The outbreaks of AIDS and COVID-19 showed clearly how infectious viruses can influence people’s lives. Investigating the changes in the host metabolism may provide a paradigm shift to consider... Show moreThe outbreaks of AIDS and COVID-19 showed clearly how infectious viruses can influence people’s lives. Investigating the changes in the host metabolism may provide a paradigm shift to consider immune-metabolic interactions as therapeutic targets. The aim of this thesis is to examine the interplay between the immune system and metabolism during viral infections, such as HIV and coronavirus. These investigations will utilize metabolomic and lipidomic mass spectrometry techniques to gain a comprehensive understanding of the metabolic changes that occur during viral infections. To enhance the coverage of the lipidome, a new method will be developed. Show less
With ageing populations, the prevalence of age-related disorders such as dementia is on the rise. As there is currently no curable treatment for dementia, the vascular component of dementia is... Show moreWith ageing populations, the prevalence of age-related disorders such as dementia is on the rise. As there is currently no curable treatment for dementia, the vascular component of dementia is increasingly recognised as a key modifiable cause. This thesis aims to investigate biological pathways between risk factors of cardiometabolic disease and cognitive function, in a population of older adults at increased risk of cardiovascular disease (CVD). We hypothesise that changes in physiological functioning caused by (sub)clinical CVD are possible mediators within the pathway leading to cognitive dysfunction. In the first part of this thesis, we studied electrocardiogram-based intervals and serum cardiac biomarkers (such as troponin) in relation to cognitive function. In the second part of this thesis, we studied the interplay of body mass index and serum leptin, loss of body weight and body weight variability, as well as metabolomics-based health scores in relation to cognitive function. We found that various cardiometabolic risk factors are associated with worse cognitive function. The results of this thesis strongly suggest that subclinical changes in cardiometabolic health may exist before cognitive dysfunction becomes apparent. Treating these cardiometabolic risk factors may be of benefit to future cognitive health. Show less
The progressive loss and degeneration of dopaminergic neurons is a major pathological hallmark of Parkinson's disease (PD). The onset and progression of PD can be triggered by multiple risk factors... Show moreThe progressive loss and degeneration of dopaminergic neurons is a major pathological hallmark of Parkinson's disease (PD). The onset and progression of PD can be triggered by multiple risk factors, for instance, genetic mutation, environmental exposure, and aging. Each factor may cause common or unique metabolic disturbances, ultimately converging into a complex metabolic disorder with diverse clinical phenotypes. Through metabolome analysis, the full picture of the metabolic landscape depicting a biological system can be revealed. Metabolites function as key elements and direct read-outs of a system’s functional status. Alterations in metabolite concentrations are informative for inferring and understanding underlying metabolic activity. In addition, stable isotope labeling techniques coupled with metabolomics can bring us an extra-dynamic vision of the metabolic landscape. Changes in labeling patterns of metabolites help identify alterations with metabolic fluxes through pathways. This thesis aimed to develop a comprehensive analytical strategy for characterizing the metabolic activity related to PD neurodegeneration, especially focused on the improvement in metabolome coverage and data quality, facilitating the use of stable isotope labeling in in-depth metabolism investigations, and developing a computational workflow for metabolic flux analysis. These methods were applied to investigate metabolic dysregulation of dopaminergic neurons due to genetic and environmental factors. Show less
De uitkomsten beschreven in dit proefschrift dragen bij aan de bestaande overtuiging dat een verfijndere classificatie voor depressie, op basis van symptoomprofielen en hun mogelijke biologische... Show moreDe uitkomsten beschreven in dit proefschrift dragen bij aan de bestaande overtuiging dat een verfijndere classificatie voor depressie, op basis van symptoomprofielen en hun mogelijke biologische onderbouwing, overwogen dient te worden. Inmiddels wordt adipositas in de dagelijkse praktijk op meer dan alleen het BMI beoordeeld, namelijk ook de tailleomtrek en het lipidenprofiel. Echter, dergelijke aandacht bestaat nog niet voor de heterogeniteit van depressie. Een grotere bewustwording van de verschillende manifestaties van depressie-symptomatologie, die het gevolg kunnen zijn van uiteenlopende pathofysiologische mechanismen, is van essentieel belang. Wanneer een patiënt met depressie een atypisch energie-gerelateerd symptoomprofiel heeft, kan het nuttig zijn om diens metabole biomarkers te controleren om mogelijke ontwikkeling van cardiometabole ziekten te voorkomen. In de klinische praktijk moeten wij ons bij de behandeling van patiënten