>Magister Scientiae - MSc / Research on natural products and medicinal plants has been conducted more with each passing year due to the great interest in isolating bioactive compounds and secondary metabolites from natural products such as plants, fungi, and many other naturally occurring products. To our knowledge, the Uromycladium tepperianum MacAlpine fungus has not been studied in depth before thus, its organic characterization was unknown, but related species have been studied, and these have shown compounds that may be used as medicine and as health benefits. Crude and macerated extracts of the Uromycladium tepperianum fungus have been fractionized using various chromatographic techniques such as solvent-solvent extraction followed by dry column chromatography to achieve the required separations. Thirty-nine compounds have been isolated from the hexane(n-hex) extract, Ethylacetate (EtOAc) extract, and n-butanol (BuOH) extract, and they belong to the following groups, steroids, terpenoids, amino-acids, flavonoids, alkaloids, phenolics, fatty-acids, flavones, and others.

>Magister Scientiae - MSc / Marine invertebrate associated (MIA) bacteria are an important source of bioactive secondary metabolites with the potential to address the current anti-microbial resistance crisis experienced globally. Secondary metabolites (SM) have historically yielded several compounds with pharmaceutical applications such as anti-viral, anti-microbial, anti-cancer, anti-inflammatory and anti-parasitic. This study aimed to use bioassay and genomic approaches in the identification of MIA bacteria isolated from South African marine invertebrates as a source of bioactive compounds and the characterisation of the produced SMs using analytical techniques. A total of 23 MIA bacteria were cultured under different conditions (one strain many compounds approach (OSMAC)) to evaluate their ability to produce anti-microbial compounds against a panel of indicator strains namely Escherichia coli 1699, Bacillus cereus ATCC10702, Pseudomonas putida ATCC12633, Mycobacterium aurum A+, Staphylococcus epidermidis ATCC14990, Aspergillus fumigatus MRC and Candida albicans NIOH.

n-Hexane and its metabolites are neurotoxic to animals and man. Studies have revealed a progressive neuropathy which affects the distal regions of motor and sensory peripheral nerves. This paper describes efforts to determine whether 2-hexanone or 2,5-hexanedione is more neurotoxic to rats when given in drinking water. Our results show that 2,5-hexanedione is more neurotoxic than 2-hexanone and that it first affects the distal axon. Concentrations of 20 mM produced no effects after 3 weeks but 40 mM increased distal latency after 2 weeks.

Tetrodotoxin (TTX) is a lethal neurotoxin isolated mainly from the organs of wild puffer fishes. Although the neurotoxicity mechanisms of TTX are well known, the TTX origin and the biosynthetic mechanisms inside its hosts remain unresolved. In recent decades, the numerous reports of TTX-producing bacteria strongly suggested its bacterial origin. However, this origin is currently being challenged by the low and inconsistent TTX productions in vitro by the previously reported TTX-producing bacteria. Culturable TTX-producing bacteria were frequently isolated and reported from the guts of TTX-bearing animals including puffer fishes, however, these bacteria were estimated to account for 0.1% of the total gut bacteria. Moreover, the identification and functions of the non-culturable gut bacteria participating in TTX biosynthesis have never been reported. I hypothesize that the puffer fish gut bacteria and the entire gut environment serve as a functional integrality responsible for TTX biosynthesis. In this study, 16S rRNA amplicon metagenomics pipeline was established to profile the entire gut bacterial structures of both toxic and non-toxic puffer fishes respectively. UniFrac based principal coordinate analysis showed that bacterial diversities were significantly different (P-value < 0.001) between the gut environments of toxic puffer fishes and the non-toxics. Vibrio and Cyanobacteria were identified as centralities of gut bacteria co-occurrence network in toxic puffer fishes, implying their key roles in TTX biosynthesis. The results of metagenome prediction and gene set enrichment indicated that arginine biosynthesis was significant enriched (P-value < 0.05) in the toxic group. To further investigate the roles of key bacteria and arginine biosynthesis in producing TTX, metabolomics pipeline was established along with 16S rRNA amplicon metagenomics to monitor the dynamics of metabolites and bacterial compositions in guts of toxic puffer fishes during their detoxification process. The average TTX concentrations in the liver after a 60-day culture (6.41 ± 3.00 µg/g) was found significantly lower (P-value < 0.01) than that of the same species from the wild (31.86 ± 22.20 µg/g). The relative abundance of Vibrio was found positively correlated with the liver TTX concentrations. With the increase of culture periods, the relative abundance of Vibrio and Cyanobacteria decreased. In addition, both the metabolites and functional genes in arginine biosynthesis metabolic pathway were found significantly down-regulated (P-value < 0.05). These results indicated that both Vibrio and Cyanobacteria bacterial symbionts participated in TTX biosynthesis using arginine as a potential precursor in the gut environment of toxic puffer fishes.

