The objective of the project described in this thesis was to study the complex induction of extracellular proteases in the filamentous fungus Aspergillus niger using information gathered with... Show moreThe objective of the project described in this thesis was to study the complex induction of extracellular proteases in the filamentous fungus Aspergillus niger using information gathered with functional genomics technologies. A special emphasis is given to the requirements for performing a successful systems biology study and addressing the challenges met in analyzing the large, information-rich data sets generated with functional genomics technologies. The role that protease activity plays in strain and process development of A. niger and other aspergilli is reviewed. The influence of several environmental factors on the production of extracellular proteases of A. niger in controlled batch cultivations was studied. Samples generated in this study were used for analysis with different functional genomics technologies. With a shotgun proteomics approach the A. niger secretome under different experimental conditions was determined. Furthermore, the effect of different quantitative phenotypes related to protease or glucoamylase activity on the information content of a metabolomics data set was investigated. Finally, the clustering of co-expressed genes is described. First, a set of conserved genes was used to construct gene co-expression networks. Subsequently, all protein-coding A. niger genes, including hypothetical and poorly conserved genes, were integrated into the co-expression analysis. Show less
The application of dedicated mass spectrometry (MS) and nuclear magnetic resonance (NMR) technologies for biomarker discovery and diagnostic purposes has increased substantially in the last decade.... Show moreThe application of dedicated mass spectrometry (MS) and nuclear magnetic resonance (NMR) technologies for biomarker discovery and diagnostic purposes has increased substantially in the last decade. In the studies presented in this thesis, we have used these technologies to identify parasite or host-derived products (biomarkers) related to infection and morbidity associated with schistosomiasis and to better understand the host-parasite interaction. The application of our peptidomics and metabonomics studies on schistosomiasis have provided some novel, valuable information but they are obviously only the first step. In addition to the potential biomarkers identified with the global biomarker discovery approaches, we showed in this thesis that a more targeted approach, looking at glycosylation, also resulted in novel information on S. mansoni infection. We have identified and characterized a set of human Apolipoprotein C-III peptides aberrantly glycosylated at the O-glycosylation site (Thr74), in urine of S. mansoni- infected individuals. The presented study is the first in which MS and NMR were used for the analysis of a cohort of human S. mansoni-infected individuals. This has resulted in the identification of a number of novel markers. Nevertheless, further studies are needed to evaluate the overall applicability of these putative biomarkers Show less
Summary of the Thesis: Vegetables have always been considered as healthy food. So also Brassica vegetables are well known all over the world as a common food due to the presence of health affecting... Show moreSummary of the Thesis: Vegetables have always been considered as healthy food. So also Brassica vegetables are well known all over the world as a common food due to the presence of health affecting compounds (Chapter 2). A vast amount of data is available for health promoting compounds in Brassicaceae vegetables. These health promoting affects are due to a range of phytochemicals including primary (carbohydrates, amino acids and organic acid) and secondary metabolites (phenolics and glucosinolates), along with vitamins and minerals. These metabolites are interconnected through different biosynthetic pathways and are affected by different external stimuli. Plant metabolic responses are specific for different kinds of stress, but use in part similar metabolic pathways (Chapter 3). Certain internal or external factors play an important role for the metabolite profile of vegetables, thus changing the nutritional value for human (Chapter 4). These factors are related to the plant response to external stress factors and helping the plant to survive. These factors includes bacteria (Chapter 5), metals ions ( Chapter 6) and post harvest storage conditions (Chapter 7). The aim of this thesis was to study the Brassica phytochemicals and their response to stress factors by using a holistic analytical approach. Show less
Het is nu gangbaar in de kliniek om aan de hand van een enkele biochemische component (een gen, eiwit of metaboliet) vast te stellen of iemand ziek is. Echter, met geavanceerde meettechnieken zijn... Show moreHet is nu gangbaar in de kliniek om aan de hand van een enkele biochemische component (een gen, eiwit of metaboliet) vast te stellen of iemand ziek is. Echter, met geavanceerde meettechnieken zijn we nu in staat zijn om tientallen tot zelfs honderden van deze componenten tegelijk te meten. Hierdoor krijgen onderzoekers een veel breder overzicht van wat er allemaal verandert tijdens een ziekte en kunnen er betere diagnostische tests worden ontwikkeld. Voor dit proefschrift heb ik mij verdiept in deze technieken en hun toepasbaarheid in artrose. Artrose is een veel voorkomende rheumatische aandoening waarvan de exacte oorzaak nog onduidelijk is. Ik heb vastgesteld dat er met name nog weinig bekend is over het aandeel van de afbraakproducten van eiwitten en van vetten. Ik heb de benodige meettechnieken opgezet om honderden van deze afbraaktproducten en vetten te kunnen meten. Hieruit bleek dat een onstekingsmediator zeer verhoogd is in artrose en dat de samenstelling van vetten in het bloed van artrose patienten anders is dan bij gezonde mensen. De vindingen van dit proefschrift geven de kracht van deze meettechnieken aan om bij te dragen tot verbeterde diagnostische tests. Show less
