma tissue section. Bioinformatic analysis revealed the enrichment of cell type-specific ligands and receptors and potentially new communications between cancer cells and CAFs by these signaling proteins. Therefore, IHC-SISPROT is sensitive and accurate proteomic approach for spatial profiling of cell type-specific proteome from tissues. N-linked glycoproteins are promising candidates for diagnostic and prognostic biomarkers and therapeutic targets. They often locate at plasma membrane and extracellular space with distinct cell type distribution in tissue microenvironment. Due to access to only low microgram of proteins and low abundance of glycoproteins in tissue sections harvested by LCM, region- and cell type-resolved glycoproteome analysis of tissue sections remains challenging. Here we designed a fully integrated spintip-based glycoproteomic approach (FISGlyco) which achieved all the steps for glycoprotein enrichment, digestion, deglycosylation and desalting in a single spintip device. Sample loss is significantly reduced and the total processing time is reduced to 4 hours, while detection sensitivity and label-free quantification precision is greatly improved. 607 N-glycosylation sites were successfully identified and quantified from only 5 μg of mouse brain proteins. By seamlessly combining with LCM, the first region-resolved N-glycoproteome profiling of four mouse brain regions, including isocortex, hippocampus, thalamus, and hypothalamus, was achieved, with 1,875, 1,794, 1,801, and 1,417 N-glycosites identified, respectively. Our approach could be a generic approach for region and even cell type specific glycoproteome analysis of tissue sections. Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with five year survival rate of around 8%. No effective biomarkers and targeted therapy are one of the major reasons for this urgent clinical situation. To explore potential protein biomarkers and drug targets located at intercellular space of pancreatic tumor microenvironment, we established chemical proteomic approach for deep glycoproteome profiling of PDAC clinical tissue samples based on the above- mentioned new proteomic methods. Taking advantage of a long chain biotin- hydrazide probe with less space hindrance, the new method outperformed traditional hydrazide chemistry method in terms of sensitivity, time efficiency and glycoproteome coverage. The method was successfully applied to enrich and validate LIF and its receptors as potential biomarkers for PDAC. In addition, to explore the full map of pancreatic tumor microenvironment glycoproteome with diagnostic and therapeutic values, we collected 114 pancreatic tissues, including 30 PDAC tumor tissues, 30 adjacent non-tumor (NT) tissues, 32 chronic pancreatitis tissues and 22 normal pancreatic tissues, and systematically profiled their glycoprotein expression pattern by using the developed glycoproteomic strategy. The deepest glycoproteome of PDAC was achieved, which covered the majority of previously reported glycoprotein biomarkers and drug targets for PDAC. Importantly, we discovered many new glycoproteins with differential expression in PDAC and normal tissue types. Moreover, LCM-based cell-type proteome profiling was achieved for 13 PDAC tissue samples, which covered more than 8000 proteins for both pancreatic stromal cells and pancreatic cancer cells in each sample. We therefore provided a valuable resource for screening novel and cancer specific glycoprotein biomarkers for pancreatic cancer with spatial resolution

