Disentangling the role of prokaryotes in regulating export flux via suspended and sinking organic matter in the southern ocean
- Authors: Dithugoe, Choaro David
- Date: 2022-10-14
- Subjects: Microbial ecology , Bioinformatics , Biochemistry , Oceanography , Metagenomics , Carbon cycle (Biogeochemistry) , Prokaryotes
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365745 , vital:65782 , DOI https://doi.org/10.21504/10962/365745
- Description: The role of phytoplankton in regulating atmospheric carbon dioxide in the marine environment has been the subject of extensive research. We lack, however, comparative insights regarding the functional contributions of bacteria, archaea, fungi, and viruses (the microbiota) to organic matter export especially in understudied polar marine environments such as the Southern Ocean. This knowledge deficit is in part due to the high levels of microbial diversity which obscures efforts to study the relationship between diversity and ecosystem functions including their roles in the sequestration of carbon and nitrogen. Elucidating their precise contributions to organic matter export may be central to potential ecosystems feedbacks to global climate change. We examined several factors which may influence organic matter export to depth including net primary production, phytoplankton biomass, temperature, and prokaryotic functional capacity in the Southern Ocean. A Marine Snow Catcher was used to collect suspended and sinking material 10 metres below mixed layer depth at Southern Ocean Time Series (SOTS) in autumn (March-April) and in the Atlantic sector of the Southern Ocean in winter (July-August) and spring (October-November) 2019. The suspended and sinking material was used to determine the particulate organic carbon and nitrogen concentrations which were then used to calculate fluxes and export ratio ((e-ratio) - particulate organic carbon flux divided by net primary production). Additionally, genomic DNA was extracted from the suspended and sinking material and sequenced to obtain Shotgun metagenomic data which was employed to reconstruct metagenome assembled genome (MAGs) and their functional capacity using bioinformatic tools such as DRAM. Data from the Atlantic sector of the Southern Ocean, demonstrate that net primary production and temperature were inversely related to the e-ratio which is consistent with previous findings from the northern region of the Southern Ocean. Genomic functional capacity from SOTS suggested that r-strategist (organisms adapted to live in unstable environments) bacteria (e.g., Gammaproteobacteria) were prominent in the suspended pool. By contrast, the sinking particle-pool appeared to be dominated by K- strategists (organisms adapted to stable environment). The opposite was true for the archaea. This finding (i.e., bacteria) differs from a previous study in the northern region of the Southern Ocean, showing that microbes with K-strategists were more abundant in the suspended fraction. K-strategists typically degrade sinking organic matter into suspended organic matter or dissolved organic matter reducing the organic carbon export efficiency. Furthermore, Data from the Atlantic sector of the Southern Ocean revealed that seasonal temperature changes might dictate the rate of regional prokaryotic degradation across the zones. Resulting in rapid degradation at the northerly warmer regions and slow degradation further south. The data further provide evidence of chemolithoautotrophic mechanisms, with prokaryotes harbouring key pathways, required to transform dissolved inorganic carbon into complex organic forms, including recalcitrant dissolved organic carbon. Collectively, the SOTS and Atlantic sector of the Southern Ocean data suggest that shifts in prokaryotic community structure and functional capacity may regulate (either degradation or synthesis of organic matter) carbon export to depth. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2022
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- Date Issued: 2022-10-14
The synthesis and assessment of thioxanthone- and xanthone- derived compounds as hosts for application in host-guest chemistry
