List of Titles

Investigation of brewery waste grains and microbial fuel cells as value-additive technologies improving solvent production yields in Clostridium acetobutylicum (ATCC 824) fermentation

- Du Toit, Ryan Guillaume

Authors: Du Toit, Ryan Guillaume
Date: 2023-10-13
Subjects: Biomass energy , Butanol , Fermentation , Microbial fuel cells , Brewery waste , Clostridium acetobutylicum
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/424643 , vital:72171
Description: The production of the solvent compounds acetone, ethanol and butanol through fermentation of organic feedstocks using Clostridia species could be a promising route for biofuel production. However, the cost of raw materials, low yields and the complexity of anaerobic fermentation continue to hinder this means of generating these compounds. The research presented in this Thesis investigated low-cost interventions that could decrease the costs of production and to direct the synthesis of fuel compounds using microbial fuel cells. Low-cost anaerobic chambers were designed and constructed for the propagation and manipulation of Clostridium acetobutylicum, selected as a low-risk microbial catalyst. Fermentation was monitored using in situ pH measurements and a combination of turbidity measurements, nutrient assays (especially total carbohydrates) and HPLC-RI detection as a means of monitoring the consumption of nutrients (glucose), production of precursor compounds (butyric acid) and the formation of solvent molecules (acetone/ethanol and butanol) during fermentation by this organism. Brewer’s spent grains were tested as a sustainable and low-cost feedstock for solvent production, comparing the effects of sterilising before fermentation, or allowing resident microflora to remain during Clostridium-catalysed solvent production. Sterilised spent grains significantly improved the production of solvent molecules (e.g. 12.97 ± 0.38 g/L of butanol yielded, compared to 0.40 ± 0.33 g/L for defined media sampled during the solventogenic phase); compared to these, the use of non-sterilised brewer’s grain decreased both the reproducibility and yields of fermentation (8.66 ± 1.6 g/L of butanol). Microbial fuel cells were studied as a possible means of altering electron transfer to/from electrode-attached Clostridia to control the metabolic shift in bacteria from acidogenesis to solventogenesis. The base line MFC (11.00 ± 4.69 g/L) fermentation experiment did produce higher acetone/ethanol than the baseline batch experiment MB (5.47 ± 4.48 g/L), indicating an improvement to solvent production in C. acetobutylicum (ATCC 824) in a MFC fermentation. In this study, MFC-1 demonstrated remarkable superiority over MB in terms of butyric acid production, yielding significantly higher concentrations while also improving acetone and ethanol production. However, the enhanced butyric acid production did not correspond to significantly increased butanol yields when compared to batch fermentation of chemically defined media. These findings highlight the potential of MFC-1 as an efficient approach for enhancing the fermentative production of valuable compounds, with a particular focus on butyric acid and acetone/ethanol. , Thesis (MSc) -- Faculty of Science, Biotechnology Innovation Centre, 2023
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Date Issued: 2023-10-13

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Towards development of a malaria diagnostic: Generation, screening and validation of novel aptamers recognising Plasmodium falciparum lactate dehydrogenase

