No description available.

Methanococcus jannaschii is a thermophilic methane producing archaebacterium. In this organism genes encoding the aspartate transcarbamoylase (ATCase) catalytic (PyrB) and regulatory (PyrI) polypeptides were found. Unlike Escherichia coli where the above genes are expressed from a biscistronic operon the two genes in M. jannaschii are separated by 200-kb stretch of genome. Previous researchers have not been able to show regulation of the M. jannaschii enzyme by the nucleotide effectors ATP, CTP and UTP. In this research project we have genetically manipulated the M. jannaschii pyrI gene and have been able to assemble a 310 kDa E. coli like enzyme. By using the second methionine in the sequence we have shown that the enzyme from this organism can assemble into a 310 kDa enzyme and that this enzyme is activated by ATP, CTP and inhibited by UTP. Thus strongly suggesting that the second methionine is the real start of the gene. The regulation of the biosynthetic pathway in Pseudomoans aeruginosa has previously been impossible to study due to the lack of CTP synthase (pyrG) mutants. By incorporating a functional uridine (cytidine) kinase gene from E. coli it has been possible to isolate a pyrG mutant. In this novel mutant we have been able to independently manipulate the nucleotide pools and study its effects on the enzymes in the biosynthetic pathway. The enzyme asapartate transcarbamoylase was repressed 5-fold when exogenous uridine was high and cytidine was low. The enzyme dihydroorotate was repressed 9-fold when uridine was high. These results suggest that a uridine compound may be the primary repressing metabolite for the enzymes encoded by pyrB and pyrC. This is the first study to be done with the proper necessary mutants in the biosynthetic pathway of P aeruginosa. In the past it has been impossible to vary the internal UTP and CTP pools in this organism.

Plants contain a host of secondary metabolites that may be of dietary use to man. A comprehensive approach to plant-based nutrition would include investigating all aspects of a nutrient, from creation through storage and consumption. Here, experiments address each of these facets for a group of important antioxidant and pigment compounds, the carotenoids. The carotenoid biosynthetic pathway regulatory mechanisms leading to lycopene accumulation are well defined in the model fruit, tomato. Those leading to accumulation of other carotenoids and flesh colors, however, are poorly understood. The variety of flesh colors available in watermelon fruit (red, orange, salmon yellow, and canary yellow) makes it an ideal candidate for investigating the regulation of the full pathway. Carotenoid accumulation was measured in ten watermelon varieties, representing the four flesh colors and three ploidy levels, throughout fruit maturation. It was found that the putative regulatory mechanisms controlling lycopene accumulation in red-fleshed fruit may be applied in a generalized fashion to each flesh color in respect to the major carotenoid accumulated at maturity. Additionally, triploid varieties were generally found to have higher accumulation levels than diploids, and tetraploids were intermediate to both. In addition to total carotenoid content, many factors are important in determining perceived benefit. Several of these factors involve components of the food matrix, cellular and subcellular species-specific characteristics of the food which act as barriers to nutrient release. Cell size, cell wall, and chromoplast (the carotenoid storage organelle) characteristics were observed in nine fruits and vegetables using light and transmission electron microscopy. Watermelon, tomato, and melon have the largest cells. Sweet potato, butternut squash, carrot, and mango have the most fibrous cell walls; mango and papaya additionally had the thickest walls. Chromoplast globular, tubular, crystalline, and membranous substructures were described for each food. These food matrix factors may be related to differences in carotenoid bioaccessibility between food sources. An in vitro digestion experiment was used to determine carotenoid bioaccessibility for each of these foods. Per serving, grapefruit yielded the most lycopene while carrot gave the most ?-carotene, ?-carotene, lutein, and phytoene, and mango proved a good source of violaxanthin.

No description available.

