To address global biodiversity loss, national and subnational actions are imperative. Malaysia is a biodiversity hotspot with a federal system of government. The literature points to gaps in governance of biodiversity. The aim of this Ph.D. was to understand issues on biodiversity governance in Peninsular Malaysia, with the following objectives: (i) identify conservation priorities; (ii) review and assess the effect of federalism; and (iii) review and analyse the governance of protected areas (PA). This research identified conservation priorities defined by multi stakeholder participation, deploying a workshop and snowball survey approach. This generated a ranked list of 35 priority issues under seven themes, with high degree of agreement among stakeholders. The prioritisation exercise and the literature revealed current federal system of governance posed biodiversity governance challenges. Building on postcolonial and political ecology frameworks, theoretical and empirical qualitative research was carried out on the impact of federalism on biodiversity governance; and the governance of protected areas. I concluded that that states did not want to give up their land for conservation as it is their source of revenue in the absence of incentives for conservation from federal government due to the dichotomy in the federal constitution. Governance of PAs is compromised with different laws operating at both state and federal level, shortage of manpower and funds. This study provides a menu of recommendation options which highlights constitutional, institutional, financial and legal reforms to strengthen governance of biodiversity. In terms of contribution, this study took an innovative approach to identify conservation priorities in Peninsular Malaysia while applying postcolonial and political ecology theory to examine biodiversity governance in a federalised developing country. I highlight the potential of this study to influence policy space and if the proposed reforms are implemented, Peninsular Malaysia has all the ingredients in terms of economic capability, sizeable forest cover and low population density for the effective conservation of biodiversity.

In mammals, adult neurogenesis in the subventricular zone (SVZ) of the lateral ventricle and the subgranular zone (SGZ) of the dentate gyrus produces neurons contribute to learning and memory functions. However, more recent evidence suggests that neurogenesis may also happen in other regions of the brain such as striatum, spinal cord, and hypothalamus (Reviewed in (Riddle, 2007)). It is important to determine if neurogenesis also occurs in non-neurogenic regions of the adult brain such as CB and 3V. This would be of importance for potential future therapeutic applications for brain repair, and also to help understand the fundamental function of the different regions of the adult brain. This thesis tested the hypothesis that neural stem cells (NSCs) are present in the mature cerebellum (CB) and the lining of the third ventricle (3V). Based on this hypothesis, one of the major goals of this thesis was to isolate and characterise NSCs isolated from CB and 3V of adult mouse and weather they could generate neuronal and glial cells in vitro. Immunohistochemical analysis for NSC-associated markers revealed that the mature CB in mouse, chick, and primates contains a population exhibiting NSCs characteristics. Results showed that this population was the Bergmann glial located in the Purkinje cell layer (PCL) of the cerebellar cortex, which express Sox1, Sox2, Sox9, BLBP, and GFAP in a similar pattern. Some of these markers are common for neural stem/progenitor cells or radial glial cells in other brain regions. Observations in the 3V revealed that tanycytes lining the ependymal layer also express NSC and astrocytic markers. Moreover, cells were isolated from the CB and 3V of adult GFP+/-Sox1 mice and tested their ability to form neurospheres, their response to EGF and FGF-2, and their differentiation into neurons, astrocytes, and oligodendrocytes. CB and 3V-isolated cells were found to grow in culture, expand, and differentiate into neuronal and glial phenotypes. It was also observed that CB-derived NSCs could survive and differentiate into neuronal and glial lineages after long term removal of either EGF or FGF-2, although cultures were optimal in the presence of both mitogens. We also observed that cells cultured in either EGF or FGF-2 for 3 weeks had