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
The transition to electric vehicles (EVs) reduces vehicle emissions to combat climate change. EVs raise concerns regarding the production of lithium-ion batteries and related emissions; while... Show moreThe transition to electric vehicles (EVs) reduces vehicle emissions to combat climate change. EVs raise concerns regarding the production of lithium-ion batteries and related emissions; while batteries can also provide energy storage services for the electricity system. Here we use the material flow analysis method to quantify the future material demand for lithium-ion batteries and the prospective life cycle assessment method to quantify future emissions of battery production. Further combined with battery technology modelling, future energy storage potential of EV batteries is evaluated. Results show the demand for battery raw materials will increase by a factor of over 15 in the next three decades, which requires a drastic expansion of battery supply chains. The increasing utilization of renewable energy and improved mining technology of raw materials for battery production will result in a 50% decrease in emissions per lithium-ion battery production between 2020-2050. Renewable energy transition contributes largely to this emission reduction, but EV battery storage can provide short-term grid services for complementing variable renewable generation. EV batteries alone could satisfy short-term grid storage demand by as early as 2030. This research reveals environmental challenges and opportunities for EV batteries as well as options to improve EV battery sustainability. Show less
Parkinson's disease is the second most common neurodegenerative disease in the world. One of its symptoms is the loss of dopaminergic neurons in the substantia nigra pars compacta. A number of... Show moreParkinson's disease is the second most common neurodegenerative disease in the world. One of its symptoms is the loss of dopaminergic neurons in the substantia nigra pars compacta. A number of phenotypes, including the aggregation of misfolded proteins, mitochondrial dysfunction, and neuroinflammatory chemicals released by microglia and activated astrocytes, may all play a role in its pathogenesis.Due to the multisystemic nature of Parkinson's disease, novel tools for developing mechanistic models that simulate its pathogenic processes have been proposed. Furthermore, as the amount of information in biological databases grows and the cost of omics experiments decreases, methods for integrating different types of biological data have become essential for increasing the level of detail in mechanistic models of biological systems.Constraint-based modelling is a valuable tool in bioengineering and biomedicine. It is used to estimate the reaction flux in a metabolic network. The constraints represent essential characteristics of a biological system, including connectivity between metabolites and reactions, thermodynamics, maximum and minimum flux rates, and the steady-state.This thesis presents studies and tools for integrating various types of specific information to genome-scale models used in constraint-based modelling. In addition, is presented the iDopaNeuro default models, genome-scale models of a culture of dopaminergic neurons derived from induced pluripotent stem cells. Show less
In this thesis, we consider various (electro)chemical phenomena at surfaces and nanoparticles and their underlying atomistic processes, which we studied using first-principles methods such as... Show moreIn this thesis, we consider various (electro)chemical phenomena at surfaces and nanoparticles and their underlying atomistic processes, which we studied using first-principles methods such as density functional theory. These phenomena range from CO2 reduction to C2 and C3 species, through solvation of adsorbates on various surface features of late transition metals, to the impact of graphene on hydrogen evolution reaction, cathodic corrosion and surface oxidation of Pt. With our thermodynamic and kinetic calculations, we provide explanations for experimental observations by unraveling underlying phenomena, support novel computational methods and techniques, and propose new atomic structures that explain prior findings and provide inroads into future electrocatalytic research. Show less
In response to the shortage of nursing staff and the so-called refugee crisis in 2015, two residential homes invited first-generation immigrants with a refugee background to participate in a... Show moreIn response to the shortage of nursing staff and the so-called refugee crisis in 2015, two residential homes invited first-generation immigrants with a refugee background to participate in a project for nursing education, orientation and internships. Between 2015 and 2018, a group of ten immigrants started working in a Dutch residential home and a group of seventeen immigrants in the German home. This dissertation investigates the social processes when these newcomers start working with the established staff, as well as the extent to which their mutual interactions and values of good care influence the enactment of geriatric care. Using ethnographic observations (305 hours), in-depth interviews (44) and six focus groups (24), the established care workers and immigrants were followed in both homes. The empirical data shows that institutional constraints, such as staff shortage, the imposition of professional norms, gossip used as a ‘weapon of the weak’, mutual suspicions of indifference, and collective images of ‘us’ versus ‘them’ affected the enactment of geriatric care. Their habitus stimulated them to tinker among each other as well as with different, sometimes conflicting, values of good care. However, both groups shared the feeling of ignorance by management, a pain of not mattering. Show less