met depressie ook meer bewust worden van de correlatie tussen symptoomprofielen van depressie en afzonderlijke biologische en klinische manifestaties. Het is cruciaal om goed te kijken naar de symptomen die bij elke patiënt tot uiting komen. De resultaten van dit proefschrift tonen aan dat patiënten met een depressie die atypische energie-gerelateerde depressieve symptomen vertonen, genetisch en klinisch kwetsbaar zijn voor aan insulineresistentie gerelateerde ziekten (namelijk adipositas, metabole ontregelingen en diabetes mellitus type 2). Een gepersonaliseerde aanpak kan behulpzaam zijn in preventie van deze chronische en complexe ziekten. Hierbij dient er rekening gehouden worden met de heterogeniteit van depressie en de associatie tussen atypische energie-gerelateerde symptomen van depressie en deze ziekten. Show less
Viral hemorrhagic fever (VHF) is a group of acute diseases caused by highly infectious viruses including Ebola, Lassa, Dengue viruses. Its high mortality rate poses high risk to public health,... Show moreViral hemorrhagic fever (VHF) is a group of acute diseases caused by highly infectious viruses including Ebola, Lassa, Dengue viruses. Its high mortality rate poses high risk to public health, however, studies on VHF have been hampered due to the non-availability of proper models and incomplete knowledge on its mechanism. In order to fill this gap, this thesis presented new bioanalytical, lab-on-chip and single-cell assays to investigate changes in vascular biology and macrophage immunometabolism induced by VHF viruses. Firstly, an organ chip was developed to mimic the hemorrhagic shock syndrome caused by VHF viruses in vitro and test experimental drug candidates. In addition, acoustic force spectroscopy was applied to investigate the effect of Dengue on the cellular viscoelastic properties of endothelial cells at single-cell level. Then, metabolic profiling of endothelial cells and macrophages upon Ebola viral protein exposure was performed on bulk-level. Finally, the immunometabolism of human macrophages upon polarization was investigated by live single-cell metabolomics, setting the stage for future host-pathogen studies at single-cell level. Overall, this thesis will facilitate the understanding of VHF viruses and the development of treatment strategies. More importantly, the technologies developed here expectedly open up opportunities to combat the viruses that threaten global society. Show less
Metabolomics is a powerful tool that can provide a comprehensive insight into the complexity of human biology and the pathophysiology of diseases. By analyzing the metabolome, which refers to the... Show moreMetabolomics is a powerful tool that can provide a comprehensive insight into the complexity of human biology and the pathophysiology of diseases. By analyzing the metabolome, which refers to the complete set of small (endogenous) molecules (with a mass <1500 Da) present within a given biological system, a direct functional read-out of an organism's physiological status can be obtained. In particular, metabolomics has emerged as a promising approach for neuroscience research, as it helps to shed light on the molecular mechanisms underlying neurodegenerative and neuropsychiatric diseases. One of the main challenges in (brain) metabolomics studies is the reliable and sensitive analysis of volume-limited biological samples. Therefore, in this thesis, innovative microscale analytical workflows based on capillary electrophoresis (CE) coupled to mass spectrometry (MS) are developed in order to generate metabolic profiles in volume-restricted samples. The ultimate aim of this thesis is to showcase that the technical reproducibility, detection sensitivity, and metabolic coverage of CE-MS are sufficient to allow use for different material-limited matrices of interest for neuroscience research. Show less
Lipid signaling is an essential biological event/process in a plethora of pathophysiological conditions. The underlying idea of this thesis is that many of the roles and the complex interplay of... Show moreLipid signaling is an essential biological event/process in a plethora of pathophysiological conditions. The underlying idea of this thesis is that many of the roles and the complex interplay of the individual signaling lipids in inflammatory processes and related conditions in health and disease is not well known, and therefore has to be studied integrally as a complex network. In order to study this complex interplay, an improved broad analytical method is necessary to analyze a wide range of different signaling lipid classes such as oxylipins, (nitro) free fatty acids, endocannabinoids, bile acids and different subclasses of lysophospholipids. Therefore, the aim of this thesis is to develop a better method to study signaling lipids, and to apply it to study the role of these molecules in several relevant biological questions for a better understanding of inflammation related pathophysiology including autoimmune diseases, neurodegeneration and regulatory effect of exercise training. Show less