- Frith, Kelly-Anne

Authors: Frith, Kelly-Anne
Date: 2020
Subjects: Plasmodium falciparum , Malaria -- Chemotherapy , Oligonucleotides , Lactate dehydrogenase , Biochemical markers , Systematic evolution of ligands through exponential enrichment (SELEX)
Language: English
Type: Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/142247 , vital:38062
Description: Malaria, caused by infection with the Plasmodium parasite, is one of the leading causes of death in under-developed countries. Early detection is crucial for the effective treatment of malaria, particularly in cases where infection is due to Plasmodium falciparum. There is, therefore, an enduring need for portable, sensitive, reliable, accurate, durable, self-validating and cost-effective techniques for the rapid detection of malaria. Moreover, there is a demand to distinguish between various infectious species causing malaria. Research in the area of malarial biomarkers has identified a unique, species-specific, epitope of P. falciparum lactate dehydrogenase (PfLDH), enhancing prospects for the development of diagnostics capable of identifying the species causing malarial infection. In recent years, improvements have been made towards the development of rapid diagnostic tests for detecting malarial biomarkers. Owing to their low cost, ease of labeling, and high thermal stability (relative to antibodies), the development and synthesis of aptamers that target the malarial lactate dehydrogenase represents one of the key innovations in the field of rapid diagnostics for malaria. This study explored the generation of aptamers that specifically target P. falciparum. Two sets of aptamers with diagnostically-supportive functions were generated independently, through parallel SELEX of recombinantly-expressed, full-length Plasmodium falciparum lactate dehydrogenase (rPfLDH), and an oligopeptide comprising the P. falciparum-specific epitope on lactate dehydrogenase (LDHp). The latter offers a promising solution for generating aptamers capable of binding with high specificity to P. falciparum. In this work, an rLDH class of aptamers was generated when SELEX was performed using the full-length rPfLDH protein as the target and the LDHp class of aptamers was generated when SELEX was performed using the oligopeptide LDHp as a target. Aptamers were successfully generated through the process of SELEX (systematic evolution of ligands through exponential enrichment) following the study and application of several optimisation steps, particularly during the amplification stage of SELEX. Optimisation steps included the study of improvements in PCR conditions; role of surfactants (Triton-X), modifying the PCR clean-up protocol; and agarose gel excision. Structurally-relevant moieties with particular consensus sequences (GGTAG and GGCG) were found in aptamers both reported here and previously published, confirming their importance in recognition of the target. Novel moieties particular to this work (ATTAT and poly-A stretches) were identified. Clades of consensus sequences were identified in both the rLDH and LDHp groups of aptamers, where sequences in the rLDH clade did not show preferential binding to rPfLDH while those in the LDHp clade (particularly LDHp 3 and 18) were able to recognise and bind only LDHp. Of the 19 sequences returned from the parallel SELEX procedures for rPfLDH (11 sequences) and LDHp (8 sequences), six rPfLDH and all eight LDHp sequences underwent preliminary screening and those with low responses eliminated. Of the eight LDHp-targeting aptamer sequences, five were preliminarily shown to bind to LDHp, whereas only two rPfLDH-targeting sequences were shown to bind to the target (rLDH 4 and 7). To this small selection of rPfLDH oligonucleotide sequences, two more (rLDH 1 and 15) were chosen for further study based on their sequences, secondary and predicted tertiary conformations. Sequences chosen for further study were therefore: rLDH 1, 4, 7 and 15 in the rLDH class, and LDHp 1, 3, 11, 14 and 18 in the LDHp class. Binding properties of the aptamers towards their targets were investigated using enzyme-linked oligonucleotide assays (ELONA), fluorophore-linked oligonucleotide assays (FLONA), electromobility shift assays (EMSA), surface plasmon resonance (SPR), and GelRed dissociation assays, while applications towards aptasensors were explored