The number of people living with diabetes worldwide is continually increasing. The majority of these people will eventually die of cardiovascular disease, the major underlying cause of which is atherosclerosis. Despite the efforts of many researchers, gaps in our knowledge still exist regarding the molecular mechanism(s) linking the two conditions. Current data suggests that the hexosamine biosynthetic pathway (HBP) may have a role in the development of hyperglycemia-accelerated atherosclerosis. About 2-3% of glucose entering a cell is diverted into this pathway where it is modified through a series of reactions to yield the end product, UDP-N-acetylglucosamine (UDP-GlcNAc); a substrate for both N- and O-linked glycosylation of various molecules. N-linked glycosylation occurs in the endoplasmic reticulum (ER) and is an important process in the maintenance of ER homeostasis. We hypothesized that a dysregulation in the HBP can ultimately trigger ER stress – an event associated with the development of atherosclerosis. We have established a method that allows us to monitor levels of UDP-GlcNAc both in cultured cells and mouse tissues through high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS). Using this technique, we’ve shown that both glucosamine supplementation and overexpression of the rate limiting enzyme of the HBP, GFAT, in cultured cells results in elevated UDP-GlcNAc levels. Furthermore, glucosamine was shown to trigger ER stress. In contrast, three GFAT inhibitors that were previously identified in a high throughput screen were shown to decrease UDP-GlcNAc levels and one inhibitor, dehydroiso-β-lapachone, appears to prevent ER stress induction. Finally, we use complementary methods to show that the HBP is augmented in the livers of hyperglycemic mice. This process may play a role in the accelerated development of atherosclerosis. Together, these results provide further insight into the role of the HBP in diabetic atherosclerosis and the established methods provide a platform for the further investigation of this mechanism. / Thesis / Master of Science (MSc)

