Characterization of termite Trinervitermes trinervoides metagenome-derived glycoside hydrolases, the formulation of synergistic core enzyme sets for effective sweet sorghum and corncob saccharification, and their potential industrial applications
- Authors: Mafa, Mpho Stephen
- Date: 2019
- Subjects: Termites , Metagenomics , Glucosides , Hydrolases , Enzymes , Feedstock
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/72414 , vital:30044 , DOI https://doi.org/10.21504/10962/72414
- Description: The current study investigated the biochemical properties of endo-glucanase (GH5E), exo-glucanase (GH5D), xylanase (GH5H) and endo-glucanase/xylanase (GH45), derived from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) for their potential role in the biotechnology industry. All these enzymes, except GH5D, exhibited activities on cellulosic and xylan-rich polymeric substrates, which only displayed activity on p-nitrophenyl cellobioside. GH5D, GH5E, GH5H and GH45 enzymes retained more than 80% of their activities at pH 5.5 and also retained more than 80% of their activities at 40ºC. Furthermore, these enzymes were thermostable at 37ºC for 72 hours. GH5E, GH5H and GH45 were generally stable over a range of metal-ion. The kinetic parameters for GH5E were 5.68 mg/ml (KM) and 34.36 U/mg protein (Vmax). GH5D activity did not follow classical Michaelis-Menten kinetics, suggesting product inhibition. GH5H displayed KM values of 5.53, 95.03 and 2.10 mg/ml and Vmax values of 112.36, 144.45 and 180.32 U/mg protein on beechwood xylan, CMC, and xyloglucan, respectively. GH45 displayed a KM of 6.94 mg/ml and a Vmax of 12.30 U/mg protein on CMC. GH5D [cellobiohydrolase (CBH)] and a commercial CBHII (GH6) enzyme outperformed a commercial CBHI (GH7) enzyme when these enzymes hydrolysed β-glucan. GH5D and CBHII also displayed a higher degree of synergy on β-glucan but failed to show synergy on Avicel. We therefore concluded that GH5D and CBHII are β-glucan-specific cellobiohydrolases. The corncob (CC) and sweet sorghum bagasse (SSB) substrates were pretreated with lime, NaOH and NaClO2. Subsequent to pretreatment, these substrates were used to investigate if GH5D, GH5E, GH5H and GH45 could operate in synergy. Results revealed that out of 12 possible core enzyme sets constructed, only two (referred to as CES-E and CES-H) displayed higher activities on pretreated CC or SSB. Simultaneous synergy was generally the most effective mode of synergy during hydrolysis of alkaline pretreated SSB and CC samples by both CES-E and CES-H. Both core enzyme sets did not display synergy on oxidative pretreated substrates. These findings suggest that lime and NaOH are more effective pretreatments for CC and SSB substrates. We used PRotein Interactive MOdeling (PRIMO) software to demonstrate that GH5D protein structure is an (α/β)8 barrel with a tunnel-like active site. Enzymes with this type of protein structure are able to perform transglycosylation, a process in which GH5D produced methyl, ethyl and propyl cellobiosides. We concluded that the GH5D, GH5E, GH5H and GH45 enzymes possess novel biochemical properties and that they form synergy during the hydrolysis of complex substrates (SSB and CC). GH5D transglycosylation could be used to produce novel biodegradable chemicals with special properties (e.g. anti-microbial properties). In conclusion, our findings suggest that GH5D, GH5E, GH5H and GH45 can potentially be used to improve biorefinery processes. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
- Authors: Mafa, Mpho Stephen
- Date: 2019
- Subjects: Termites , Metagenomics , Glucosides , Hydrolases , Enzymes , Feedstock
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/72414 , vital:30044 , DOI https://doi.org/10.21504/10962/72414
