Computational Modelling of the Coastal Protection Function of Salt Marshes with Flexible Vegetation Cover

Salt marshes are intertidal coastal wetlands that are typically found in sheltered locations such as estuaries. They exhibit a diverse vegetation cover with flexible grasses and rigid shrubs. This vegetation provides coastal protection by attenuat-ing currents and waves. Unlike traditional hard defences, they offer co-benefits by stabilising shorelines and enhancing natural habitats. However, it has remained unclear how salt marshes with a flexible vegetation cover contribute to coastal protection under storms with surge and wave components.In this thesis, I have developed a new coupled current-wave-vegetation model which includes the effect of vegetation flexibility on wave attenuation. The wave-vegetation model builds on novel laboratory experiments using artificial vegeta-tion in the Swansea University Wave Flume, where wave damping, water velocity fields, and plant motion were measured simultaneously for the first time. A new work factor is introduced to explicitly account for vegetation flexibility in compu-tational models. Furthermore, a momentum sink term parameterisation is found to best resemble current-vegetation interactions. The advanced coupled model is successfully applied to simulate flood risk in the Taf Estuary under six contrast-ing vegetation scenarios.My results highlight how the vegetation cover affects the coastal protection pro-vided by salt marshes. All modelled vegetation species constrain flood currents to the main estuary channel and damp incoming waves. Although flexible grasses are 50% less effective in wave damping than rigid shrubs in the Taf Estuary. The wave conditions, wind conditions and local topography further affect the protec-tion provided. Additionally, rigid species can amplify orbital velocities above the canopy by inducing wave-averaged currents, but flexible species do not.It is recommended that the biomechanical properties of vegetation, including the flexibility, are included when modelling the coastal protection by salt marshes. My new computational modelling framework provides evidence to support the continuing uptake of salt marshes as sustainable coastal defences

Improving flexibility in substrate metabolism:a pharmacological and lifestyle approach

Overweight increases the risk of cancer, non-alcoholic fatty liver disease, cardiovascular disease, and the development of diabetes type 2. These metabolic diseases are characterised by less pronounced carbohydrate and fat oxidation fluctuations over 24 hours. This thesis focuses on a better understanding of 24-hour substrate metabolism and investigates whether pharmacological and lifestyle interventions that stimulate a more pronounced overnight fast can improve metabolic health. First of all, it was demonstrated that treatment with a pharmacological compound, an SGLT2 inhibitor, increased 24-hour and nocturnal fat oxidation and reduced carbohydrate oxidation in individuals with prediabetes. Second, it was demonstrated that acutely prolonging the overnight fast by 6.5 hours in individuals with non-alcoholic fatty liver disease and age matched controls, resulted in higher nocturnal fat oxidation and lower nocturnal carbohydrate oxidation. Third, repeatedly prolonging the overnight fast in individuals with type 2 diabetes lowered 24-hour carbohydrate oxidation, but did not result in higher fat oxidation. However, fasting and 24-hour glucose levels improved. In conclusion, it was shown that individuals with overweight or obesity have a disturbed 24-hour substrate metabolism, and that this can be improved by pharmacological and lifestyle interventions, eliciting a more pronounced overnight fast

A microbial take on bird life:Illuminating environmental context of bird microbiota dynamics and immune function

In a world dominated by invisible bacteria and other microorganisms, birds themselves are mobile ecosystems for microorganisms; every bird with its own microbiota. With a variety of functions, microbiota contribute to health and functioning of the bird in its environment. But should the microbiota be considered a trait of the individual bird or does the microbiota rather represent a reflection of the bird’s microbial environment? The answer to this question has fundamental merit to evolutionary ecology. Understanding the developmental process of microbiota and its symbiosis with the host, and understanding how the microbiota is maintained, insight can be gained into how symbiosis with microbiota affects health and disease and evolutionary success of failure. This thesis demonstrates that the effect of the microbial environment on the microbiota of larks in the Netherlands is substantial. Subsequent comparison with the microbiota of larks from the desert of Saudi Arabia and tropical grasslands of Kenia underscores the importance of the microbial environment to microbiota variation, also at a large geographical scale. By manipulating the microbial environment of zebra finches, not only the swift changes of bird microbiota upon a changing environment were apparent, also the antibody concentration in blood changed. The immune system can thus respond fast and flexibly to the microbial environment. The acquired experience can also be transferred to the next generation through maternal antibody deposition to the eggs. In conclusion, the microbial environment is of ecological relevance for a bird’s physiology and microbiota dynamics

DNA repair pathways in radiation induced cellular damage: a molecular approach

__Abstract__ DNA damage, especially double-strand breaks, can be induced by endogenous or exogenous darnaging agents, such as ionizing radiation. Repair of DNA damage is very important in maintaining genomic stability. Incorrect repair may lead to chromosomal aberrations, translocations and deletions. Consequently, incorrect repair might result in oncogenic transformation of cells, which can lead to the development of cancer. Thus, unreaveling the pathways of double-strand break repair is essential in understanding the genetic interactions that lead to ancogen ie changes. Biochemica I studies have provided insight into the molecular mechanisms by which various proteins involved in repair of double-strand breaks perfarm these essential tasks. The next step ahead is analyzing the relationship between the individual biochemical activities of doublestrand break repair proteins and their coordinated action in the context of the living cell. This thesis describes the cellular behaviour and cooperation of the mammalian double-strand break repair genes Rad51, Rad52, Rad54 and Mre11 after induction of DNA damage by ionizing radiation. Furthermore, the possible use for a predictive assay that measures individual radiosensitivity in humans, ba