Drug induced organ toxicity is the main problem of the drug development and drug usage in the clinic. The liver and kidneys are the most sensitive organs towards drug induced toxicity. The liver... Show moreDrug induced organ toxicity is the main problem of the drug development and drug usage in the clinic. The liver and kidneys are the most sensitive organs towards drug induced toxicity. The liver neutralizes xenobiotic to which human are exposed to while the kidneys remove waste products from the blood. Due to their detoxification function, these organs are continuously exposed to high amount of toxicants leading to potential injury. Investigating the molecular and cellular mechanisms contributing to drug-induced liver injury (DILI) and drug-induced kidney injury (DIKI) will open new avenues that can help in the prediction of induced organ injury caused by drugs as well as other xenobiotics.In this thesis, we mapped the dynamics of cellular stress responses in the liver and kidneys upon the exposure of a set of model compounds in order to gain a more holistic insight in DILI and DIKI. We conducted multiple extensive in vitro and in vivo studies to understand the dynamics of these cellular responses and determined the translation of our findings from in vitro to in vivo. Transcriptomics analysis was central in the research which was complemented with other methodologies, such as reporter cell assay, immunohistochemistry, to unravel the mechanisms of drug-induced organ toxicity in both liver and kidney. Show less
Facioscapulohumeral muscular dystrophy (FSHD) is caused by incomplete epigenetic repression of the D4Z4 repeat resulting in misexpression of the repeat-encoded DUX4 gene in skeletal muscle. Two... Show moreFacioscapulohumeral muscular dystrophy (FSHD) is caused by incomplete epigenetic repression of the D4Z4 repeat resulting in misexpression of the repeat-encoded DUX4 gene in skeletal muscle. Two mechanisms are known to drive this D4Z4 epigenetic dysregulation: a contraction of the D4Z4 repeat or mutations in DNMT3B or SMCHD1, both epigenetic regulators of the repeat that are responsible for the establishment or maintenance of the repeat’s epigenetic repressive state in somatic cells. However, the aforementioned (epi)genetic changes lead to FSHD only if the individual also has a disease-permissive D4Z4 allele which allows for stable DUX4 expression in skeletal muscle. This disease permissivity of D4Z4 alleles has been attributed to the presence of a DUX4 polyadenylation signal adjacent to the D4Z4 repeat which is used for transcription termination. Despite knowing the root cause of FSHD, to date, there is no curative therapy available for FSHD and in some cases, the genetic etiology of the disease remains unknown. In this thesis, we identified a new FSHD disease gene called LRIF1 and performed its follow-up functional studies in human somatic cells and mouse embryonic stem cells. In addition, we also pursued a new targeted gene therapy for FSHD by employing CRISPR-based mutagenesis of the DUX4 polyadenylation signal. Show less
This thesis examines the normative dimensions of the acts that constitute international crimes. It offers a conceptualisation of the normative dimensions of these acts as processes of construction... Show moreThis thesis examines the normative dimensions of the acts that constitute international crimes. It offers a conceptualisation of the normative dimensions of these acts as processes of construction and meaning making. Using the crimes of attacks on cultural property, pillage, sexual violence and reproductive violence as case studies for analysis, the thesis develops an interdisciplinary methodological approach which centralises the narratives and discourses that emerge around particular crimes as central to how they are given normative content in practice. This analysis reveals a diverse, flexible and dynamic normative picture of these crimes, which demonstrates how their normative meanings are not natural or given, but are instead produced through an ongoing process of meaning making that takes place throughout the legal process in a continuum of cases. Understanding the normative dimensions of the acts that constitute international crimes in these terms not only exposes a diversity of interests that transcends their dominant characterisations as violations of basic security rights, but also uncovers the processes through which their normative foundations are constructed and transformed internally through practice. This thesis ultimately offers a dynamic, pluralist and socially constructed account of wrong in international criminal law, which recognises the relationship between criminal wrong and transformations in the wider social and political order, and contributes to developing a more granular understanding of the nature of the representational work that international criminal justice does in the world. Show less
It is well known that military deployment can lead to mental health problems in veterans, but the long-term impact is still unclear. This thesis discusses the results of the PRISMO-study, a large... Show moreIt is well known that military deployment can lead to mental health problems in veterans, but the long-term impact is still unclear. This thesis discusses the results of the PRISMO-study, a large cohort study in a group of Dutch Afghanistan veterans with a follow-up period of ten years. It shows that at ten years post-deployment, 8% of the cohort reported severe symptoms of posttraumatic stress disorder (PTSD). Agoraphobia, anxiety, depression, and hostility symptoms are also reported more frequently at ten years post-deployment compared to pre-deployment. Furthermore, this thesis demonstrates the large heterogeneity in PTSD symptom development among veterans. Of note is the delayed onset group that experienced increasing symptom levels between five and ten years post-deployment and did not show significant symptom reduction. The results from this thesis also show that various psychological factors, such as social support, and biological factors, such as DNA methylation, are associated with the development of PTSD or other mental health symptoms after deployment. Combining these factors in a prediction model for PTSD symptoms has not led to a useful screening instrument. It does, however, offer important leads for the identification of risk factors for PTSD and the development of intervention programs. Show less