Antibodies to tropomyosin, cardiac troponin I, myosin, and the beta-adrenergic receptors have been implicated in myocarditis, dilated cardiomyopathy, and heart failure. However, in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), there are only a few studies on how autoantibodies play a role in autoimmune mediated heart disease, despite the prevalence of these conditions. Ro52 antibodies have been implicated in fetal heart block, but their role in adult myocarditis remains elusive. In this study, we look beyond Ro52 and characterized the relevant autoantibodies in adult patients with SLE and RA myocarditis. An optimized immunoprecipitation followed by liquid chromatography mass spectrometry methodology was performed to determine putative auto-antigens in the human heart. The quantity and specificity of auto-antibodies was correlated with clinical measures of myocardial cellular infiltration, as determined by fluorodeoxyglucose (FDG)-positron emission tomography (PET) in patients with SLE and RA. We created autoantibody profiles that are complimentary to SLE and RA patients' clinical profile. Autoantibodies that correlated with cellular infiltration included TPI1, TPM1, MYL2, XRCC6 and APOA4. We then explored methodologies for testing patient autoantibodies using engineered cardiac tissues derived from human induced pluripotent stem cells (iPSCs). These tissues are increasingly used for drug discovery, pharmacology and in models of development and disease. While there are numerous platforms with engineered cardiac tissues, they often require expensive and non-conventional equipment and utilize complex video processing algorithms. As a result, only specialized academic labs have been able to harness this technology. In addition, methodologies and tissue features have been challenging to reproduce between different groups and models. Here, we describe a facile technology (milliPillar) that covers the entire pipeline required for studies of engineered cardiac tissues: (i) platform fabrication, (ii) cardiac tissue generation, (iii) electrical stimulation, (iv) automated real-time data acquisition, and (v) advanced video analyses. We validate these methodologies and demonstrate the versatility of the platform by showcasing the fabrication of tissues in different hydrogel materials and by using cardiomyocytes derived from different iPSC lines in combination with different types of stromal cells. We also validate the long-term culture (100 days) of tissues within the platform and provide protocols for automated analysis of force generation and calcium flux using both brightfield and fluorescent imaging. Lastly, we demonstrate the compatibility of the milliPillar platform with electromechanical stimulation to enhance cardiac tissue function. milliPillar tissues were cultured in the presence of patient autoantibodies to recapitulate the phenotype of myocardial disease, and the calcium transients and force generation were measured. Our results indicated that milliPillar tissues exhibited a decrease in force generation after 6 days in culture with SLE autoantibodies. Separately, our results indicated a prolonged calcium transient after 7 days in culture with SLE and RA autoantibodies. Changes to the downstroke of the calcium transient correlated most with patients’ autoantibody profiles and cellular infiltration. We confirmed autoantibody binding to live tissues/cells in 25% of the patients with SLE and myocarditis. Finally, we used changes in cardiac tissue function in the presence of autoantibodies to classify patients with SLE myocarditis with an accuracy of 87.5%.

This work deals with the optimization of the method for determination of conjugated linoleic acid (CLA) using gas chromatography. The summary about formation and occurrence of CLA in animal materials, its biological effects in human organism and methods suitable for its determination is introduced in the theoretical part of this study. The experimental part verify, if the gas chromatography is applicable method for assesment of CLA in selected biological matrices. The chosen method was introduced and verified at FCH of Brno university of technology. At the end the applicability of this method to CLA determination is discussed here.

Le développement du concept de chimie analytique « verte » représente l’une des préoccupations majeures du tout début du 21ème siècle ; elle a amené les différents acteurs du domaine à s’interroger sur le bien-fondé du développement de méthodes ayant un impact sur l’environnement et sur l’homme. Dans le domaine de l’analyse des lipides, les séparations par classe nécessitent de travailler sur une très large gamme de polarité, conséquence directe de la diversité des structures et des solubilités mises en jeu. La chromatographie en phase normale (NPLC) permet de réaliser l’élution des composés par ordre de polarité croissante. La mise en solution des classes lipidiques nécessite le recours à des mélanges de solvants incluant le chloroforme, le n-heptane, dichlorométhane. Les solvants organiques classiquement utilisés en NPLC, bien que performants, soulèvent aussi de nombreux problèmes liés à leur toxicité pour l'homme et l'environnement, leur volatilité, ou encore leur origine quand ils sont issus des hydrocarbures fossiles. Une des voies envisagée est la substitution de ces solvants par des solvants alternatifs, tels ceux proposés par les différents acteurs de la chimie verte. L'intérêt suscité par ces solvants est prometteur en termes de réduction de l'utilisation de solvants avec un impact significatif sur l'environnement. Les propriétés de la chromatographie en phase dioxyde de carbone supercritique sont semblables à la NPLC et offrent également une alternative verte à cette méthode. Ce travail a mis en évidence que des méthodes de séparation pourraient être développées avec des solvants alternatifs au n-heptane, au méthanol et au chloroforme. Leur utilisation est compatible avec la chromatographie liquide et la chromatographie supercritique et offre une meilleure sélectivité en termes de séparation des classes de lipides. La compatibilité de solvants alternatifs avec ELSD et la spectrométrie de masse a également été évaluée, ce qui a montré que l'absence de pureté suffisante pourrait être un problème. Cependant, ce problème a également été observé avec l'utilisation de solvants commerciaux, qui présentaient des impuretés telles que des acides gras, des polymères et des antioxydants. / Green analytical chemistry development represents one of the main issues of the 21th century. Many investigators in analytical chemistry are actually involved in the development of well-established analytical methods that prevent irreversible damage to humans and environment. In the domain of lipid analysis, structural diversity as well as difference in solubility of these compounds is leading to work with a very large polarity range to separate lipids by classes. The normal-phase liquid chromatography (NPLC) allows realising the elution of compounds in order of increasing polarity. The solubilisation of lipid classes requires the use of a mixture of several solvents, among them chloroform, n-heptane, dichloromethane. Moreover, organic solvents traditionally used in NPLC, although well performing are raising different problems due to their original source, i.e. fossil hydrocarbons, volatility and toxicity for humans and environment. One of the ways to avoid such solvents is the substitution with alternative solvents, as proposed by various players in green chemistry. The interest raised by these solvents, is promising in terms of reduction of solvent use with a significant environmental impact. The properties of supercritical fluid chromatography using CO₂ are similar to NPLC and also offer a green alternative to this method. This work has highlighted that separation methods could be developed with alternative solvents to n-heptane, methanol and chloroform. Their use is compatible with liquid and supercritical chromatography and offer better selectivity in terms of separation of lipid classes. The compatibility of alternative solvents with ELSD and mass spectrometry was also evaluated, which showed that the unavailability of sufficient purity could be an issue. However, this problem was also observed with the use of commercial solvents, which presented impurities such as fatty acids, polymers and antioxidants.