different effects on both CB and LV cells in terms of cell fate specification toward neuronal and glial lineages. This finding suggests the heterogeneity of NSCs population in the adult brain. The identification and mapping of the different NSC populations present in the adult brain offers some important opportunities for regenerative medicine approaches. In order to better characterise the cerebellar population of cells identified above, adult Bergmann glial was observed in a mouse model of cerebellar damage caused by the loss of PCs in pcd5J mutant mice. Calbindin immunostaining at different time-points showed that PC degeneration was visible at P21, then progressed rapidly and became considerable at P26 (nearly 70-80% loss), and by P100 all PCs were lost. Immunohistochemical analysis on sections of CB from pcd and wild type counterparts revealed an increase in Bergmann glia cells at P100 as well as the upregulation of GFAP expression. GFAP+ BG exhibited thick disorganised processes in the molecular layer (ML) at P100 in the mutant mice, with some cell bodies mispositioned in the ML, and significant shrinkage of both ML and internal granular layer (IGL). The increase in the number of Sox1+, Sox2+, and Sox9+ BG in 3 month old mutant mice was not visible at earlier time points analysed. These findings indicate that the PCs loss in pcd5J mice precede and possibly trigger the increase in the Sox1+, Sox2+ and Sox9+ cell population in the CB. Our results also showed that no proliferation activity was observed in the pcd mouse CB at revealed by Ki67 staining, suggesting that the CB microenvironment might not be permissive for neurogenesis even after PCs loss. In vitro isolation of NSCs the CB of P21 pcd mice was carried out, and although cultures appear slower to establish than wild type controls these cells did form neurospheres and express NSC markers. Further characterisation of CB-derived NSCs from pcd mice and their growth and differentiation potential will help better understand the dynamics and possible therapeutic targets for neurodegenerative disorders affecting the CB. The characterisation of CB and 3V derived NSCs from adult mouse CB has provided important information regarding their differences with NSCs derived from neurogenic region in the brain, the lateral ventricle (LV).

Genomic elements such as proteins or genes are the basic unit of the genome and involved in the functioning of every biological process. Predicting, therefore, the function of these genomic elements is the first step in the understanding of functioning of plants under various stress conditions. To date, various types of computational methods have been developed to predict the function of a given protein sequence. The recent increase in the development of a number of methods has created its own set of problems leading to difficulty in applying on newly sequenced genomes especially non-model crops. Due to these reasons, the immediate requirement for development of sophisticated computational methods to predict the function of a given protein sequence is raised. This thesis presents three novel computational tools developed based on transfer learning algorithms to predict the function of a given protein sequence and these tools are: 1) TL-RBPPred, for prediction of RNA-binding proteins, outperformed SPOT-Seq, RNApred, RBPPred and BLASTp on HumanSet (AUC of 0.977), YeastSet (AUC of 0.971), ArabidopsisSet (AUC of 0.972) and GlymaxSet (AUC of 0.97); 2) TL-DBPPred, for prediction of DNA-binding proteins, outperformed DNABP, enDNA-Prot, iDNA-Prot, nDNAProt, iDNA-Prot|Dis, DNAbinder and BLASTp on an testing dataset (AUC of 0.988); and 3) TL-TFPred, for prediction of transcription factors, outperformed PlantTFcat, iTAK and BLASTp on testing dataset (AUC of 0.999) in terms of prediction accuracy. Further, both TL-RBPPred and TL-DBPPred were tested on the transcriptome of the non-model crop, Bambara groundnut (Vigna subterranea (L.) Verdc.), to identify RNA-binding and DNA-binding proteins, respectively. The results obtained from these tests indicated that these two methods outperformed in terms of prediction accuracy (AUC) as compared to existing current state-of-the art tools such as SPOT-Seq, RBPPred, iDNA-Prot and iDNA-Prot|Dis. Based on the performance, the developed methods will be useful in predicting the function of given protein sequences (DNA, RNA-binding and transcription factor) of model species as well as non-model crops.