using electrochemical impedance spectroscopy (EIS) and fluorescent microscopy. Some inconsistencies were seen for specific aptamer to target binding interactions using specific techniques; however, generally, binding to the targets was observed across the techniques assessed. These varied responses demonstrate the need to screen and validate aptamers using a variety of techniques and platforms not necessarily specific for the proposed application. From the aptamer binding screening studies using ELONA, the most promising aptamers generated were identified as LDHp 11, rLDH 4, rLDH 7 and rLDH 15. Aptamer rLDH 4, which was generated against rPfLDH, exhibited preferential and specific binding to the lactate dehydrogenase from P. falciparum, over the recombinantly-expressed lactate dehydrogenase from Plasmodium vivax (rPvLDH), albeit with lowered responses compared to LDHp 11 in ELONA and EMSA studies. However, in kinetic ELONA studies rLDH 4 showed binding to both rPfLDH and rPvLDH. Aptamer rLDH 7 showed high affinity for rPfLDH and rPvLDH in kinetic studies using ELONA. However, screening studies with ELONA indicates that aptamer rLDH 7 may not be suitable for diagnostic tests in serum samples given its non-specific binding to human serum albumin (HSA). Aptamer rLDH 15 exhibited species specificity for rPfLDH in screening studies using ELONA but showed affinity towards rPvLDH (albeit lower relative to its affinity for rPfLDH) in kinetic studies using ELONA. LDHp 11, generated against the PfLDH peptide, showed a clear preference for rPfLDH when compared to rPvLDH and other control proteins, in both sets of ELONA studies conducted, as well as EMSA, thus possessing a strong ability to identify the presence of Plasmodium falciparum owing to its generation against the species-specific epitope. While LDHp 1 demonstrated binding to plasmodial LDH in a flow-through system (SPR), so reiterating ELONA responses, it did not perform well in the remaining methodologies. Aptamers rLDH 1 and 15 and LDHp 3, 14 and 18 exhibited a mixed set of results throughout the target protein screening analyses and were, thus, not considered for selective binding in P. falciparum parasite bodies. In studies aimed at exploring biosensor assemblies utilising the developed aptamers, both rLDH 4 and LDHp 11, along with rLDH 7, LDHp 1 and pL1, demonstrated in situ binding to the native PfLDH in fluorescent microscopy. LDHp 11 exhibited FITC-based fluorescence equivalent to the anti-rPfLDHp IgY antibody in confocal fluorescent microscopy indicating superior binding to the native PfLDH compared to the remaining aptamers. An examination of electrochemical impedance as a platform for a biosensor assembly did not, in these studies, exhibit the required sensitivity using physiologically relevant concentrations of analyte expected for pLDH following infection with Plasmodium spp. Malstat/LDH activity was explored for application in a colorimetric aptasensor. A decrease in both rPfLDH and rPvLDH activity was observed following incubation with the tested aptamers, but rLDH 1, rLDH 7 and LDHp 14 did not exhibit similar decreases in rPvLDH activity. Aptamers rLDH 1, 4 and 7 and LDHp 11 and 14 were, therefore, not selected as candidates for LDH capture in LDH activity-based diagnostic devices for P. falciparum. The decreases in pLDH activity in the presence of aptamers could hold promise as direct or antagonistic malaria therapeutic agents. Preliminary studies on the application of aptamers as malaria therapeutic agents, while of interest, should be viewed with due caution given the challenges of aptamers reaching the intracellular native plasmodial LDH hosted within the red blood cells. In conclusion, this work has shown the ability of the LDHp 11 aptamer, generated in these studies, to selectively bind rPfLDH over rPvLDH, and to bind to the native PfLDH in fluorescent microscopy, indicating that this aptamer holds promise as a biorecognition element in malaria biosensors and other diagnostic devices for the detection, and differentiation, of P. falciparum and P. vivax. The use of a species-specific epitope of P. falciparum as a target in aptamer generation paves the way for similar such studies aimed at generating aptamers with species selectivity for other Plasmodium species.
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Date Issued: 2020