- Description: The current study investigated the biochemical properties of endo-glucanase (GH5E), exo-glucanase (GH5D), xylanase (GH5H) and endo-glucanase/xylanase (GH45), derived from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) for their potential role in the biotechnology industry. All these enzymes, except GH5D, exhibited activities on cellulosic and xylan-rich polymeric substrates, which only displayed activity on p-nitrophenyl cellobioside. GH5D, GH5E, GH5H and GH45 enzymes retained more than 80% of their activities at pH 5.5 and also retained more than 80% of their activities at 40ºC. Furthermore, these enzymes were thermostable at 37ºC for 72 hours. GH5E, GH5H and GH45 were generally stable over a range of metal-ion. The kinetic parameters for GH5E were 5.68 mg/ml (KM) and 34.36 U/mg protein (Vmax). GH5D activity did not follow classical Michaelis-Menten kinetics, suggesting product inhibition. GH5H displayed KM values of 5.53, 95.03 and 2.10 mg/ml and Vmax values of 112.36, 144.45 and 180.32 U/mg protein on beechwood xylan, CMC, and xyloglucan, respectively. GH45 displayed a KM of 6.94 mg/ml and a Vmax of 12.30 U/mg protein on CMC. GH5D [cellobiohydrolase (CBH)] and a commercial CBHII (GH6) enzyme outperformed a commercial CBHI (GH7) enzyme when these enzymes hydrolysed β-glucan. GH5D and CBHII also displayed a higher degree of synergy on β-glucan but failed to show synergy on Avicel. We therefore concluded that GH5D and CBHII are β-glucan-specific cellobiohydrolases. The corncob (CC) and sweet sorghum bagasse (SSB) substrates were pretreated with lime, NaOH and NaClO2. Subsequent to pretreatment, these substrates were used to investigate if GH5D, GH5E, GH5H and GH45 could operate in synergy. Results revealed that out of 12 possible core enzyme sets constructed, only two (referred to as CES-E and CES-H) displayed higher activities on pretreated CC or SSB. Simultaneous synergy was generally the most effective mode of synergy during hydrolysis of alkaline pretreated SSB and CC samples by both CES-E and CES-H. Both core enzyme sets did not display synergy on oxidative pretreated substrates. These findings suggest that lime and NaOH are more effective pretreatments for CC and SSB substrates. We used PRotein Interactive MOdeling (PRIMO) software to demonstrate that GH5D protein structure is an (α/β)8 barrel with a tunnel-like active site. Enzymes with this type of protein structure are able to perform transglycosylation, a process in which GH5D produced methyl, ethyl and propyl cellobiosides. We concluded that the GH5D, GH5E, GH5H and GH45 enzymes possess novel biochemical properties and that they form synergy during the hydrolysis of complex substrates (SSB and CC). GH5D transglycosylation could be used to produce novel biodegradable chemicals with special properties (e.g. anti-microbial properties). In conclusion, our findings suggest that GH5D, GH5E, GH5H and GH45 can potentially be used to improve biorefinery processes. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
Ectomycorrhizal fungal assessment of South African Pinus patula seedlings and their biological control potential to enhance seedling growth
- FitzGerald, Véronique Chartier
- Authors: FitzGerald, Véronique Chartier
- Date: 2019
- Subjects: Ectomycorrhizal fungi , Pinus patula Diseases and pests Biological control South Africa , Fusarium , Forest nurseries , Seedlings Growth , Seedlings Diseases and pests
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/67902 , vital:29167
- Description: The South Africa forestry industry, covering 1.3 million hectares, is dependent on exotic pine and eucalyptus species. Nursery seedlings are not inoculated with ectomycorrhizal (ECM) fungi or other beneficial microbes. Fusarium circinatum is an economically important pathogen affecting seedling survival. The purpose of this investigation was to assess levels of naturally occurring ECM colonisation in South African nurseries and to determine the effects of seedling inoculation with selected ECM and bacterial isolates on plant growth and resistance to the fungal pathogen F. circiantum. Pinus patula seedlings from 10 different South African nurseries were assessed for ECM colonisation using a grid line intersect method and molecularly identified using morphological and next-generation Illumina sequencing. Explants from ECM basidiocarps, collected from Pinus stands, were plated onto MMN medium to obtain isolates which were verified using molecular techniques. Mycorrhizal helper bacteria (MHB) were also isolated from these basiocarps, tested for MHB properties, siderophore production, phospahte solubilising and IAA production. ECM and associated bacterial isolates were used to inoculate