To increase clinical success rate of drugs, a better understanding of drug action mechanism and disease dynamics is required. Metabolomics, which studies small molecules involved in biochemical... Show moreTo increase clinical success rate of drugs, a better understanding of drug action mechanism and disease dynamics is required. Metabolomics, which studies small molecules involved in biochemical processes in organisms, has shown to be a useful tool for this better understanding. In this thesis, we focus on the endocannabinoid system (ECS) and profiling its related metabolic pathways using liquid chromatography - mass spectrometry (LC-MS) based metabolomics techniques. The endocannabinoid system (ECS) is a signaling system involved in multiple physiological and pathological processes. Due to its wide distribution and complex network of metabolic interactions, the development of drugs targeting the ECS has seen high failure rates. To get a better understanding of the behavior of the ECS and related pathways, LC-MS platforms with wide coverage of the major ECS-related metabolites, or with high sensitivity that reaches low levels of metabolites, were developed and optimized. Furthermore, these metabolomics platforms were applied in clinical studies looking into cardiometabolic health, and revealed correlations between endogenous metabolite signaling, cardiometabolic health and the benefits of exercise. Show less
This thesis focuses on the development of sample-preparation methods for small amounts of samples and applying the developed methods to muscle tissues to investigate the mechanisms involved in... Show moreThis thesis focuses on the development of sample-preparation methods for small amounts of samples and applying the developed methods to muscle tissues to investigate the mechanisms involved in sarcopenia. A fully automated, high-throughput, and high enrichment sample-preparation method, electroextraction, was developed. The metabolomics mechanism analysis of sarcopenia by using mouse models facilitate the understanding of metabolic processes underlying sarcopenia and can help to identify treatment options in the future. Show less
Streptomyces bacteria are a valuable source of natural products, many of which are used in the clinic or in biotechnology. In our search for novel antibiotics we discovered lugdunomycin, a natural... Show moreStreptomyces bacteria are a valuable source of natural products, many of which are used in the clinic or in biotechnology. In our search for novel antibiotics we discovered lugdunomycin, a natural product with a highly complex chemical architecture that is produced by Streptomyces sp. QL37. It is derived from the angucyclines, a well-known class of molecules known for their antibacterial and anticancer activities. Though angucyclines are produced in high quantities under most conditions, lugdunomycin is produced in minimal amounts. This thesis describes novel insights into the transcriptional control of the lugdunomycin biosynthetic gene cluster and into the lugdunomycin biosynthesis pathway. These insights may be applied to improve the yield of lugdunomycin and expand the chemical diversity of angucyclines. Using molecular biology, bioinformatic approaches and omics studies, such as metabolomics and transcriptomics, we have characterized the lugdunomycin biosynthetic gene cluster, the regulatory genes (lugRI–lugRV) required for transcriptional activation of the cluster, and the oxygenase genes (lugOI–lugOV) that play a key role in the different chemical rearrangements of the angucyclines. Furthermore, this thesis contains a detailed review of the regulatory network that controls antibiotic production in Actinobacteria. Show less
In this thesis, I study 1) metabolic alterations in tuberculosis related to wasting syndrome in human patients as well as in rodent and fish animal models. 2) effects of the mutation of the leptin... Show moreIn this thesis, I study 1) metabolic alterations in tuberculosis related to wasting syndrome in human patients as well as in rodent and fish animal models. 2) effects of the mutation of the leptin gene on cachexia and diabetes in rodent and zebrafish animal models. 3) how tuberculosis infection and resulting metabolic reprogramming are dependent on leptin signaling in mice and zebrafish larvae. Show less
Neurodegenerative diseases, including Parkinson’s disease (PD), are increasing in prevalence due to the aging population. Despite extensive study, these diseases are still not fully understood and... Show moreNeurodegenerative diseases, including Parkinson’s disease (PD), are increasing in prevalence due to the aging population. Despite extensive study, these diseases are still not fully understood and the lack of personalised treatment options that can target the cause of the diseases, rather than the symptoms, has led to a greater demand for improved disease understanding, therapies and diagnostic procedures. In this thesis, we use systems biology approaches to construct disease-specific models intended for biomarker discovery, therapeutic treatment strategy identification and drug repurposing in PD. Systems biology is a mathematical field of research that analyses biological systems via construction of a computational model using experimental data. This is achieved by integration of omics data, including genomics, proteomics, transcriptomics and metabolomics. A specific approach used to identify the physico- and biochemical bounds within a biological system is constraint-based modelling, which requires the input of absolute quantitative metabolomics data. To improve our absolute quantitative coverage of the metabolome, we developed and improved new quantitative metabolomics methods using a targeted mass spectrometry workflow to obtain data intended to be integrated into constraint-based metabolic models for the study of PD. Show less
