Climate change is a challenge for both current and future generations. New biological resources have to be developed in order to meet the demand for energy as well as the demand for food. One way... Show moreClimate change is a challenge for both current and future generations. New biological resources have to be developed in order to meet the demand for energy as well as the demand for food. One way of doing this is to make use of so-called smart crops, as they have improved yields and a small environmental footprint. Model plant organisms, such as Arabidopsis thaliana, can contribute to the development of smart crops as they have been studied extensively by the research community. The purpose of this research is to unravel the pathways leading to the enhanced growth characteristics phenotype of two phenotypically engineered Arabidopsis mutants from a systems biology perspective, by using metabolomics. In metabolomics, metabolites are studied both qualitatively and quantitively under specific growth conditions. Since metabolites are the end products of cellular processes, the metabolome is most closely related to the phenotype of plants. To obtain the metabolic profile directly from the leaves of Arabidopsis, high-resolution magic angle spinning (HR-MAS) NMR is used. Combined with multivariate analysis, biomarkers, related to the mutant phenotype, are determined. The biological interpretation of the biomarkers will be performed in a systems biology approach to obtain a model to explain the mutant phenotype. Show less
Treating chronic diseases such as rheumatoid arthritis and type 2 diabetes mellitus is a hot topic that has been discussed widely and investigated extensively, but never solved, due in part to... Show moreTreating chronic diseases such as rheumatoid arthritis and type 2 diabetes mellitus is a hot topic that has been discussed widely and investigated extensively, but never solved, due in part to their high complexity. Integrating disease-related information using a systems approach may help improve our knowledge of stages of the disease, thus improving the accuracy of diagnosing chronic disease. With respect to integrative thinking, traditional Chinese medicine (TCM)‒based concepts may provide a suitable holistic model, as TCM describes disease syndromes/phenotypes as an experience-based reference from the systems level. Systems-based metabolomics provides a comprehensive picture of small molecular metabolites as a readout and provides biological interpretations of the pathophysiology of disease. The rapid, highly sensitive, non-invasive measurement of ultra-weak photon emission (UPE) -- which measures spontaneously emitted photons at the surface of the skin--has been proposed for supporting TCM-based diagnostics and for reflecting the whole body’s physiological and pathological status. Combining metabolomics with TCM-based diagnostics will provide a robust model for investigating the biological processes that underlie UPE. This thesis aimed to investigate system-wide perturbations by using/combining metabolomics, UPE and TCM-based diagnostics, to provide i) a systems view of chronic disease, and ii) personalized phenotyping guided by TCM-based principles. Show less
On the basis of systems thinking, in this thesis metabolomics, Chinese medicine (CM), as well as Western medicine (WM) were combined to achieve a more comprehensive systems diagnosis of patients... Show moreOn the basis of systems thinking, in this thesis metabolomics, Chinese medicine (CM), as well as Western medicine (WM) were combined to achieve a more comprehensive systems diagnosis of patients with chronic diseases. Specifically, metabolomics has been applied to characterize patients by small molecule profiles, which can be applied in phenotyping patients and matching these with optimal therapies. Chinese and Western medicine have different perspectives on diagnosis and could be highly complementary to each other, so combining both could have advantages in personalized diagnosis. Therefore, in this thesis a combination of systems approaches is used, including metabolomics, CM-based diagnosis principles as well as WM to provide systems diagnosis of patients with chronic diseases, in particular rheumatoid arthritis (RA). With systems diagnosis, we could better identify potential biomarkers to predict the WM therapeutic response of patients with RA and monitoring disease progression. Show less
Cellular responses to DNA damage are highly variable and strongly depend on the cellular and organismic context. Studying the DNA damage response is crucial for a better understanding of cancer... Show moreCellular responses to DNA damage are highly variable and strongly depend on the cellular and organismic context. Studying the DNA damage response is crucial for a better understanding of cancer formation and ageing as well as genotoxic stress-induced cancer therapy. To do justice to the multifaceted cellular changes, elicited by DNA damage, use of high-throughput techniques and integration with bioinformatics tools is of great value. This thesis summarizes recent advances in the field of systems biology studies of the DNA damage response and furthermore shows integrated approaches of the study of DNA damage response signaling networks in embryonic stem and cancer cells. By integration of transcriptional changes and the