Esophageal cancer and lung cancer are among the most common cancers worldwide with millions of new cases annually. Esophageal cancer patients at an advanced stage suffer from a poor five-year survival rate. However, only fewer than 30% of esophageal cancer cases were diagnosed at an early stage. For lung cancer, malignant pleural effusion (MPE) is an important hallmark for late-stage patients with metastasis. However, other causes of pleural effusions including tuberculosis bring difficulties in the diagnosis of MPE. It is necessary to develop novel diagnostic biomarkers and elucidate the pathological mechanism of esophageal cancer and lung cancer. Metabolic reprogramming is an emerging hallmark of cancer. It has been clear that metabolites play a critical role in cancer development and impose vulnerabilities that could be targeted for cancer therapy. The overall objective of this study is to comprehensively characterize the metabolic dysregulation in esophageal cancer and lung cancer for biomarker discovery and pathological elucidation, by using liquid chromatography--mass spectrometry (LC-MS)-based metabolomics and lipidomics. Paired tumors and normal adjacent tissues from esophageal squamous-cell carcinoma (ESCC) patients were first analyzed through global metabolomic and lipidomic profiling. Tumors were clearly separated from the normal tissues based on the partial least-square discriminant analysis (PLS-DA) model (R2Y >0.85 and Q2Y >0.79 in metabolomic profiling and R2Y >0.70 and Q2Y >0.67 in lipidomic profiling). A preliminary list of 41 polar metabolites and 65 lipids were identified to be significantly perturbed in tumor tissues. Kynurenine, spermidine, citicoline, as well as several glucosylceramides and phosphatidylcholines (PC) showed excellent predictive potential with area under curve (AUC) values better than 0.95 in receiver operating characteristic (ROC) models. Major elevated metabolic pathways were polyamine biosynthesis, glycerophospholipid metabolism, methionine mechanism, arginine and proline mechanism, and kynurenine metabolism, suggesting active amino acid biosynthesis and lipid biosynthesis in ESCC. The potential biomarkers and dysregulated pathways discovered above in ESCC tissue was further validated using targeted metabolomic, lipidomic and proteomic profiling. Polyamine biosynthesis was found to be activated in ESCC through the overexpression of tumor promoting ornithine decarboxylase and spermidine/spermine synthases. Upregulated levels of S-adenosylmethionine and DNA (cytosine-5)-methyltransferase 1 implied DNA hypermethylation in ESCC. Elevated purines in tumors were generated through the overexpression of methylenetetrahydrofolate dehydrogenases. Active phospholipid biosynthesis in tumors was promoted by overexpression of choline transporters and synthase of citicoline, which may accelerate the tumor growth. Dysregulation of coenzyme A species with different fatty acyl chains showed the same trend as of phospholipids, implying the specific activation of relevant acyltransferases in the phospholipid remodeling pathway. Moreover, essential amino acids exhibited a higher upregulation trends in patients with high-grade tumor or with cancer recurrence. Collectively, this study revealed the detailed metabolic dysregulations in ESCC tumor tissues, discovered potential metabolite biomarkers and identified therapeutic targets of ESCC. In order to explore the clinical application of the discovered biomarkers, metabolomic and lipidomic profiling was further performed on ESCC plasma samples. Eight metabolites were found to be simultaneously upregulated in ESCC tumors and plasma samples, indicating their potential as tumor-derived plasma biomarkers. Among them, a panel of five tumor-derived plasma biomarkers consisting of