We are living in an information era where the amount of image and video data increases exponentially. It is important to develop intelligent visual understanding systems to satisfy our need for... Show moreWe are living in an information era where the amount of image and video data increases exponentially. It is important to develop intelligent visual understanding systems to satisfy our need for searching information of interest. An important example of such a system that, with the current increasing concern for public security, is urgently required, is an automated person Re-Identification (ReID) system. This thesis mainly focuses on exploring ReID systems via deep learning methods. To enable ReID systems to meet the so-called open-world challenges, we explore three themes that are challenging yet practical in real application scenarios: lifelong learning, unsupervised domain adaptation and cross-modality challenge. Furthermore, this thesis provides numerous experiments and in-depth analysis, which can help motivate further research on the three research themes. Show less
Human skin equivalents (HSEs) are in vitro 3D-skin models that mimic many aspects of the native human skin (NHS) and can be a valuable tool. In this thesis, several (medium based) approaches have... Show moreHuman skin equivalents (HSEs) are in vitro 3D-skin models that mimic many aspects of the native human skin (NHS) and can be a valuable tool. In this thesis, several (medium based) approaches have been investigated to improve the barrier characteristics of this HSE to mimic that of NHS. Show less
Bone and joint disorders have an enormous personal- and societal impact. Diagnosis and treatment of these disorders are most efficient if targeted screening, accurate diagnosis, and targeted... Show moreBone and joint disorders have an enormous personal- and societal impact. Diagnosis and treatment of these disorders are most efficient if targeted screening, accurate diagnosis, and targeted treatment are available. To enable targeted screening, the population at risk must be well-defined, and categorized if required. Subsequently, screening- and diagnostic methods must have good, or excellent predictive value and finally, treatment must target the disease, thus spare healthy tissues and processes and thereby avoid adverse events.The aim of this thesis is to gain new insights about the diagnostic process- and treatment of pathological conditions of the bone and joints, namely male urological cancer-induced bone loss and inflammatory arthritis. Show less
This thesis focuses on the application of lipid-based nanomedicine in drug delivery, including small molecular antitumor drugs and biomacromolecules including mRNA, and evaluates their biological... Show moreThis thesis focuses on the application of lipid-based nanomedicine in drug delivery, including small molecular antitumor drugs and biomacromolecules including mRNA, and evaluates their biological performance. We have modified liposomes and LNPs with fusogenic coiled-coil peptides to enhance the drug/mRNA delivery efficiency (Chapter 2-4), and also investigated how the lipid composition of LNPs influences the immune response (Chapter 5). Show less
The largest genus within the Phyllanthaceae family is a group called Phyllanthus L. Recent studies have shown, that Phyllanthus is paraphyletic with the genera Glochidion, Breynia and Synostemon... Show moreThe largest genus within the Phyllanthaceae family is a group called Phyllanthus L. Recent studies have shown, that Phyllanthus is paraphyletic with the genera Glochidion, Breynia and Synostemon nested within it. In this thesis, I study the evolution and systematics of Phyllanthus and how to solve the apparent paraphyly. First we explore past morphological subgroups to come to a subdivision, which was tested using molecular phylogenetics. Several species of Phyllanthus are also used in traditional medicine and by utilizing the living collections of the Hortus botanicus Leiden, we tested for antibacterial and antifungal bioactivity. The phylogeny resulting from this study is used to study the historical biogeography and diversification of the tribe and to propose a new classification where Phyllanthus is separated into several smaller genera. Show less
To design the ideal water oxidation catalyst, understanding of the catalytic mechanism and decomposition pathways is essential. The aim of the research described in this thesis is to provide... Show moreTo design the ideal water oxidation catalyst, understanding of the catalytic mechanism and decomposition pathways is essential. The aim of the research described in this thesis is to provide mechanistic insight on the water oxidation reaction catalyzed by homogeneous electrocatalysts and topostulate design criteria for the ideal water oxidation catalyst. Show less
