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Direct cell reprogramming is a rapidly growing field that has challenged traditional concepts of cellular identity. The expression of Neurogenin 2 (NGN2) results in rapid reprogramming of human pluripotent stem cells (PSCs) into functional excitatory neurons. My lab has previously demonstrated that gene targeting the components of a Tet-On system overexpressing NGN2 into two separate safe harbour sites overcome gene silencing and results in optimised transgene expression in hiPSCs (Opti-Ox), and consequently yields highly homogenous cultures of neurons within less than four days. The mechanisms that mediate this remarkable cellular metamorphosis however remain poorly understood. To explore this, I first sought to establish a protocol for long-term culture of electrophysiologically functional NGN2 induced neurons (iNs). This was achieved by co-culturing with primary rat-derived glial cells, enriched for astrocytes. iNs demonstrated functional activity around two weeks post-induction and by three weeks, formed networks of synchronous bursts that were mediated by glutamatergic AMPA-receptors. Based on these phenotypical hallmarks, I designed a time course-based genomic analysis that investigated the transcriptional and chromatin accessibility states of cells undergoing NGN2 reprogramming. Bulk RNA and ATAC-sequencing were performed at Day 0, 6h, 12h, Day 1, 36h, Day 2, Day 3, Day 4, Day 14 and Day 21 post-NGN2 induction. I also performed a scRNA-seq of the same time points, except for 6- and 36-hours post-induction, to investigate any heterogeneity in the time course and complement findings from the bulk RNA-seq. In order to differentiate direct from indirect NGN2 down-stream effectors, ChIP-seq of NGN2 binding acquired on day 1 after induction was subsequently overlaid with bulk-seq data. In addition, to study the genome-wide effects of astrocyte-enriched rat glia, I performed the same assays on neurons co-cultured with glia at Day 4, 14 and 21. Together, they revealed rapid transcriptional and accessibility changes induced by NGN2 within 6 hours of reprogramming. The subsequent events show a stark similarity to the familiar stages of neurogenesis found in development or conventional differentiation protocols - shutting down of non-neuronal networks, in this case pluripotency, establishment of neuronal commitment in an NSC-like stage by Day 1 post-induction, cell cycle exit by Day 3 or Day 4 and subsequent onset of neuronal differentiation, followed by neuronal maturation. Up until now, this entire process was believed to be a highly homogenous occurrence, but findings from the scRNAseq analysis showed that in addition to glutamatergic neurons, our NGN2 iNeurons are made up of two additional types of neurons: cholinergic neurons with a visceral motor phenotype and neurons with a hybrid profile of cholinergic and glutamatergic transcription. Comparison with neurons co-cultured with glia found an enrichment for synaptic genes and ontologies. Specifically, there was an enrichment for neuronal activity regulated genes in the post-synaptic compartment. Candidate transcription factors crucial to these processes and the states described above were identified from the transcriptional and epigenomic datasets. It is likely that some of these factors could potentially be crucial regulators of neuronal differentiation and function, not only in this protocol, but in development as well. Therefore, one major aim for the future would be to further explore the role these genes play in NGN2 reprogramming through gene knockdown or overexpression experiments along with investigation of their genomic binding sites. Ultimately, this could also lead to the discovery of new reprogramming strategies for producing neurons with enhanced maturity and functionality without the need of human or rodent glia. By uncovering broad, yet essential neuronal processes such as neuronal fate commitment and maturation, the dataset I have generated can be used as a useful resource for studying these processes and designing relevant disease models using this simple, yet robust and efficient protocol for generating functional excitatory human neurons.