arginine, acetylspermidine, methylguanosine, dimethylguanosine and cystine showed good diagnostic potential in the cross validation. These biomarkers are related with polyamine biosynthesis and purine metabolism, which are critical to support tumor growth. For lung cancer, MPE from lung adenocarcinoma patients were investigated by LC-MS/MS-based metabolomic and lipidomic profiling. In PLS-DA models, the MPE samples were clearly separated from benign pleural effusion samples from pulmonary tuberculosis patients. A group of 17 polar metabolites and 45 lipids were identified to be significantly perturbed in MPE. For diagnostic purposes, ether lipid biomarkers, including PCs, lyso-PCs and phosphatidylethanolamines, showed an excellent predictive ability with the highest AUC value of 0.953 in ROC models. Furthermore, downregulated ether lipids and upregulated oxidized polyunsaturated fatty acids in MPE reflected the elevated oxidative stress and peroxisome disorder in lung cancer patients, which offers deeper understanding in lung cancer pathology.

Tetrodotoxin (TTX) is a lethal neurotoxin isolated mainly from the organs of wild puffer fishes. Although the neurotoxicity mechanisms of TTX are well known, the TTX origin and the biosynthetic mechanisms inside its hosts remain unresolved. In recent decades, the numerous reports of TTX-producing bacteria strongly suggested its bacterial origin. However, this origin is currently being challenged by the low and inconsistent TTX productions in vitro by the previously reported TTX-producing bacteria. Culturable TTX-producing bacteria were frequently isolated and reported from the guts of TTX-bearing animals including puffer fishes, however, these bacteria were estimated to account for 0.1% of the total gut bacteria. Moreover, the identification and functions of the non-culturable gut bacteria participating in TTX biosynthesis have never been reported. I hypothesize that the puffer fish gut bacteria and the entire gut environment serve as a functional integrality responsible for TTX biosynthesis. In this study, 16S rRNA amplicon metagenomics pipeline was established to profile the entire gut bacterial structures of both toxic and non-toxic puffer fishes respectively. UniFrac based principal coordinate analysis showed that bacterial diversities were significantly different (P-value < 0.001) between the gut environments of toxic puffer fishes and the non-toxics. Vibrio and Cyanobacteria were identified as centralities of gut bacteria co-occurrence network in toxic puffer fishes, implying their key roles in TTX biosynthesis. The results of metagenome prediction and gene set enrichment indicated that arginine biosynthesis was significant enriched (P-value < 0.05) in the toxic group. To further investigate the roles of key bacteria and arginine biosynthesis in producing TTX, metabolomics pipeline was established along with 16S rRNA amplicon metagenomics to monitor the dynamics of metabolites and bacterial compositions in guts of toxic puffer fishes during their detoxification process. The average TTX concentrations in the liver after a 60-day culture (6.41 ± 3.00 µg/g) was found significantly lower (P-value < 0.01) than that of the same species from the wild (31.86 ± 22.20 µg/g). The relative abundance of Vibrio was found positively correlated with the liver TTX concentrations. With the increase of culture periods, the relative abundance of Vibrio and Cyanobacteria decreased. In addition, both the metabolites and functional genes in arginine biosynthesis metabolic pathway were found significantly down-regulated (P-value < 0.05). These results indicated that both Vibrio and Cyanobacteria bacterial symbionts participated in TTX biosynthesis using arginine as a potential precursor in the gut environment of toxic puffer fishes.