The formation of embryoid bodies has long been utilized to initiate differentiation of embryonic stem cells in vitro. The embryoid body provides an effective means of recapitulating early stages during embryogenesis and formation of the three germ layers. Current methodology for embryoid formation is extensive but exhibits a lack of standardisation and coherence. Here is shown a 3D culure system for controlled embryonic stem cell aggregation via a non-cytotoxic cell surface modification and cell-cell cross-linking. Embryoid body formation was found to be a complex relationship between embryonic stem cell aggregation, proliferation, death, cluster agglomeration, extracellular matrix deposition and structural reorganisation. Engineered embryoid bodies formed more rapidly and were significantly larger than those in control samples. Embryoid body characterisation revealed a layered internal structure resulting from poor nutrient and gaseous diffusion and consequent core necrosis after ≥ 5 days in suspension culture. Immuno-labelling and PCR amplification analysis of Brachyury, Nestin, Gata-4 and Oct-4 showed differentiation of mesoderm, ectoderm and endoderm on the embryoid body surface and internal undifferentiated cells, respectively. Engineering appeared to enhance mesoderm differentiation, a progenitor of the osteogenic lineage. Embryoid bodies in settled culture spread outwards to form a plateau of collagen matrix which was later mineralized through differentiated osteoblast function. Quantification through Alizarin Red stained bone nodules and alkaline phosphatase activity demonstrated osteogenic differentiation enhancement within engineered samples. Dex-loaded poly-(lactic co-glycolic) acid polymer microparticles were found to be an effective method for delivery of osteo-inductive factors to internal undifferentiated embryonic stem cells within the embryoid bodies. These findings show that the proposed 3D culture system provides reliable and repeatable methodology for the controlled formation of embryoid bodies which exhibit enhanced osteogenic differentiation. It is hoped that these engineered embryoid bodies could be used to efficiently generate homogeneous bone tissue for clinical application.

On the Tibetan Plateau, there is a long history of animal farming practices. Although Tibetan pastoralism had been successful in the past to support the population, the problems of increasing demand and impact in the face of more scarce resources and global climate change are challenging pastoralists. The problem is even more pronounced in the Tibetan Plateau’s unique natural and socioeconomic conditions. Based on the perception of the problem, the Chinese government started a reform programme aiming at changing the nomadic practices in Tibet. Tibet today is in transition, not only in terms of pastoralism, but also that of culture, of institutions, and of economy, nevertheless the transition in pastoralism as a livelihood and source of income will have significant implications. The usefulness of the resilience concept in examining a complex system’s innovation, development, disturbance and reorganisation makes them suitable tools in the study of historical changes and the future of Tibet, as the area is under human management, and subject to the influence of changes in nature and external policies. In this study remote sensing and mathematical modelling approaches are used to assess ecological resilience in the region. The advantage of remote sensing allows the researcher to observe and analyse a large area as well as recent changes, and to examine the spatial pattern of these changes. The model simulates the dynamics of the grassland system given the current condition. The key functions linked to the system’s resilience can be examined in this model and provide information on the system’s sustainability. The simulation shows that the nomadic pastoralism system can better adapt to disturbances of known intensity and frequency than the sedentary style. However, the trend of climate change and population increase may require a change of organisation and practices for the system to be sustained.

Cytochrome family P450 4A encode a major group of enzymes which are involved in the mechanism of peroxisome proliferation in rodents. Induction of CYP4A expression by peroxisome proliferators is due to transcriptional activation, mediated via the peroxisome proliferator activated receptor alpha. Cyp4a enzymes catalyse the w-hydroxylation of fatty acids and eicosanoids, and it has been suggested they thereby play a pivotal role in blood pressure regulation. Murine Cyp4a10, Cyp4a14 and Cyp4a12 genes have been reported by Bell et al (1993) and Heng, et al (1997). There is contradictory evidence in the literature concerning the expression of lauric acid hydroxylase (LAH) and Cyp4a-related protein in mouse liver and kidney. We have previously shown that Cyp4a12 is expressed at high level in a male-specific fashion in liver and kidney of mouse (Bell et al 1993). However, various workers have reported the presence, or absence, of Cyp4a proteins, or LAH, in male mouse liver. Work by Hiratsuka et al (1996) demonstrate that ddY mice show a male specific expression of LAH and Cyp4a-related protein in the liver, while other strains Balb/c and C57BL/6 exhibit no sex difference in neither enzyme or protein. In the kidney, ddY, Balb/c and C57BL/6 all show sexual dimorphism in the expression of both LAH and Cyp4a related protein. The aim of this project was to characterise the expression of mouse Cyp4a12 and resolve the conflicting results in the literature. Findings demonstrate that there is a male specific expression of Cyp4a12 in male liver and kidney. The data differs from Hiratsuka et al in that their findings present no sex difference in Balb/c and C57BL/6 expression of Cyp4a proteins. Hiratsuka et al also determined that in the kidney of ddY, Balb/c and C57BL/6 there is no sex difference in expression of neither enzyme or protein. Data here agrees with these findings and suggests that the sexual dimorphism exhibited by the LAH and Cyp4a related protein in the kidney is due to constitutive expression of Cyp4a12. Thus it appears that there is till a discrepancy between the Cyp4a12 hepatic expression pattern presented here and that of the enzyme and protein determined by Hiratsuka et al. An explanation may infer that the LAH and Cyp4a-related protein measured by Hiratsuka et al is not only Cyp4a12 but also another member of the Cyp4a family. Further work is required to establish what Cyp4a is expressed predominately in the female. Work by Henderson et al (1994) supports the case that this Cyp4a candidate may be Cyp4a10. Continuing studies will clarify the expression pattern of the Cyp4a and also investigate the mechanism of regulation of the Cyp4a family genes and the expression of male specific genes.