Marine sponges are important members of reef ecosystems, as they play ecological roles that are essential for the health of the reef. From a chemical perspective, sponges have been widely studied,... Show moreMarine sponges are important members of reef ecosystems, as they play ecological roles that are essential for the health of the reef. From a chemical perspective, sponges have been widely studied, showing great chemical diversity with biological activity, although this chemical diversity can often not be linked to for instance variation in environmental conditions experienced by sponges. Metabolomics, with its holistic overview of the metabolites present in samples, has provided new tools to gain insight into the function of metabolites in the intricate relationship between sponges and their environment. Among sponges, giant barrel sponges have stood out for their predominance in many reefs, their longevity and the fact that they are widely spread across oceans. this thesis showed how environmental, genetic and biological factors individually or as a result of their interaction can influence the metabolome of giant barrel sponges. This is only the first step towards a better understanding of the role that chemical compounds play in interactions between sponges and the surrounding environment. The advances in this field will rely, among others, on the development of technologies that would allow real time measurement of the metabolome and the study of the interaction between the metabolome and other omics. Show less
Heart failure is a major health care problem with high mortality. Although advances have been made in treatment of patients suffering from heart failure with reduced ejection fraction, this is not... Show moreHeart failure is a major health care problem with high mortality. Although advances have been made in treatment of patients suffering from heart failure with reduced ejection fraction, this is not true for patients suffering from heart failure with preserved ejection fraction. The mechanism underlying heart failure with preserved ejection fraction is still unclear. Recent evidence suggests that factors circulating in blood might have an effect on the microvessels, including those in the heart. To diagnose and treat microvascular diseases, we aim to explore the association of circulating plasma factors with microvascular integrity. As current human 2D models with cultured endothelial cells lack sufficient complexity to assess the function of microvascular endothelial-pericyte interactions, research on microvascular loss largely depends on animal models. To mimic the microarchitecture and functions of the human blood vessel in a more efficient way for drug discovery, we developed the microvessel-on-a-chip. This system allowed us to screen microvascular destabilization factors in blood and study the efficacy of potential drugs for microvascular diseases. In conclusion, our platform may serve as a unique tool for microvascular destabilization studies as well as for the development of novel therapeutic strategies to combat microvascular complications. Show less
The challenge of achieving fast quantification in metabolomics is the presence of severe matrix effects during the MS analysis of complex samples. Complex samples also result in challenges during... Show moreThe challenge of achieving fast quantification in metabolomics is the presence of severe matrix effects during the MS analysis of complex samples. Complex samples also result in challenges during metabolite identification as complex MS/MS spectra and peak overlap in 1H NMR complicate structure elucidation. The goal of this thesis is to tackle these challenges by the development and application of innovative fractionation approaches and state-of-the-art MS and NMR analyses. Show less
By growing in a soil plants change the biotic and abiotic properties of the soil in which they grow. This can influence the performance of plants that grow in the same soil subsequently and is... Show moreBy growing in a soil plants change the biotic and abiotic properties of the soil in which they grow. This can influence the performance of plants that grow in the same soil subsequently and is known as plant soil feedback (PSF). Species largely differ in how they influence the soil while they grow in it and how they react to conditioned soil. So far PSF was mainly shown to influence biomass of plants and certain specific chemical compounds in plants. This thesis demonstrates how the whole metabolome of a range of different plants changes due to different microbiomes in the soil and that the influence of soil on the metabolome of plants can be stronger than the effect of herbivory. Furthermore, this thesis shows how these PSF change over time and on different spatial scales and which methods are most suitable to study the metabolomic response of plants. Show less