Thesis (MSc (Physiological Sciences))--University of Stellenbosch, 2009. / Aims and Background: According to the World Health Organization type 2 diabetes will constitute a major global burden of disease within the next few decades. In agreement, reports show that rapid urbanization and lifestyle changes in South Africa are major factors responsible for these projections. Therefore, any perturbations that alter the regulatory steps that control myocardial glucose uptake by the cardiac-enrich glucose transporter, GLUT4, will lead in the development of diabetic cardiomyopathy and cardiac hypertrophy. Although considerable efforts are been put into unraveling molecular mechanisms underlying this process, less is known regarding the spatio-temporal regulation of GLUT4. In light of this, our specific aim was to establish in vitro fluorescence microscopy- and flow cytometry-based models for visualization and assessment of myocardial GLUT4 translocation using H9c2 cardiac-derived myoblasts. After successful establishment of our in vitro-based model for myocardial GLUT4 translocation, our second aim was to determine the role of the hexosamine biosynthetic pathway (HBP) in this process. Here, we employed HBP modulators to alter flux and subsequently evaluate its effect on myocardial GLUT4 translocation. To further strengthen our hypothesis, we also investigated the role of the HBP in hearts of an in vivo type 2 diabetes mouse model. Hypothesis: We hypothesize that increased flux through the HBP impairs myocardial GLUT4 translocation by greater O-linked glycosylation of the insulin signaling pathway, ultimately leading to myocardial insulin resistance. Methods: Rat cardiac-derived H9c2 myoblasts were cultured until ~ 80-90 % confluent for 3 days and thereafter subcultured in Lab-Tek chamber slides (~ 15, 000 cells per well) for 24 hours. Cells were then serum starved for 3 hours by insulin administration of 100 nM for 0, 5 and 30 minutes, respectively. We employed a method to quantify the relative proportion of GLUT4 at the sarcolemma using immunofluorescence microscopy- and flow cytometry-based models for visualization and assessment of myocardial GLUT4 translocation. Using these methods we investigated the role HBP have during GLUT4 translocation. The HBP were then activated through the following: a) high glucose and glutamine concentrations; b) low glucose and glucosamine stimulation; and c) over-expression of the HBP rate- limiting enzyme, i.e. GFAT. Subsequently, cardiac-derived myoblasts were fixed and probed for ~ 24 hours with antibodies specific for intracellular- and membrane-bound GLUT4, anti-myc GLUT4 (9E10) and O-GlcNAc. To assess GLUT4 translocation and O-GlcNAcylation we employed the following secondary antibodies: FITC Green for intracellular-bound GLUT4; and b) Texas Red for membrane-bound GLUT4 (immunofluorescence microscopy) and Phycoerythrin for flow cytometry-based model. Cells were thereafter viewed by multi-dimension imaging using an inverted system microscope (Olympus IX81) and a BD FACS Aria cell sorter for flow cytometric analysis. We also assessed HBP in an in vivo context by probing heart tissue - from insulin resistant db/db mice - with a GFAT monoclonal antibody. Results: The db/db mouse represents an ideal model to confirm our hypothesis in an in vivo context. In agreement, our preliminary results show increased GFAT expression versus heterozygous db/+ controls. Our in vitro model show myocardial GLUT4 translocation at 5 minute peak response when H9c2 cardiac-derived myoblasts were stimulated with 100 nM insulin, and GLUT4 vesicles return to normal after longer insulin stimulatory times (10, 15 and 30 minutes. Myocardial Glut4 v translocation was impaired when cells were stimulated with 100 nM wortmannin. Our transfection based model (immunofluorescence microscopy- and flow cytometry-based models) confirms 5 minute peak response under real time conditions. High glucose concentration (25 mM glucose), glucosamine concentrations (2.5 mM, 5 mM, and 10 mM) and over-expression of GFAT led to an impairment of myocardial GLUT4 translocation. Employment of an HBP activator (50 μM PUGNAc) also caused impairment of myocardial GLUT4 translocation. Myocardial GLUT4 translocation was restored when cells were treated with an HBP inhibitor (40 μM DON). High glucose concentrations (25 mM glucose), glucosamine concentrations (2.5 mM, 5 mM, and 10 mM) and over-expression of GFAT resulted in an increase in O-GlcNAcylation. HBP activation (50 μM PUGNAc) showed an increase in O-GlcNAcylation, while administration of 40 μM DON reversed this effect. Discussion and conclusion: We successfully established an in vitro experimental system to assay myocardial GLUT4 translocation. Our data show that dysregulated flux through the HBP impairs myocardial GLUT4 translocation. It is likely that the HBP becomes dysregulated during the pre-diabetic/early diabetic state and that O-GlcNAcylation of members of the insulin signaling pathway occurs during this stage. This will lead to myocardial insulin resistance, and in the long term, will contribute to the onset of the diabetic cardiomyopathy. Investigations to find unique inhibitors of this maladaptive pathway should therefore result in the development of novel therapeutic agents that will lead to a reduction in the growing global burden of disease for type 2 diabetes and associated cardiovascular diseases.

The thesis deals with the creation of the biosynthetic pathways of selected alkaloids of opium poppy. Then is following the design primers for selected genes and optimization of PCR reaction of these genes for amplification and sequencing of the longest fragments. The PCR reaction was optimized for the 7OMT, TNMT and CODM genes. These genes are involved in biosynthetic pathways of morphine, codeine, papaverine, noscapine and sanguinarine. Each gene was split in half. The primers were designed separately for each half of the gene. Altogether were designed 13 pairs primers. 5 pairs primers were optimized by gradient PCR and gel electrophoresis. These primers were used for sequencing analysis.

Triacylglycerols (TAGs) are stored in variable amounts (1-90 % by dry weight) in seed and non-seed tissues of various plant species. We analyzed the deep transcriptional profiling data obtained for eight species (brassica, castor, nasturtium, euonymus, oil palm, date palm, and avocado), to gain insights into tissue- and species-specific regulation and biosynthesis of TAG in plants. In all tissues analyzed, an increased expression was noted for genes mostly associated with fatty acid biosynthesis in plastid, but much less increase in those for TAG assembly in the endoplasmic reticulum. In most oil-rich tissues, transcripts associated with hexose metabolism in plastid also showed higher expression, relative to cytosol; this is likely associated with the need for high pyruvate flux directed toward plastid fatty acid synthesis. Additionally, expression of WRINKLED1 transcription factor, a regulatory element associated with oil biosynthesis in seed and non-seed tissues of monocot and dicot plants, was observed in most oil-rich tissues. Transcripts for other regulatory factors that are candidates associated with TAG synthesis in seed and non-seed tissues are also identified. In summary, our studies point to distinctive modes of regulation of fatty acid biosynthesis and TAG assembly that are conserved in both seed and non-seed oil-rich plants.