Esophageal cancer and lung cancer are among the most common cancers worldwide with millions of new cases annually. Esophageal cancer patients at an advanced stage suffer from a poor five-year survival rate. However, only fewer than 30% of esophageal cancer cases were diagnosed at an early stage. For lung cancer, malignant pleural effusion (MPE) is an important hallmark for late-stage patients with metastasis. However, other causes of pleural effusions including tuberculosis bring difficulties in the diagnosis of MPE. It is necessary to develop novel diagnostic biomarkers and elucidate the pathological mechanism of esophageal cancer and lung cancer. Metabolic reprogramming is an emerging hallmark of cancer. It has been clear that metabolites play a critical role in cancer development and impose vulnerabilities that could be targeted for cancer therapy. The overall objective of this study is to comprehensively characterize the metabolic dysregulation in esophageal cancer and lung cancer for biomarker discovery and pathological elucidation, by using liquid chromatography--mass spectrometry (LC-MS)-based metabolomics and lipidomics. Paired tumors and normal adjacent tissues from esophageal squamous-cell carcinoma (ESCC) patients were first analyzed through global metabolomic and lipidomic profiling. Tumors were clearly separated from the normal tissues based on the partial least-square discriminant analysis (PLS-DA) model (R2Y >0.85 and Q2Y >0.79 in metabolomic profiling and R2Y >0.70 and Q2Y >0.67 in lipidomic profiling). A preliminary list of 41 polar metabolites and 65 lipids were identified to be significantly perturbed in tumor tissues. Kynurenine, spermidine, citicoline, as well as several glucosylceramides and phosphatidylcholines (PC) showed excellent predictive potential with area under curve (AUC) values better than 0.95 in receiver operating characteristic (ROC) models. Major elevated metabolic pathways were polyamine biosynthesis, glycerophospholipid metabolism, methionine mechanism, arginine and proline mechanism, and kynurenine metabolism, suggesting active amino acid biosynthesis and lipid biosynthesis in ESCC. The potential biomarkers and dysregulated pathways discovered above in ESCC tissue was further validated using targeted metabolomic, lipidomic and proteomic profiling. Polyamine biosynthesis was found to be activated in ESCC through the overexpression of tumor promoting ornithine decarboxylase and spermidine/spermine synthases. Upregulated levels of S-adenosylmethionine and DNA (cytosine-5)-methyltransferase 1 implied DNA hypermethylation in ESCC. Elevated purines in tumors were generated through the overexpression of methylenetetrahydrofolate dehydrogenases. Active phospholipid biosynthesis in tumors was promoted by overexpression of choline transporters and synthase of citicoline, which may accelerate the tumor growth. Dysregulation of coenzyme A species with different fatty acyl chains showed the same trend as of phospholipids, implying the specific activation of relevant acyltransferases in the phospholipid remodeling pathway. Moreover, essential amino acids exhibited a higher upregulation trends in patients with high-grade tumor or with cancer recurrence. Collectively, this study revealed the detailed metabolic dysregulations in ESCC tumor tissues, discovered potential metabolite biomarkers and identified therapeutic targets of ESCC. In order to explore the clinical application of the discovered biomarkers, metabolomic and lipidomic profiling was further performed on ESCC plasma samples. Eight metabolites were found to be simultaneously upregulated in ESCC tumors and plasma samples, indicating their potential as tumor-derived plasma biomarkers. Among them, a panel of five tumor-derived plasma biomarkers consisting of arginine, acetylspermidine, methylguanosine, dimethylguanosine and cystine showed good diagnostic potential in the cross validation. These biomarkers are related with polyamine biosynthesis and purine metabolism, which are critical to support tumor growth. For lung cancer, MPE from lung adenocarcinoma patients were investigated by LC-MS/MS-based metabolomic and lipidomic profiling. In PLS-DA models, the MPE samples were clearly separated from benign pleural effusion samples from pulmonary tuberculosis patients. A group of 17 polar metabolites and 45 lipids were identified to be significantly perturbed in MPE. For diagnostic purposes, ether lipid biomarkers, including PCs, lyso-PCs and phosphatidylethanolamines, showed an excellent predictive ability with the highest AUC value of 0.953 in ROC models. Furthermore, downregulated ether lipids and upregulated oxidized polyunsaturated fatty acids in MPE reflected the elevated oxidative stress and peroxisome disorder in lung cancer patients, which offers deeper understanding in lung cancer pathology.