- Authors: Greyling, Lizé
- Date: 2019
- Subjects: Chemistry, Organic , Biochemistry
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/42525 , vital:36665
- Description: In this work, the host capabilities of two structurally related compounds, N,N’-bis(9-phenyl-9- thioxanthenyl)ethylenediamine (H1) and N,N’-bis(9-phenyl-9-xanthenyl)ethylenediamine (H2) were compared in the presence of a wide variety of guest species. Additionally, the selectivity displayed by these host compounds were examined when exposed to mixtures of guests in order to ascertain whether it would be feasible to employ them in alternative separation strategies for the purification of industrially relevant chemicals. H1 and H2 were synthesized by reacting thioxanthone and xanthone with phenylmagnesium bromide. The resultant alcohol was then treated with perchloric acid and, finally, two of these molecules were effectively linked by utilizing ethylenediamine to afford the two host compounds. Initially, H1 and H2 were investigated for their inclusion abilities by recrystallizing each from a number of potential isomeric and non-isomeric guest compounds such as the xylenes and ethylbenzene, methylanisoles and anisole, methylpyridines and pyridine, methylcyclohexanones and cyclohexanone, heterocyclic five- and six- membered ring compounds, alkylsubstituted benzenes, anilines, and dihaloalkanes. H1 displayed excellent inclusion ability when presented with the above-mentioned compounds, and a 1:1 H:G ratio was consistently preferred in each case. H2 also proved to be successful in this regard but did not include the methylcyclohexanones and cyclohexanone nor the heterocyclic five-membered ring solvents. Furthermore, varying host:guest ratios were observed for the complexes formed with H2. Mixed competition experiments were carried out in the presence of either isomeric or related but non-isomeric guest species. When H1 and H2 were independently recrystallized from mixtures of the former, selectivity orders correlated for both hosts, but it was observed that H2 exhibited an enhanced selectivity for the preferred guests in each case, compared with H1. Interestingly, in mixtures of the latter, host behaviours were distinctly opposing (with the exception of the dihaloalkanes). H1, and even more so H2, demonstrated very high selectivities for p-xylene, aniline and N,Ndimethylaniline from the xylene and aniline guest series, respectively, where selectivities were found to be ~90% or higher for host recrystallization experiments from respective mixtures of these guests. Single crystal X-ray diffraction, Hirshfeld surface and thermal analyses were employed in order to elucidate the reasons for any selectivity observations. The inclusion of these guests was, in most cases, found to be as a result of interactions between host and guest species, which included π∙∙∙π stacking, C‒H∙∙∙π, hydrogen bonding and various other short contact types. Guest compounds were accommodated in either cavities or channels and this was dependent on the nature of the guest. The host molecule conformations showed H1 to adopt a bent tricyclic fused ring system with the N atoms of the linker in a synclinal arrangement, while in complexes with H2, the fused ring system was near-planar and the N atoms adopted an antiperiplanar geometry. These key differences resulted in a very ordered host‒host packing for H2 as a direct result of the more planar O-containing ring and linear linker; for H1, on the other hand, the buckled S-containing ring and gauche-orientated N atoms resulted in a less ordered packing, which ultimately related to the differences in the behaviour of the two host species. Hirshfeld surface analyses, in general, did not provide much information to explain the host selectivities, with the exception of complexes containing the five-membered ring guest heterocyclics. Thermal analyses were completed on all suitable host-guest complexes and, in most cases but not all, the onset and peak temperatures (terms Ton and Tp, respectively) were related to the thermal stability of the complexes, which were used to rationalize the selectivities of these host compounds.