Solid surfaces that spend long periods of time in aquatic environments are susceptible to the accumulation of marine fouling organisms and this phenomenon is known as marine biofouling. This is a natural process which has significant impacts on marine industries. Research to develop new antifouling solutions focuses on the development of non-toxic solutions that can deter biofouling. A non-toxic antifouling approach that has gained interest in recent years is to modify the surface’s structure to disrupt organism settlement (Kirschner and Brennan 2012; Magin et al. 2010; Myan et al. 2013). Many studies determined that uniform arrays of single layered, micro-topographies are effective at deterring the initial settlement of fouling organisms. In contrast, most studies that tested uniform arrays of single layered, macro-topographies concluded that these topographies are not suitable for antifouling applications. Both single layered, micro-topographies and single layered, macro-topographies were determined to have limitations at mitigating biofouling. This resulted in the interest to develop hierarchical topographies. Hierarchical topographies are surfaces that consist of features that are varied in size and shape. It was suggested that the diverse nature of hierarchical topographies might be able to deter biofouling from a wider array of organisms. This research fabricated and tested a wide range of topographies (uniform, non-uniform, micro, macro, hierarchical, etc.) in a field study. A field study was preferred over lab experiments because results will reflect the antifouling efficacy of the surfaces in a marine environment. These results will indicate the topographies’ viability and future potential for industrial applications. Antifouling efficiency was evaluated by measuring fouling resistance (during the field test) and fouling removal (after the field test) of all topographies. Physical attributes (pattern geometry, pattern size, and surface roughness) of topographies were characterised with Scanning Electron Microscopy (SEM) and Laser Scanning Confocal Microscopy (LSCM). Statistical analysis was carried out to evaluate the significance of the topographies’ physical attributes on the antifouling efficiency of the topographies. The research hypotheses predicted that topography size, geometry and surface roughness will affect the topographies’ ability to resist biofouling. All patterned surfaces were predicted to have a higher resistance to biofouling in comparison to un-patterned control surfaces (i.e. smooth surfaces). The possibility that hierarchical topographies would have better fouling resistance properties than micro-topographies was considered as well. Hierarchical topographies and micro-topographies were also hypothesised to demonstrate better resistance to biofouling than macro-topographies. Topographies with straight ridges and hierarchical shapes were predicted to be more fouling resistant than sandpaper surfaces. Topographies with average roughness (RSa) that were less than 100µm were assumed to exhibit better antifouling efficacy in comparison to topographies with average roughness greater than 100µm. Results showed that pattern size and pattern geometry affects the antifouling efficiency of topographies. Unexpectedly, surface roughness did not show strong correlations with the fouling resistance of the topographies. With the exception of Sandpaper 50 and Sandpaper 1mm samples, all topographies were more fouling resistant than the control samples (i.e. smooth surfaces). Among the 16 topographies, sandpaper 1mm samples demonstrated the worst defence against biofouling. The mean total fouling coverage on these samples after 10 weeks of tests was 98.7%. Straight, single layer ridges demonstrated the best resistance to total fouling during the field test. Barnacle and polychaete settlement trends were affected by the size and geometry of single layer, single sized topographies. After 10 weeks, the mean total fouling coverage on these ridges was only 37.5%. The field test also showed that the topography with the best prolonged resistance to fouling was the 1mm straight ridges. The combination of structured surfaces and a low modulus material is likely to have contributed to the fouling removal properties of all topographies. Lastly, results from the field study also showed that hierarchical topographies do not necessarily have better antifouling properties than single layer, single sized topographies. The field study demonstrated that the physical attributes of topographies contributed to their antifouling efficiency. It has been suggested that the physical characteristics of topographies induces hydrodynamic variations that affects the surfaces’ antifouling properties. However, it is difficult to observe these changes in lab experiments or through field studies because these variations take place at a very small scale. Recent research has applied Computational Fluid Dynamics (CFD) to numerically simulate and analyse flow characteristics in the surrounding areas of antifouling topographies. As a continuation from the field study, the next study in this research applied CFD to analyse flow characteristics over several topographies that were tested in the field study. This was to determine if the settlement trends exhibited by organisms in the field study could have been affected by hydrodynamic variations that were induced by the presence of the topographies. The CFD analysis showed that rotational vortices formed between topography patterns. These vortices could have aided in the accumulation of biofouling material on all topographies during the field test. The analysis also showed that the topographies’ resistance to fouling could be attributed to high shear stress and strain rate zones at the peaks of the topographies. Comparisons between CFD and field test results indicate that higher stresses and strain rate zones around the topographies are likely to lead to a surface’s better resistance to marine biofouling. This is likely because high shear stress and strain rate zones could have disrupted organism motility and made the surface less conducive for settlement.