abstract: This work aims to characterize protein-nanoparticle interactions through the application of experimental techniques to aid in controlled nanoparticle production for various applications from manufacturing through medical to defense. It includes multiple steps to obtain purified and characterized protein and then the production of nanoparticles using the protein. This application of protein requires extremely pure homogenous solution of the protein that was achieved using numerous protein separation techniques which were experimented with. Crystallization conditions, protein separation methods and protein characterization methods were all investigated along with the protein-nanoparticle interaction studies. The main protein of study here is GroEL and the inorganic nanoparticle used is platinum. Some studies on MBP producing gold nanoparticles from an ionic gold precursor were also conducted to get a better perspective on nanoparticle formation. Protein purification methods, crystallization conditions, Car-9 tag testing and protein characterization methods were all investigated along with the focus of this work. It was concluded that more Car9 studies need to be carried out before being used as in the form of a loop in the protein. The nanoparticle experiments were successful and platinum nanoparticles were successfully synthesized using GroEL. The direction of further research in protein-nanoparticle studies are outlined towards the end of the thesis. / Dissertation/Thesis / Masters Thesis Chemical Engineering 2019

Please read the abstract in the section 00front of this document / Dissertation (MSc)--University of Pretoria, 2010. / Chemistry / unrestricted

A decreased concentration of pepsinogen A in serum was found to be a marker of gastric cancer, similarly as a low ratio of pepsinogen A to pepsinogen C. In the present study we have compared properties of immunoglobulin fraction isolated from the egg yolks after immunization of laying hens with pepsinogen isolated from porcine gastric mucosa with those of present in rabbit antiserum obtained after the animal immunization with the same antigen. The characteristics of chicken antibodies against porcine pepsinogen and the comparison with rabbit antibodies raised against the same antigen was carried out using the following methods: ELISA, affinity chromatography on immobilzed antigen and bovine serum albumin, SDS and native electrophoresis and MALDI-TOF MS/MS. While the rabbit specific antibodies interacted with the used antigen and only slightly with bovine serum albumin and there was a diference between pre-immune IgG and specific IgG, in the case of chicken antibodies IgY it did not work. No diference was observed between ELISA tests performed with pre-immune serum and the serum after immunization with porcine pepsinogen and a high interaction of IgY with bovine serum albumin in pre-immune serum and specific IgY after the immunization were detected. Similar results were obtained in experiments with...

The determination of non-esterified fatty acids (NEFA) in plasma is possible by many routine biochemical methods. For more detailed metabolic studies it is required to analyse the fatty acid (FA) profile. The NEFA profile determination is usually performed by the capillary gas chromatography (GC), but the sample preparation is not uniform. NEFA may be isolated by the extraction process or by the preparative thin-layer chromatography (TLC). The aim of this study was to compare these two separation procedures. The samples of pooled plasma from volunteer donors were analyzed by capillary GC after previous separation procedure by the TLC and the liquid-liquid extraction. The results were compared by the t-test for both the absolute concentration of individual FA provided by the internal standard (margaric acid) method and the relative abundance (Rel%). The reproducibility of the results was significantly better for the liquid-liquid extraction method than the TLC. The relative standard deviations (RSD) of the FA groups (unsaturated, monosaturated and polysaturated) were from 4.3 to 11.3 % vs. 8.6 to 33.8 % for the relative abundance and from 16.5 to 25.5% vs. 15.4 to 47.4% for the absolute concentration. For each FA, which were represented by more than 0.1 Rel %, RSD ranged from 4.5 to 47.8% vs. 9.5 to...