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- Date Issued: 2019
The extraction, quantification and application of high-value biological compounds from olive oil processing waste
- Authors: Postma-Botha, Marthie
- Date: 2018
- Subjects: Organic compounds , Biochemistry , Biomass energy , Olive oil industry
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/34383 , vital:33371
- Description: Olive oil processing waste (pomace) as a by-product of the olive oil industry is regarded as a rich source of high-value biological compounds exhibiting antioxidant potential. The objective of the present work was to obtain a concentrated extract of high-value biological antioxidants from the pomace. The effect of extraction conditions on the concentration of the bioactive compounds in the extracts was investigated. The simultaneous recovery of both hydrophilic and lipophilic high-value biological compounds exhibiting antioxidant potential was achieved through a one-step extraction method under reduced pressure using a non-toxic solvent blend. A multilevel experimental design was implemented with the aim of optimising the recovery of selected compounds, namely, hydroxytyrosol, tyrosol, oleuropein, α-tocopherol and squalene from olive pomace by using solvent blends of n-heptane, d-limonene, ethanol and water. The factors considered were: extraction time, percentage composition of solvent blends and extraction temperature. The results suggested that a good recovery of the hydrophilic polyphenolic compounds, namely, hydroxytyrosol, tyrosol and oleuropein, as well as the lipophilic compounds, α-tocopherol and squalene may be achieved at a solvent temperature of 60°C at 400 mbar with a solvent blend of 30% n-heptane, 50% ethanol and 20% water and an extraction time of two hours. It was found that freeze-drying the pomace before extraction minimised production of artefacts, avoided degradation of biophenols, ensured long term stability of a reproducible sample and achieved better recovery of important hydrophilic and lipophilic bioactive compounds. Since the bioactive compounds are temperature sensitive, the extraction was performed under reduced pressure in order to reduce solvent reflux temperature and to improve extraction efficiency. The quantitative and qualitative determinations of the aforementioned high-value compounds were performed by high-performance liquid chromatography (HPLC), which revealed that the hydrophilic polyphenolic as well as the lipophilic α-tocopherol and squalene were present. In this study hydroxytyrosol, tyrosol, oleuropein, α-tocopherol and squalene were extracted from the pomace of two olive cultivars (Frantoio and Coratina). A comparison among the two cultivars showed quantitative differences between the two cultivars in all five high-value biological compounds and in the antioxidant capacity of the extracts evaluated by measuring the radical scavenging effect on 1,1-diphenyl-2- picrylhydrazyl (DPPH) free radical. Coratina cultivar was found to have a significantly higher antioxidant capacity than Frantoio due to the much greater oleuropein content in the Coratina compared to the Frantoio although Frantoio had a significantly greater amount of hydroxytyrosol. The stability of olive waste extracts stored at four temperatures was also investigated and the results show that increased temperatures caused greater extent of degradation of both the hydrophilic polyphenolic and lipophilic compounds. The proposed optimum storage condition for the olive pomace extracts was found to be at 5°C in the absence of light. The extracts were incorporated into two cosmetic formulations and were found, from a stability study, to be stable at room temperature and optimally stable at 5°C in the absence of light.
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- Date Issued: 2018
LIPOPROTEINS AND THEIR SUBFRACTIONS IN TYPE 2 DIABETES PATIENTS FROM MTHATHA, EASTERN CAPE, SOUTH AFRICA
- Authors: JIM JOSEPH THYTHARAYIL
- Date: 2017
- Subjects: Biochemistry
- Language: English
- Type: Thesis, Doctoral
- Identifier: http://hdl.handle.net/11260/2116 , vital:40897
- Description: Cardiovascular disease is the main cause of mortality in diabetic patients and the risk of mortality due to cardiovascular disease is 2-4 times higher in diabetic patients when compared to the general population. The dysregulation of lipid metabolism due to abnormal insulin concentration or activity is one of the major reasons for the increased cardiovascular risk associated with diabetes. The main objective of the study was to analyse the alterations in the sub-fractions of lipoproteins in type 2 diabetic patients from hospitals and clinics around Mthatha. The results of the study showed that the concentration of small dense low density lipoproteins (LDL) was highly elevated in the diabetic patients with diabetic patients having four times the odds of having a pattern of increased small dense LDL than people without diabetes. The diabetic patients also had a very high concentration of oxidized low-density lipoprotein and lipoprotein (a). These alterations in lipid concentration exposed the diabetic patients to high risk of cardiovascular disease. This atherogenic alteration in lipid concentration could not be detected by the traditional lipid profile and hence analysis of lipoprotein sub-fractions can help in better management and decrease cardiovascular events in diabetic patients.