The human polycore minisatellite probes 33.6 and 33.15 developed by Prof. Alec Jeffreys and colleagues have been shown to detect hypervariable minisatellites in many taxonomically dispersed species. The mRNA derivatives of these two probes, pSPT19.6 and pSPT18.15, have here been used to probe the genomes of four species currently maintained in captivity. The wild populations of these species, Rothschild's mynah, the Rodrigues fruit bat, the British Merlin and the New Zealand falcon, are threatened with extinction to varying degrees. By using the technique of DNA fingerprinting, it has been possible to assess the levels of minisatellite variation remaining in these stocks, to confirm or refute the parent/offspring allocations made within, and in the case of Rothschild's mynah, to demonstrate that at least two of the founders of the stock were closely related. In addition, it has been possible to show that there is a significant positive relationship between the similarity coefficient calculated between two adults and the inbreeding coefficient calculated for their offspring.

This thesis is divided into two main chapters. The first chapter relates to studies undertaken to gain insights into the mechanism of action on liver growth by the peroxisome proliferator (PP) ciprofibrate and the chemical cyproterone acetate (CPA) in rodents. Peroxisome proliferators are a class of chemicals that have diverse effects in rats and mice including increased DNA synthesis and peroxisome proliferation. Peroxisome proliferators include herbicides, plasticisers, hypolipidemic drugs and synthetic fatty acids. These chemicals act through ligand activation of nuclear membrane receptors termed ‘peroxisome-proliferator-activated receptors’ (PPARs), which ultimately activate nuclear transcription. PPs induce a cellular process in liver characterised by dramatic increases in the size and number of peroxisomes, correlated with both hepatocyte hypertrophy (i.e. an increase in the size of liver cells) and hyperplasia (i.e. an increase in the number of liver cells during replicative DNA synthesis and cell division). However, the mechanism of action of increased hepatocyte growth is not currently understood. Understanding the mechanism by which increased liver growth is induced by PPs in rodents will hopefully provide insights into how natural liver growth occurs and might have medical benefits for human health if the mechanism of PP toxicity can be overcome. Knowledge gained from the mechanism of PP activation might also then be applied to other chemical carcinogens. Therefore, firstly the mode of action of the peroxisome proliferator ciprofibrate was investigated. Previous work had indicated that two successive doses of ciprofibrate treatment separated by 24hr led to two rounds of liver cell replication, but it was not clear whether the same or different hepatocytes were involved in this growth response. To study this phenomenon, histochemical experimental work was undertaken to assess whether the same or different hepatocyte cells were stained during the two rounds of cell division following ciprofibrate treatment. The two histochemical stains used were EdU and BrdU, which are both base-pair analogues that stain nuclei undergoing DNA replication. It was hypothesized that if EdU was used to stain cells at 24 hr and then BrdU at 48 hr, that if the same cells were responding to ciprofibrate treatment then cells would be co-stained by both dyes, whereas if different cells were responding then there would be little or no double staining of hepatocyte cells. It was found that different cells were stained by the two dyes, indicating that ciprofibrate treatment was targeting different cells. Secondly, the mode of action of the carcinogen cyproterone acetate (CPA) on hepatocyte growth was investigated. Previous work had investigated the effects of CPA on hepatocyte growth in male and female rats and had suggested differences in response between the sexes. In the present study female rats were treated with CPA, to assess whether differences in labelling indices were present compared to previous male results. Female F-344/NHsd rats, aged 14-15 weeks, were treated with CPA and then injected with BrdU at 22 hr, and rats were killed 2 hr later. Results confirmed that the female rats had a considerably higher labelling index (50%) compared to male rats (6%). This suggested that upregulation of gene expression in female rats was much higher, which might provide an exciting opportunity to identify sets of genes involved in carcinogenic responses. To investigate whether there was any overlap between genes induced by ciprofibrate and CPA treatment a preliminary study was designed where female rats were gavaged with CPA and then killed 3 hr later. Real-time PCR analysis of a small number of target genes showed no consistent changes in expression between the present CPA and previous ciprofibrate treatment results, suggesting largely different modes of action of these chemicals. The second chapter of this thesis relates to studies undertaken to gain insights into neurodegenerative disorders. Neurodegeneration is a gradual loss of structure or function of neurons, which may lead to neuronal death. Neurodegenerative diseases including Parkinson’s, Alzheimer’s, and Huntington’s occur as a result of neurodegenerative changes. Several studies have suggested that PPARs have critical roles in reducing the brain inflammation which in turn might have a significant effect on reducing the fundamental processes involved. Work was performed using a mouse model of dementia with lewy body disease (Psmc1fl/fl; CaMKIIα-Cre) to represent neurodegenerative disorder, and involved parallel, in vivo and in vitro investigations to determine whether the development of neurodegenerative diseases occurs at the same rate in vitro and in vivo i.e. a comparison of rapidity of pathogenicity progression was made. Astrocytes were used to track the development of disease, given that these play a key role in neurological disorders, using an immunohistochemistry approach. A PPAR-γ analogue was used to investigate the role of PPARs in reducing astrocytes proliferation. To optimise the validity of the results, four controls were used including an antagonist T0070907 which abolished the effect of rosiglitazone treatment alone. The results on the effect of PPAR-γ agonist and rosiglitazone, after a week of treatment, showed that the PPAR-γ agonist inhibited astrocytes activation in both the cortex and hippocampus of the mutant mice organotypic slice culture. The number of GFAP +ve astrocytes was significantly decreased in mutant mice with 100 µM rosiglitazone in both areas, whereas 50 µM rosiglitazone showed a decrease in the number of astrocytes in the cortex, but the effect was less in the region of the hippocampus. This finding suggests that PPs such as rosiglitazone may have potential uses as therapeutic drugs to inhibit neurodegeneration.

In the absence of telomerase, Saccharomyces cerevisiae telomeres erode leading to senescence. Rare cells can survive after this stage as they can elongate their telomeres utilizing homologous recombination. Two different types of survivors can be easily distinguished by Southern blot. Type I survivor cells, elongate the telomere by amplifying Y elements and require RAD51, RAD54, RAD55 and RAD57 for establishment. Type II survivors elongate their telomere by amplifying TG1-3 repeats, however, they require the following genes to be established: RAD50, MRE11 and XRS2, RAD59, SGS1 and KU80 in some cases. Both types require the gene RAD52. In this study several candidate genes were deleted individually in diploid type II survivor strains. The main aim of this work was to see if these genes were required for type II telomere maintenance. Most of these genes are not required for type II telomere maintenance at least until ~150 generations after deleting these genes. The exceptions were KU80 and RPB9. Ku80Δ strains switched to a new survivor type that is similar to type I and continued for the long term. RPB9 was required for two independent type II survivor strains to survive, whereas the third type II strain did not require this gene at ~150 generations after deleting the gene. After many generations (~ 350), this strain switched to type I. At long term propagation (~500 generations) after deletion of the candidate genes, all type II strains displayed telomere shortening until the propagation was stopped. However, Rad50Δ strains switched to type I after long term. Finally, the absence of the candidate genes did not affect the sensitivity of type II survivor strains to temperature. On the other hand, type II survivor strains with some genes deleted displayed sensitivity to UV.