There is currently much interest in the comparative health benefits of various meat products, including pasture-fed beef. However, little is known about the specific pasture-finishing diets (mixed forages, alfalfa, or sainfoin, compared to grain) on meat quality, consumer preferences, and human health. Thus, additional information is needed to better understand and develop new animal feeding regimes for optimum animal growth, meat flavor, and meat nutritional quality. The objective of the current study was to examine how animal diets, including secondary metabolites in the diet, affect meat chemical characteristics, meat quality, and nutritional value. In study 1 (Chapter 3), grain- vs. pasture-fed beef rib steaks were evaluated. Ribs from pasture-fed animals had a much lower fat content (P < 0.01), which was its main positive nutritional attribute. Pasture-fed beef had more (P < 0.05) omega-3 polyunsaturated fatty acids (PUFAs) and conjugated linoleic acid (CLA) than grain-fed beef, but was only a moderately good source of PUFA, compared to salmon. Pasture-fed beef had higher antioxidant capacity and lower measures of oxidation (P < 0.05). Pasture and grain diets influenced the volatile profile of cooked meat. Flavor descriptors barny, gamey, and grassy were associated with pasture feeding, and were uniquely shown in this study to be positively correlated with specific aroma volatiles benzaldehyde, toluene, dimethyl sulfone, 3- heptanone, 2-ethyl-1-hexanol, and hexadecanoic acid methyl ester (P < 0.05). In study 2 (Chapter 4), the effects of legume pasture-finishing of beef cattle on meat quality were evaluated, comparing alfalfa pasture (containing saponins) versus sainfoin pasture (containing tannins). No strong differences (P > 0.05) were found between the two legume diets in all meat characteristics, indicating that sainfoin was similar to alfalfa as a cattle forage. Similar (P > 0.05) low TBA values after 12 d of storage at 2 °C were obtained from both diets, comparable to pasture-fed beef from study 1. This verified the prolonged retail shelf life benefit of forage-fed beef, compared to grain-fed beef. In study 3 (Chapter 5), lambs fed four different diets, plain/control (P), tanninsrich diet (T), saponins-rich diet (S), or choice of them (C), were evaluated on metabolomics profiles using GC/MS technique. Forty metabolites were detected (30 named and 10 unknown). A principal component analysis (PCA) plot showed a clear separation of P, T, and S diet treatments while the C diet was overlapped with S and P diets, indicating that S or P diets were preferred while the T diet was avoided. In summary, the effects of ruminant diets on meat characteristics depended on the type and concentration of plant secondary compounds (PSC), especially the PSC levels contained in the pastures.

For many years, substitutes for butterfat have been the subject of much controversy. Their acceptance as being nutritionally equal to butterfat has often been question. The importance of this problem lies primarily in its economic and nutritional significance. A recent study of pulic attitudes toward dairy products conducted by Alfred Politz Research, Inc. for the American Dairy Association, shows that 48.4 per cent of the poulation believed that butter is a more nutritions food than oleomargarine. Only 6 per cent thought that oleomargarine is more nutritious while 27.2 per cent believed they are about the same. The remainder, 18.4 per cent, stated that they did not know. Margarine tax laws were in force for some time while vegetable oils were being tested as a human food. In addition to chemical examination, many investigations were conducted with rats, calves, and humans. Although there were still conflicting results, the tax laws were repealed and substitutes wen on the market to compete with butter. Many investigators still question the decision that substitutes are qual to butter, nutritionwise. Many investigations (4, 6, 21, 34) have shown that butter contains one or more growth factors which have not, as yet been identified. Chemical methods have failed to identify any of these factors, and so other methods have been considered. It is a well known fact that interrelationships exist between fat metabolism and the metabolism of other substances. It has been shown (11) that dietary fat affects the metabolism of other nutrients such as calcium and phosphorus. Although not clearly understood, it has been demonstrated (25, 37) that the kidney plays an important role in fat transport and metabolism. The value of urinalysis as a method of indicating the metabolism as a whole is well known, as well as is the high sensitivity of metabolic systems to minute quantities of some substances. The possibility of detecting growth factors or other substances through a study of excreted metabolites seems worthy of consideration in this study. Recent work with paper chromatography at the University of Texas (48) has indicated that each individual has a specific urinary metabolic pattern. Similarities have been found in the patterns of identical twins and schizophrenics. It was also found that the diet changed this pattern to a certain extent, although this was not studied extensively. The problem reported here is a study of urine obtained from highly inbred rats fed animal and vegetable fats analyzed by use of paper chromatography.

