Towards understanding the role of ‘silicon’ in life

Silicon is an essential trace element that is required for physiological bone growth and health. Though silicon has been shown to have an essential effect on mineralised tissues, current research is still lacking understanding of many aspects of the mechanism involved and further knowledge enhancement is needed to fulfil this research gap. Another area of silica science where understanding is relatively more developed is the study of living organisms such as bacteria and plants that deposit silica during a process called biosilicification though even here the chemistry of the silica phase is incompletely understood. The main aims of this PhD research were to focus on understanding the role of silicon in different organisms. An Optically Sectioned Planar Format Indicator Displacement Assay (O-IDA) was developed to study silica-biomolecule interactions. An analytical tool to map surface charge properties of silica in silicifying organisms (both non-living and living samples) was implemented. And, a study to understand the role of silicon in animals through a transcriptome evaluation method, RNA sequencing with evaluation of differential gene expression, was performed. A fluorophore, PDMPO (2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole), was utilised to develop O-IDA and to implement the analytical tool to map surface charge. The binding affinities of a number of small molecules with different functionalities (amino acids, a drug, a polyamine) and large biomolecules (7-mer peptides) were studied through O-IDA where ΔGads values ranging from −12.82 to −7.82 kcal mol−1 were obtained where Ibuprofen was best and peptide L7 (LDHSLHS) was the worst silica binder. Hence, O-IDA has potential to be used to screen silica binders. The implementation of the surface charge mapping tool allowed a proxy measure of silica chemistry/acidity through zeta potential estimation. On application to various silicifying organisms, an exemplary sample of the basal stem of Equisetum arvense cell wall showed a range of -25 to -33 mV zeta potential values which led to an estimation of varying silica particle sizes to up to 100 nm. An RNA transcriptome using an animal bone tissue enhanced the understanding of the mechanisms involved in utilising silicate from diet for bone health. The detected biological pathways demonstrated the role of silicon as anti-inflammatory (affected pathways; osteoclast differentiation, T cell differentiation, phagosome and cytokine cytokine receptor interaction) and anti-oxidative (affected pathways; glutathione metabolism and ribosome) on bone tissue which promote osteogenesis through possible non-genetic routes