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The role of cancer procoagulant on the MTOR pathway
- Authors: Chiuswa, Chengetanai
- Date: 2016
- Subjects: Cancer -- Research , Neovascularization , Biochemistry , Blood coagulation factors -- Biotechnology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/7303 , vital:21316
- Description: Cancer procoagulant (CP) is a cysteine protease found in tumour cells and amnion chorion membranes. The main function of CP is not yet known, but it has potential roles in tumour growth and metastasis. Initially, CP was believed to increase coagulation in cancer patients; however, research has shown that increase in CP concentration does not correlate with an increase in coagulation. The location of CP in amnion chorion membranes and tumour cells only led to the hypothesis that CP might be involved in inducing blood vessel and or lymph vessel formation. CP was shown to induce lymphangiogenesis (lymph vessel formation) in human telomerase reverse transcriptase-human dermal endothelial cells (hTERT-HDLEC) (Tshaka, 2011). CP-induced tube formation was inhibited by rapamycin; indicating that CP may be signalling via the mammalian target of rapamycin (mTOR) pathway. The aim of this study was to investigate the effect of CP on the mTOR signalling pathway using human umbilical endothelial vein cells (HUVECs) as a model. CP was isolated from amnion chorion membranes and purified using two anion exchange chromatography steps. Purified CP (2 μg/ml) was used to induce tube formation in endothelial cells (HUVECs) seeded on growth factor reduced (GFR) Matrigel. In addition, the 2 μg/ml CP was used to treat cultured HUVECs. Sodium dodecyl sulphate polyacrylamide electrophoresis (SDS-PAGE) and western blotting were used to determine phosphorylation levels of protein kinase B (Akt) and ribosomal protein S6 kinase (S6K). CP was successfully isolated and purified using anion exchange chromatography. The effect of CP on tube formation was not significant relative to the control in the HUVEC cell line. The role of CP on Akt and S6K phosphorylation still needs to be verified by using sensitive methods of quantification such as enhanced chemiluminescence (ECL) and enzyme linked immunosorbent assay (ELISA). The levels of CP activity were shown to be higher in early tumour growth than in advanced cancer suggesting that certain physiological factors could be increasing CP activity during early tumour growth. This study investigated the effect of cobalt chloride on CP activity in breast cancer cell lines. Cobalt chloride reduced CP activity in MCF-7 and promoted CP activity in MDA-MB-231.
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- Date Issued: 2016
Biochemistry Honours: BCH 514
- Authors: Bradley, G , Mazomba, N , Wilhelmi, B
- Date: 2010-08
- Subjects: Biochemistry
- Language: English
- Type: Examination paper
- Identifier: vital:17849 , http://hdl.handle.net/10353/d1010477
- Description: Biochemistry Honours: BCH 514, supplementary examination August 2010.
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- Date Issued: 2010-08
Chemical studies of 1,5-benzodioxepanones
- Authors: Gelebe, Aifheli Carlson
- Date: 1991
- Subjects: Biochemistry , Pigments (Biology) , Benzopyrans
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4423 , http://hdl.handle.net/10962/d1006895 , Biochemistry , Pigments (Biology) , Benzopyrans
- Description: Chromone and flavanone derivatives were prepared by condensation of the corresponding 2-hydroxyacetophenones (with diethyl oxalate or the appropriate aromatic aldehyde respectively) and cyclisation of the condensation products. Saeyer-Villiger rearrangement of these flavanones, with MCPBA, resulted in expansion of the C-ring. Spectroscopic techniques have been used to establish the regioselectivity of the rearrangement and hence, the identity of the rearranged products as 1,5-benzodioxepan-4-ones. The 1,5-benzodioxepan-4-ones were subjected to detailed ¹H and ¹³C n.m.r. analysis and a combination of low and high resolution mass spectrometry has been used to study the mass fragmentation pathways of these ring-expanded products.
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- Date Issued: 1991
""Of molecules and men"" : inaugural lecture delivered at Rhodes University
- Authors: Kaye, Perry T
- Date: 1989
- Subjects: Biochemistry , Chemistry, Organic , Chemistry
- Language: English
- Type: Text
- Identifier: vital:643 , http://hdl.handle.net/10962/d1020712 , ISBN 0868101842
- Description: Inaugural lecture delivered at Rhodes University , Rhodes University Libraries (Digitisation)
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- Date Issued: 1989