The isoprenoid biosynthetic pathway (IBP) has been highly implicated in a number of cellular malignancies, including proliferation, invasion, and migration. Epidemiological studies have found clinically relevant inhibitors of the IBP, such as the statin family and nitrogenous bisphosphonates, reduce the risk of prostate cancer advancement. In vitro work has implicated statin's and nitrogenous bisphosphonate's inhibition of GGPP and protein geranylgeranylation as the components responsible for their reduction of prostate cancer progression. However, their depletion of nearly all isoprenoid intermediates as well as their organ specificities make understanding the specific role of protein geranylgeranylation in prostate cancer metastasis impossible. Consequently, we have developed a novel library of seven alkyl bisphosphonate ethers found to potently reduce GGDPS with little to no activity against the related FDPS enzyme. Inhibition of GGDPS in three human prostate cancer cell lines reduced GGPP and protein geranylgeranylation without affecting protein farnesylation, translating into a reduction in cell migration and invasion. Interestingly, the GGDPS inhibitors reduced protein geranylgeranylation at lower concentrations in the highly metastatic PC3 cell line as compared to the less metastatic LNCaP and 22Rv1 cell lines. Additionally, the PC3 cell line was found to have higher levels of endogenous IBP intermediates as compared to the less metastatic cells. Translation in vivo using two murine models of human prostate cancer metastasis found a reduction in soft tissue tumor burden that corresponded to a biochemical reduction in protein geranylgeranylation. In conclusion, selective reduction of GGPP and protein geranylgeranylation was sufficient to reduce the metastatic potential of prostate cancer in vitro and in vivo.

Natural products have long furnished medical science playing a significant role in drug discovery and development. Their importance notwithstanding, it is estimated that less than 1% of microorganisms can be cultivated from environmental sources using standard laboratory techniques. It is therefore necessary to develop biochemical and genetic techniques to access these uncultivable genomes. Here as a point of departure toward this goal, two cDNA libraries of two microorganisms were constructed along with five fosmid libraries with DNA isolated from marine environmental samples. We describe the construction of cDNA libraries from marine microbial species and detail experiments to exploit these libraries for their natural product biosynthetic pathways and other metabolic enzymes they harbor. However, no useful biosynthetic pathways were detected within the cDNA libraries. Genetic selection by complementation was additionally explored as a method to identify and localize biosynthetic gene clusters within marine microbial DNA libraries. Genetic selection is a fast and economic method which utilizes selection of a part of a pathway to represent the presence of an entire pathway for the complementation of known mutant strains. We describe genetic selection to localize biotin biosynthetic pathways of Hon6 (Chromohalobacter sp.) as a proof of principle experiment for the identification and localization of biosynthetic pathways in general. Instead of developing purification methods or manipulating cultivation conditions, large fragments of non-culturable bacterial genomes can be cloned and expressed using recombinant DNA technology. A strong transcriptional promoter to control high-level gene expression is required in recombinant expression plasmids. We aimed to develop new tools to control gene expression through the use of riboswitches. Riboswitches are metabolite-sensing ribonucleic acid (RNA) elements that possess the remarkable ability to control gene expression. The thiamine pyrophosphate (TPP) riboswitch system was chosen as it will enable use of E. coli as a suitable host strain. This system is particularly attractive because it has one of the simplest structures among the riboswitches elucidated to date. The use of the TPP riboswitch will also enable modulation of pathway gene expression by varying the TPP coccentration as many gene products are toxic. The violacein gene cluster from Chromobacterium violaceum was selected and placed under the control of this riboswitch. We describe modulation of heterologous gene expression by the ThiC/Riboswitch and detail experiments to investigate the expression and manipulation of the gene cluster under various promoters.