seedlings and growth was assessed over a 5 month period. Colonisation of seedlings in production nurseries was low (2-21%). Morphologically the ECM fungi T. terrestris, Suillus sibiricus, and the genera Russula, Pseudotomentella were identified. Molecularly the ECM fungi T. terrestris, Inocybe jacobi and the genera Sphaerosporella and several other ECM containing families were identified along with many saprotrophic/endophytic fungi belonging to genera such as, Penicillium, Ramasonia and Talaromyces. Inoculated seedlings showed a significant increase in growth in comparison to the un-inoculated control seedlings. ECM fungal colonisation levels of these seedlings were significantly increased and colonisation was promoted by the Suillus isolate, Salmon Suillus. Seedling growth in the presence of the pathogen F. circinatum was significantly increased and promoted by the Lactarius isolate Lactarius quieticolor. Inoculation of seedlings in the nursery would ensure the production of stronger healthy plants which may be more tolerant to fusarial infection increasing survival in the plantation. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
- Authors: FitzGerald, Véronique Chartier
- Date: 2019
- Subjects: Ectomycorrhizal fungi , Pinus patula Diseases and pests Biological control South Africa , Fusarium , Forest nurseries , Seedlings Growth , Seedlings Diseases and pests
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/67902 , vital:29167
- Description: The South Africa forestry industry, covering 1.3 million hectares, is dependent on exotic pine and eucalyptus species. Nursery seedlings are not inoculated with ectomycorrhizal (ECM) fungi or other beneficial microbes. Fusarium circinatum is an economically important pathogen affecting seedling survival. The purpose of this investigation was to assess levels of naturally occurring ECM colonisation in South African nurseries and to determine the effects of seedling inoculation with selected ECM and bacterial isolates on plant growth and resistance to the fungal pathogen F. circiantum. Pinus patula seedlings from 10 different South African nurseries were assessed for ECM colonisation using a grid line intersect method and molecularly identified using morphological and next-generation Illumina sequencing. Explants from ECM basidiocarps, collected from Pinus stands, were plated onto MMN medium to obtain isolates which were verified using molecular techniques. Mycorrhizal helper bacteria (MHB) were also isolated from these basiocarps, tested for MHB properties, siderophore production, phospahte solubilising and IAA production. ECM and associated bacterial isolates were used to inoculate seedlings and growth was assessed over a 5 month period. Colonisation of seedlings in production nurseries was low (2-21%). Morphologically the ECM fungi T. terrestris, Suillus sibiricus, and the genera Russula, Pseudotomentella were identified. Molecularly the ECM fungi T. terrestris, Inocybe jacobi and the genera Sphaerosporella and several other ECM containing families were identified along with many saprotrophic/endophytic fungi belonging to genera such as, Penicillium, Ramasonia and Talaromyces. Inoculated seedlings showed a significant increase in growth in comparison to the un-inoculated control seedlings. ECM fungal colonisation levels of these seedlings were significantly increased and colonisation was promoted by the Suillus isolate, Salmon Suillus. Seedling growth in the presence of the pathogen F. circinatum was significantly increased and promoted by the Lactarius isolate Lactarius quieticolor. Inoculation of seedlings in the nursery would ensure the production of stronger healthy plants which may be more tolerant to fusarial infection increasing survival in the plantation. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
Gem-bearing granitic pegmatites in Malawi: their mineralogy, geochemistry, age, and fluid compositional variations
- Kankuzi, Charles Frienderson
- Authors: Kankuzi, Charles Frienderson
- Date: 2019
- Subjects: Granite , Pegmatites , Geochemistry , Fluid inclusions , Nonferrous metals
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/97905 , vital:31505 , DOI https://doi.org/10.21504/10962/97905