phosphorylation and metabolic response of cisplatin-treated embryonic stem cells, with RNAi-based knockdown screens we identify novel DNA damage response signaling networks, linking process such as Wnt signaling, translation arrest or altered metabolic pathways to the cellular response to DNA damage. Furthermore, genes, whose knockdown sensitizes embryonic stem cells to DNA damage-induced killing, are tested in cancer cells of varying genetic backgrounds identifying a small subset of genes, which represent potential drug targets for sensitization of cancer cells. Altogether, our systems approach for studying the DNA damage response identifies novel DNA damage-induced signaling networks and molecules, which modulate survival in the presence of DNA damage, potentially providing new targets for therapeutic intervention or biomarker discovery. Show less
The current health care system is severely challenged by for instance rising costs, fewer new blockbuster drugs and increasing numbers of hospitalizations due to side effects. Especially in the... Show moreThe current health care system is severely challenged by for instance rising costs, fewer new blockbuster drugs and increasing numbers of hospitalizations due to side effects. Especially in the area of chronic diseases the current disease fighting strategy is failing and a more personalized medicine approach is needed. In this thesis new sub-types of rheumatoid arthritis are characterized with metabolomics analysis and symptoms patterns. The sub-types are based on diagnostic knowledge from Chinese medicine. The two sub-types of RA patients were found to have differences in apoptosis regulation of T-cells and differences in urine acylcarnitine levels. A questionnaire was designed to distinguish the two sub-types and to evaluate symptom patterns of arthritis patients. In the future the response to treatment of these sub-types of patients can be studied and specific treatment can be targeted to these sub-types. Show less
This thesis was to combine metabolomics and Chinese medicine (CM) diagnosis to search for biomakers or metabolic profiles to subtype of type 2 diabetes (T2DM). An explorative study of 50 males with... Show moreThis thesis was to combine metabolomics and Chinese medicine (CM) diagnosis to search for biomakers or metabolic profiles to subtype of type 2 diabetes (T2DM). An explorative study of 50 males with pre-diabetes was designed and two subtypes (A and B) could be identified by urine metabolomics. More metabolic disturbances were indicated in subtype B. The effects of rimonabant and a multi-component preparation (SUB885C), both with reported effects of regulating weight and the improvement on metabolic risks, were assessed by lipidomics on ApoE*3Leiden.CETP Mice. A 4-week rimonabant intervention brought a significant weight reduction, but moderate effects on lipid profile. SUB885C was able to produce multiple anti-atherogenic changes in lipids of the mice to improve metabolic parameters. A combined approach of lipidomics, biochemistry and herbal component profiling was used to evaluate the effects of the ginseng roots of 3__6 years on the regulation of dyslipidemia in diabetic Goto-Kakizaki rats. The more than 4 year ginseng proved to be valuable for drug development to regulate lipids. To conclude, the early metabolomics investigations performed in this thesis converged analytical bioscience, clinical approach and the diagnostic perspectives in other health system to provide the systems biology view on the pre-stage of T2DM. Show less
Metabolomics is the comprehensive analysis of small molecules involved in metabolism, on the basis of samples that have been obtained from organisms in a given physiological state. Data obtained... Show moreMetabolomics is the comprehensive analysis of small molecules involved in metabolism, on the basis of samples that have been obtained from organisms in a given physiological state. Data obtained from measurements of trait levels in twin families can be used to elucidate the importance of genetic and environmental variation for individual differences in trait levels. I describe the results of various analyses using metabolomics data from twin families. These data originated from analysis of blood plasma lipids by liquid chromatography-mass spectrometry, and from analysis of blood plasma and urine by proton nuclear magnetic resonance spectroscopy. Data analyses with a newly developed method, based on hierarchical clustering analysis of family members, suggested that shared genetic variation and shared environmental variation are important for similarities in blood plasma lipid profiles among individuals. Also, a method called __quantile equating__ was developed and applied that enables combination of semiquantitative metabolomics data sets originating from different measurement __blocks__. Univariate quantitative genetic analyses based on structural equation modeling revealed interesting differences in heritability among different metabolites. In multivariate analysis, relationships among genetic sources of phenotypic variation in different metabolites were investigated. These results bear relevance for the interpretation of the results from genome-wide association analyses. Show less
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
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