Our immune system is supposed to protect us from infections, but it can also attack our own tissues if not properly controlled. This can lead to autoimmune diseases like rheumatoid arthritis (RA).... Show moreOur immune system is supposed to protect us from infections, but it can also attack our own tissues if not properly controlled. This can lead to autoimmune diseases like rheumatoid arthritis (RA). People with RA have antibodies to the body’s own proteins (self), but it is not known how they arise. The data described in this thesis show that these antibodies cross-react with self-proteins carrying different post-translational modifications, suggesting that multiple proteins may be involved in the initial loss of the immune system’s ability to discriminate between self- and foreign-proteins. As another unique feature, these antibodies carry additional sugars at an unexpected site in the molecule. Our data show that these sugars (variable domain glycans) can prevent binding to potential self-proteins, affect complement activation, and set the threshold for immune B-cell activation. In addition, our data show that the abundance of these sugars increases toward disease onset and predicts the development of chronic, persistent disease or the chance of subsequent remission. Taken together, these sugars may help B cells to escape the tight control mechanism in our body that are in place to prevent the development autoimmunity. This new “sugar mechanism” could be beneficial for diagnosis and future treatment. Show less
Epithelial-mesenchymal plasticity (EMP) and tumor cell migration play an important role in cancer progression, and an improved understanding of the mechanisms underlying these concepts is essential... Show moreEpithelial-mesenchymal plasticity (EMP) and tumor cell migration play an important role in cancer progression, and an improved understanding of the mechanisms underlying these concepts is essential for developing new targeted approaches. In this thesis, we studied these mechanisms using mathematical and computational approaches.First, we summarized and reviewed previous computational approaches that have been used to decipher EMP regulation. We then created mathematical models to explore (1) how different regulatory networks can explain epithelial-mesenchymal transition (EMT) in different cell contexts, and (2) how EMP and immune regulation can interact to cause tumor immunoevasion.Next, we studied the role of cell density in migration characteristics of triple-negative breast cancer cell lines by using a combined experimental and computational approach. We show how clustering and pseudopodial dynamics, potentially influenced by EMT-related factors, can alter the migratory behavior of these cell lines.Jointly, our work has shown that computational modeling can be used to test hypotheses based on experimental data, and generate testable hypotheses, making it a valuable addition to wet-lab experiments. Importantly, we identified mechanisms related to potential therapeutic targets, hopefully leading to improved targeted therapies and reduced cancer mortality. Show less
Cardiovascular healthcare is continuously evolving. Biochemical,-and surgical discoveries from past decades improved patient survival to outstanding heights. However, with an ever growing aging... Show moreCardiovascular healthcare is continuously evolving. Biochemical,-and surgical discoveries from past decades improved patient survival to outstanding heights. However, with an ever growing aging patient population and scarce resources, cardiovascular healthcare has to become more value-driven. Value Based Healthcare (VBHC) research is becoming increasingly important in that matter, which questions the relevance (i.e. value) of contemporary evidence-based interventions in relation to patients’ health status and personal preferences.It is difficult to obtain a comprehensive view of ‘valuable outcome’ for both patients and professionals as individual and subjective perspectives on the value of treatment are ever present. This thesis presents a methodological ‘toolbox’ to assess clinical cardiovascular care, unravel the ‘value of care’ for its stakeholders and develop it further in a meaningful way. Patients were assessed on a national level using claims data, which enables insight into care patterns and helps unravel if that which is perceived as valuable by the professional (i.e. guideline evidence), is truly applied in daily practice. Second, cardiovascular care on a local hospital level is qualitatively assessed via Human Factors (HF) science, a novelty in clinical research. In line with VBHC, it helps to understand how the patient and professional experience healthcare within a certain context. Show less
To advance drug discovery for cardiovascular patients, new pre-clinical models and quantification methods are needed to improve clinical predictivity. This thesis aims to explore several approaches... Show moreTo advance drug discovery for cardiovascular patients, new pre-clinical models and quantification methods are needed to improve clinical predictivity. This thesis aims to explore several approaches to bringing new solutions for disease modeling which reflect the human heart. Firstly, we review the current status of the Heart-on-chip (HoC) field and the cutting edge (bio)materials which enable more physiologically relevant culture methods for stem cell-derived cardiomyocytes (hiPSC-CMs). Then, we use a polydimethylsiloxane chip to culture hiPSC-CM, hiPSC-endothelial cells and hiPSC-cardiac fibroblasts combined with a microfluidic flow-channel to mimic physiological blood flow. Subsequently, we fabricated and tested a platform for 3D-culture of heart tissues designed ultimately for medium- to high-throughput drug screening. Moreover, we create a stand-alone software application for automated and robust analysis of in vitro models of striated muscle. We have used a previously published mathematical tool and applied it to static, live, 2D, 3D, hiPSC-CM, primary CM and skeletal muscle, providing evidence of its versatility. This was successfully applied to study hiPSC-CMs from patients with hypertrophic cardiomyopathy and carrying a heterozygous mutation in the MYBPC3 gene. Finally, we discuss the results and conclusions presented in this thesis, and provide an outlook of future research directions in this exciting field. Show less