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The creation and validation of aptamers binding to murine 3T3-L1 Preadipocytes: preliminary implications for controlled cellular attachment, differentiation and cell fate

- Rubidge, Mark Lourens

Authors: Rubidge, Mark Lourens
Date: 2017
Subjects: Oligonucleotides , Fat cells , Stem cells , Ligand binding (Biochemistry) , Fluorimetry
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10962/65247 , vital:28714
Description: The controlled seeding of a variety of stem cells in vitro has been reported to alter the patterns of their subsequent differentiation. This has been attributed to the control of the surface microenvironment onto which adherent stem cells are cultured, especially control of the proximal density of neighbouring cells. Simultaneously, advances in the generation of aptamers - synthetic ligand molecules developed using in vitro selection techniques targeting complex molecules - have aided in the production of molecules capable of selectively binding to a variety of commercial stem cell lines. Combining the aforementioned research fields, the project reported in this thesis aimed to generate DNA-based aptamers capable of assisting with the selective binding of murine 3T3- L1 preadipocytes to a solid surface. This was performed with a view to, eventually, control the seeding densities of the adherent preadipocytes on the surface of the tissue culture dish in subsequent researchers. In the process of meeting this goal, several optimisations of the in vitro process by which aptamers binding to cells are generated (Cell-SELEX) were performed: an analysis into a variety of methods used for the removal of the single stranded aptamer candidate sequences attached to the surface of 3T3-L1 preadipocytes, a comparison of methods for the generation of single-stranded aptamer sequences from double-stranded DNA template molecules and a method for quantifying the removed ssDNA from the cell surface. Their use is further reported in this work. Initially, it was determined that a fluorimetric evaluation of the unbound single stranded DNA was the optimum technique to use to evaluate the relative amounts of aptamer DNA binding to target cells during cell-SELEX; this arose from the release of DNA, and other cell lysate contaminates, which interfered UV/ Vis quantification. The evaluation into different methods of ssDNA removal from the cell surface showed that although trypsinisation of the cells demonstrated the highest level of aptamer detachment (quantified by fluorimetry), there is a decrease the number of potential targets that aptamers could attach to. The most common method for detaching bound DNA aptamer molecules from cellular targets reported in literature, the use of high temperatures, was selected for cell-SELEX to increase the variability in potential target sites on the cell surface. Using techniques optimised in this work, fluorescently-tagged single-stranded oligonucleotide aptamers were later generated with a positive selection pressure to bind to the surface of the 3T3-L1 preadipocytes, but not to their differentiated adipocyte counterparts. After eight cycles of cell-SELEX, fluorescent spectroscopic analysis depicted a 74 % binding retention of the selection pool in the positive preadipocyte selection pool, as opposed to a 0.69 % binding of sequences to the negative differentiated preadipocytes. Following the isolation and identification of candidate sequences, seven separate sequences were identified as being successfully generated from the selection process. Bioinformatic characterisation of these placed sequenced aptamer candidates into two separate families, that were then analysed in opposition to each for their binding affinity toward each other. Using fluorescently-tagged sequences, the binding selectivity of the generated aptamers was validated using both epifluorescent microscopy and confocal microscopy. At this stage, an aptamer sequence selected from prior in-house research to serve as a negative control also demonstrated significant binding to the extracellular matrix of both preadipocytes and mature adipocytes. 5’-thiolated aptamer sequences were used to form self-assembled monolayers on the electrode surfaces of the impedimetric Roche xCELLigence Real-Time Cell Analysis. The use of aptamer sequences to capture the seeded preadipocytes, demonstrated a slight increase in the extent of binding of the preadipocytes to the gold electrode surface and produced some preliminary indications of alterations to the pattern and rate of subsequent differentiation in the preadipocytes. This provides preliminary evidence that aptamers developed to bind specifically to a stem cell line in vitro show potential to be used as to capture said cell when cast in a self- assembled monolayer assembly. This provides a future opportunity to control the seeding densities of the cells in vitro. The effects of cellular differentiation at a set of predefined cellular densities can be demonstrated on a desired stem cell line. , Thesis (MSc) -- Faculty of Faculty of Science, Biotechnology Innovation Centre, 2017
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Date Issued: 2017

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Critical studies in carbon electrode materials with applications in the electroanalysis of the mycotoxin citrinin