Marineosins A and B are two spiroaminal-ring containing tripyrrole compounds isolated from the marine actinomycete, Streptomyces CNQ-617, and were found to possess potent and selective cytotoxic activity against leukemia and melanoma. Marineosins belong to the prodiginines class of natural products, examples of which are undecylprodiginine and streptorubin B. Unlike marineosins, prodiginines structures are characterized by the presence of fully conjugated tripyrrole nucleus linked to an alkyl chain (that lacks any oxygen). Cyclic prodiginines arise from an oxidative cyclization of the alkyl chain onto the tripyrrole, a step catalyzed by Rieske-oxygenase like enzymes such as RedG. The biosynthesis of prodiginines is directed via the red gene cluster. The unique structural differences between marineosin and other prodiginines spurred the proposal of a number of hypotheses for its biosynthesis, none of which have been experimentally tested. A red gene cluster homolog which has only one extra dehydratase-encoding gene; marA has been identified from the genomic library of Streptomyces CNQ-617, and the identified cluster was proposed to direct the biosynthesis of marineosin. In this study, the identified putative gene cluster was expressed in the heterologous host, S. venezuelae, and marineosin production in the new strain; JND2 was confirmed via LC/MS and 1H-NMR. The new engineered strain also produces a myriad of marineosin related shunt metabolites and pathway intermediates. This study hence presents the first identified gene cluster proved to direct the biosynthesis of marineosin; the mar gene cluster and proves that the cloned cluster encodes most, if not all the enzymes required to direct the biosynthesis of marineosin. Deletion of the Rieske-oxygenase encoding gene; marG (a RedG homolog) from the mar gene cluster led to the accumulation of 2-hydroxyundecylprodiginine; G410 with an m/z 410.28 and molecular formula C25H35O2N3. This data proves that MarG is not responsible for the introduction of the spiromaminal ring oxygen on the alkyl chain, but is required for catalyzing macrocyclic ring formation between C-8 and C-9 of G410. Undecylprodiginine production in marG deletion mutant was not observed which indicates that undecylprodiginine is likely not an intermediate along the pathway for marineosin biosynthesis, and indicates that the spiroaminal ring oxygen is introduced early in the pathway, possibly due to the incorporation of a 3-hydroxy-butyric acid starter unit. Deletion of the dehydratase-encoding gene; marA, from the mar gene cluster led to the accumulation of compounds JN408 and JN422 with m/z 408.26 and 422.24 and molecular formulae C25H33O2N3, and C25H31O3N3, respectively. Purification and structure elucidation of JN408 proves it to be an oxidized marineosin analog which has fully aromatic tripyrrole rings while; purification and structure elucidation of JN422 proves it to be a 9-keto-JN408 derivative. Both JN408 and JN422 compounds have a spiroaminal ring which indicates that MarA does not catalyze spiroaminal ring formation but catalyzes the reduction of pyrrole ring B of JN408 to yield marineosin. Therefore, we are proposing that MarA acts as a dehydrogenase, rather than a dehydratase. We are proposing that the intramolecular spiroaminal ring formation is catalyzed by either MarG or occurs non-enzymatically. JN422 is a shunt metabolite produced due to promiscuous activity of either MarG or an unidentified oxidase in the mar cluster, possibly MarT. From the data generated in this study, we present the first experimentally supported pathway for the biosynthesis of marineosin and the opportunity to generate novel compounds with potentially useful biological activities.