Narcissus is an economically important crop with a large number of species, hybrids and/or varieties in cultivation. It is one of the most popular ornamental plants. The Netherlands is among the... Show moreNarcissus is an economically important crop with a large number of species, hybrids and/or varieties in cultivation. It is one of the most popular ornamental plants. The Netherlands is among the top producers of Narcissus in the world. The ornamental value of Narcissus is quite well known but they can also be a valuable resource of natural compounds. Among these compounds, galanthamine has been successfully commercialized as medicine for the treatment of early to mild Alzheimer’s Disease (AD). The characteristic symptoms of this disease are loss of memory and impairment of multiple cognitive and emotional functions. The objective was to find out how galanthamine levels could be enhanced to convert this floricultural crop into a medicinal crop. There are different factors that influence the production of galanthamine and other metabolites in the bulbs. Effect of various factors such as preanalytical methods, bulb location and age along with effect of biotic and abiotic factors on the growth and yield were studied. From the results, it is evident that factors have detrimental effect on the total bulb yield and galanthamine levels. Show less
Plant exudates appeared long time ago in the history line of life in the early Devonian. They are typical saps produced by specialized cells. They can be naturally excreted outside or right after... Show morePlant exudates appeared long time ago in the history line of life in the early Devonian. They are typical saps produced by specialized cells. They can be naturally excreted outside or right after plants are damaged or infected. Through time, diverse cultures recognized them as valuable sources of natural medicines. Of various types of plant exudates, the most outstanding are gums, mucilage, essential oils, oleoresins, resins, phloem like saps, and latexes. Regardless of their commercial importance, in the aspect of biology, plant exudates are believed to be involved in plant defense mechanisms, but their roles still remain unclear. In this thesis, based on diverse experiments, many features of plant exudates were unveiled. Interestingly, even if plant exudates possess a broad chemical diversity, their specialized biological functions resulted in less variation of their metabolomes as compared with their bearing tissues. This lower variation indicates that plant exudates might partake of a general-broad defense against herbivores and pathogens in their bearing tissues. This defense involves both mechanical and chemical traits which might complement and modulate each other, eventually resulting in a chemo-mechanical defense layer. Of the diverse chemicals in plant exudates, terpenes are one of the most common metabolites in these saps. Show less
The major and ultimate aim of metabolomics is to obtain an answer to a specific biological or clinical question. For that, many strategies have been applied in this field, including NMR and MS... Show moreThe major and ultimate aim of metabolomics is to obtain an answer to a specific biological or clinical question. For that, many strategies have been applied in this field, including NMR and MS-based approaches. CE-MS is one of the techniques in this field but remains underappreciated because of issues such as compromised sensitivity and poor reproducibility. In this thesis, we proposed standardized protocols for CE-MS studies using a sheathless interface and applied them in the metabolic analysis of ultra-small biological samples, such as low numbers of HepG2 cells. Another CE-MS technique used in this thesis is the traditional sheath liquid CE-MS, and it was successfully used in the metabolic profiling of plasma samples. We also introduced CE-MS with both interfaces in the field of nanosciences with our efforts in revealing the adsorption characteristics of polar metabolites to the surface of nanomaterials. This work clearly demonstrates that CE-MS can be reliably performed for metabolomics studies with acceptable repeatability. The use of sheathless CE-MS interface enables us to have in-depth profiling for ultra-small samples, and may become a powerful tool in the emerging field of single-cell analysis. Show less
We showed that constitutive and inducible chemical and morphological defenses against Western flower thrips differ between tomato and chrysanthemum plants. Furthermore, we demonstrated that both... Show moreWe showed that constitutive and inducible chemical and morphological defenses against Western flower thrips differ between tomato and chrysanthemum plants. Furthermore, we demonstrated that both plant species respond differently to bacteria-derived defense elicitors, such as the phytotoxin coronatine. This highlights the plant species-specificity of these interactions and the possible limitation for the use of pathogen-associated molecular patterns to enhance the plant immune system. This study thus provides knowledge and novel strategies for Western flower thrips control. Yet, further comprehensive work is needed to evaluate the influence of these induction strategies on plant fitness. Show less