- Niland, Michael John

Authors: Niland, Michael John
Date: 2013
Subjects: Electrodes, Carbon , Mycotoxins
Language: English
Type: Thesis , Doctoral , PhD
Identifier: vital:4555 , http://hdl.handle.net/10962/d1018256
Description: Guided by increasing legislation, the analysis of food borne toxins, including mycotoxins, seeks to address market related demands for the development of analytical systems to monitor this threat to food security and human health. This Thesis is directed at the assessment of the application of electrochemistry for direct electroanalysis and characterisation of the mycotoxin citrinin (CIT) in aqueous media as well as fundamental investigations of the surface of polished and oxidised glassy carbon electrodes (GCE). This study provides the first known account of CIT detection through electrochemical methods. Although electrochemically active, CIT current responses (Ip) were highly irreproducible at polished GCE with a coefficient of variation (C.V.) of 20.16 %. As stability of Ip across multiple electrode preparations is a key requirement in electroanalysis, investigations were directed at attaining stability in CIT Ip. Achieving stability in CIT Ip was investigated via two approaches, including: accounting for Ip variability between electrode preparations as a result of variable GCE surface conditions as a post-data-acquisition analysis and secondly, removing Ip variability through modification of GCE. Accounting for variability in Ip was investigated through the application of double layer capacitance as an indicator of the activity of an electrode, and in so doing serving as a relative mediator of Ip responses between electrodes. Application of this procedure dropped CIT C.V. to a third of starting value across polished GCE (C.V. = 7.18 %), chemically oxidised GCE (Pi-GCE, C.V = 8.47 %) and functionalised multi-walled carbon nanotube modified GCE (fMWCNT, C.V. = 25.79 %) and was effective with analysis of structurally distinct molecules, 2,4-dimethylaniline (2,4-DMA) and 1,2,4-trihydroxybenzene (Triol). Furthermore, it afforded the ability to determine discreet solution overlapping data sets of Ip. Stabilising Ip through GCE surface modification was achieved by anodic electro-oxidation of GCE and allowed for direct electroanalysis of CIT and subsequent characterisation and analysis of CIT in complex media as it reduced C.V. of CIT Ip to 0.73 %. Fundamental investigations of the electrode surface condition are described such that the source of variability could be identified and the interactions of CIT with the electrode understood. Two surface oxidation techniques were applied in modification of GCE; anodic electro-oxidation (EOx GCE) and chemical oxidation using piranha solution (Pi-GCE), analysis of which has previously not been reported. Fundamental analyses to determine surface morphology and chemistry of Pi-GCE, EOx-GCE and polished GCE were conducted using high resolution scanning electron microscopy (HRSEM), scanning electrochemical microscopy (SECM), energy dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), fourier transform infrared spectroscopy (FTIR) and via electroanalytical methods. These studies showed that both oxidation procedures introduced a variety of oxide species at GCE surface, and further that the extent of those species was similar with total % O being 27.67 % and 33.47 % at Pi-GCE and EOx-GCE respectively. Although chemically similar, each surface was morphologically distinct. Electrochemical analyses at the surfaces revealed Pi-GCE to behave more similarly to polished GCE than EOx-GCE. As CIT responses were found to be stable at EOx-GCE (C.V. = 0.73 %) as opposed to Pi-GCE (C.V. = 22.87 %), stability of CIT Ip was likely to be as a result of a physical interaction with electrode morphology rather than interaction on a chemical basis. Morphological analyses revealed polished GCE and Pi-GCE to be highly morphologically irregular at the micro-scale. Although comparatively smooth, the surface morphology of EOx-GCE does not account for the stability of Ip. This study thus proposed a theory to describe the mechanism by which the limited conductivity and porosity of EOx-GCE allow for it to provide a relatively stable surface area within the oxide layer, adjacent to the electrode surface, and thus provided a stable platform for electroanalysis. Voltammetric characterization of CIT at EOx-GCE revealed that anodic oxidation in aqueous media involved an uneven number of electrons to protons via an ECE mechanism. This was illustrated to be nt = 2e- accompanied by the transfer of 1H⁺ per molecule oxidised. A proposed reaction scheme for the initial stages of CIT oxidation was suggested to involve both hydroxyl and carboxyl moieties of the CIT molecule. CIT oxidation was shown to arise as a result of a relatively complex mass transport regime which included both adsorptive and diffusive derived Ip₁. The LOD in buffered aqueous media was found to be 16 nM, a highly competitive result in relation to chromatographic techniques. Further application of EOx-GCE in complex media illustrated that CIT associates non-specifically with the components of food samples, primarily proteins. As a result of this, extraction of CIT from such media is mandatory. Liquid-liquid extraction illustrated a recovery in CIT Ip₁ and in so doing provided a means of accurately and sensitively detecting CIT from food samples with an LOD of 20 nM. These responses were corroborated by HPLC analyses on the same extractions and illustrate the applicability of electroanalysis as an analytical technique.
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Date Issued: 2013

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