The overarching aim of this thesis was to explore how vegetation spp. influence potent nitrous oxide (N2O) production and reduction to harmless dinitrogen (N2) in the soil. In the rhizosphere, organic carbon (C) exuded from plant roots (e.g. rhizodeposits), and recalcitrant soil organic matter (OM) is transformed during catabolic processes to fuel most heterotrophic organisms including in soil denitrification. C is known to drive soil denitrification, but knowledge on whether the more active microbial community would select for C derived from plant roots against soil OM pool is limited. Experiments were conducted targeting vegetation with distinct traits from two land use scenarios. In a glasshouse experiment, two rice cultivars were grown in two agricultural soils of contrasting soil OM contents with C and N stable isotopes applied at three growth stages to quantify plant-derived C influence on N2O production and reduction processes. The relationship between plant-derived C and nitrate reducers' N2O and N2 was generally positive but were stronger during flowering and maturity growth stages especially in low OM soil. The 15N-N2O/(N2O+N2) product ratio was low (< 0.10), indicating a high nitrate reducing condition and was associated with high plant-derived C input when N availability was low due to N demand during flowering and maturity stage. Also, N2O production was lowered in low OM soil, but the N2O reduction to N2 was enhanced in high OM soil when planted with the late-flowering and high yielding cultivar. In the girdling experiment, two tropical trees spp. from different genera were girdled, and the soil was treated with N stable isotope. Girdling of the two trees were conducted to stop the C transfer from photosynthesis to root by removing a ring-section of the phloem. The 15N-N2O/(N2O+N2) product ratio was also low (< 0.10) for the girdling experiment indicating a high nitrate reducing condition. A positive relationship was observed between CO2 emissions and nitrate reducers' N2O production when trees were not girdled. However, the N2O production was lowered when the tree C flow for fast-growing pioneer spp. was cut off while girdling did not impact N2O production for the old-growth tree genera. Overall, it was demonstrated that plant direct and indirect influence on N2O production and reduction to N2 varied between crop/trees, growth strategies/stages and the level of soil OM-C and -N. The information obtained from this study is crucial for the development of strategies to mitigate N2O emissions through soil OM management and selection of plant species or cultivars in rice cultivation and understanding the impact of tropical forest disturbance (i.e. girdling) on N cycle.

Islamic banking deposits are fundamentally structured in a different way than the conventional banking deposits. Each type of Islamic banking deposits, such as savings, demand, and timed deposits, is devised using the approved Shari’ah contracts such as qard, wadiah, murabahah, and mudarabah. These contracts are opposed to the conventional concepts, as they are based on the concept of a ‘lender-borrower’ relationship. In addition, the Shari’ah-approved contracts are unique as they feature a different nature of risk and return. This is especially the case for mudarabah contracts (henceforth referred to as profit-sharing contracts). The uniqueness of profit-sharing contracts in deposit products has been given due recognition in theory and also in practice, as most of the Islamic banks in Malaysia offered this product. In addition, the unique features and characteristics of profit-sharing based deposit accounts are also highlighted in the prudential standards issued by prominent regulatory bodies such as AAOIFI and IFSB which, have been adopted by the Bank Negara Malaysia (Central Bank of Malaysia). Nevertheless, it is argued by many Islamic banks practitioners, especially in Malaysia, that the concept of profit-sharing in deposits products is not practical in reality, because the depositors do not behave according to, nor accept the principles that have been laid down in the Shari’ah. Thus it is argued that both the depositors and the Islamic bankers have treated the product similar to any other conventional banking deposits products. The main aim of this study, hence, is to explore and examine the level of awareness, knowledge, perceptions, and attitude of the Islamic banking depositors in Malaysia towards characteristics of profit-sharing deposits accounts in accordance with the fundamental Shari’ah principles but also the regulations prevailing. In addition, this research also attempts to explore the significant determinant factors that encourage the depositors to engage with Islamic banking deposits accounts in general and profit-sharing deposits accounts in particular. In fulfilling the aim of the study, primary data collection research was adopted through a survey questionnaire technique. The questionnaires were distributed to eight Islamic banks representing various types of Islamic banks in Kuala Lumpur and Selangor. The questionnaire asked various pertinent questions, which intended to elicit the depositors’ opinions, perceptions, and attitudes towards the unique characteristics of profit-sharing contract as specified in Shari’ah muamalah principles. The characteristics among others are: (i) concept of uncertain deposits returns; (ii) concept of non-guarantee for the deposits; (iii) concept of profit equalization reserve. A total 649 of the returned questionnaires were complete and fit for analysis purpose. The data were analysed using various statistical analysis techniques ranging from simple frequency distribution analysis to the more advanced analyses such as non-parametric statistical analysis, factor analysis, and logistic regression. In general, the results of the study show that the level of awareness of the need to have Islamic banking deposits accounts because of religious reasons is considered as high among the Malaysian depositors. Nevertheless, the results also indicate that a high level of awareness is not being translated into a high level of understanding concerning the objectives of the products which are structured in accordance to the Shari’ah-compliant contracts. This can be seen in the major findings of this study: the characteristics of profit-sharing contracts, which arguably are the most desirable Shari’ah-compliant contracts, are not acceptable to the depositors. This indirectly implies that they are still strongly influenced by the nature of conventional banking products. In addition, the logistics regression results further proved that related factors (‘financial services’ and ‘income’) emerged as the main determinants in creating demand for profit-sharing deposits accounts. The results of the research should draw the attention of the Islamic bankers and also the regulators to finding ways for improving the level of understanding among the depositors. However, the critical successful factor in educating the depositors is highly dependent on the level of knowledge exhibited by the Islamic bankers themselves, which can be a real concern as highlighted by the findings of this study.