- Description: The gem bearing granitic pegmatites from different pegmatite fields across Malawi intrude all important geological entities from the Palaeoproterozoic in the north, the Mesoproterozoic in central Malawi and the Pan-African basement in the south. U/Pb zircon and Rb/Sr mineral isochron ages indicate pegmatite emplacement from the Palaeoproterozoic to Pan-African and Mesozoic time. Most pegmatites are related to the Pan-African cycle; no Mesoproterozoic pegmatites were observed in this study. Within the Pan-African pegmatite groups there are two important subgroups. Some pegmatites show Sr isotopic compositions that indicate mantle components contributing to the parental granites from which the pegmatites evolved. Others show higher Sr initials, indicating crustal granites as primary pegmatite sources or significant crustal contamination. Only for few pegmatites, such as the Palaeoproterozoic and Ordovician gem tourmaline pegmatites in the Chitipa and Dowa Districts, the granitic source is evident from their field context. For all others the granitic origin is interpreted by mineralogical and geochemical evidence. All analysed pegmatites belong to either the Rare Element Class or the Miarolitic Class, but they vary in their degree of fractionation. The more evolved pegmatites are more enriched in incompatible elements such as Be, Li, B, and Ta, which resulted in the formation of gem minerals such as beryl, aquamarine, tourmaline and topaz, which may or may not be associated with tantalite. The Rare Element pegmatites can be further subdivided into the REL-Li subclass, beryl type, beryl-columbite subtype, and in the complex type and elbaite subtype. The Miarolitic pegmatites include Mi-Li subclass and beryl-topaz type. Fluid inclusion studies (heating-cooling stage, Raman spectroscopy) identified a variety of fluid compositions that were present at different times and different places, indicating a variety of fluid sources. They range from aqueous-saline to CO2–rich carbonic fluids (CO2 +C3H8+ N2), or aqueous-carbonic fluids (H2O-CO2-CH4 and H2O-CO2-H2-H2S-CH4). The dominant solutes and species for the pegmatites show genetic variations over time and orogen (Paleo-/Meso-/Neoproterozoic). Uniform homogenisation temperatures and salinities in individual samples indicate that the gem-bearing pegmatites contained homogeneous fluids at the time of their capturing in quartz. Based on fluid inclusion data, the estimated trapping conditions of inclusions in quartz for all studied pegmatites except for one pegmatite suggest low pressures between 0.9 to 2.6 kb at temperatures of 400-600 C. The other pegmatite formed at slightly higher pressures of 2.2 to 3.6 kb. However, the pressure range for all the pegmatites is in agreement with the known liquidus conditions of Rare-Element pegmatite crystallisation. The shallow crustal emplacement level (3.4-9.8 km) and the greater depth (8.3 to 13.6 km) favoured the formation of gemstones. , Thesis (PhD) -- Faculty of Science, Geology, 2019
- Full Text: false
- Authors: Kankuzi, Charles Frienderson
- Date: 2019
- Subjects: Granite , Pegmatites , Geochemistry , Fluid inclusions , Nonferrous metals
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/97905 , vital:31505 , DOI https://doi.org/10.21504/10962/97905
- Description: The gem bearing granitic pegmatites from different pegmatite fields across Malawi intrude all important geological entities from the Palaeoproterozoic in the north, the Mesoproterozoic in central Malawi and the Pan-African basement in the south. U/Pb zircon and Rb/Sr mineral isochron ages indicate pegmatite emplacement from the Palaeoproterozoic to Pan-African and Mesozoic time. Most pegmatites are related to the Pan-African cycle; no Mesoproterozoic pegmatites were observed in this study. Within the Pan-African pegmatite groups there are two important subgroups. Some pegmatites show Sr isotopic compositions that indicate mantle components contributing to the parental granites from which the pegmatites evolved. Others show higher Sr initials, indicating crustal granites as primary pegmatite sources or significant crustal contamination. Only for few pegmatites, such as the Palaeoproterozoic and Ordovician gem tourmaline pegmatites in the Chitipa and Dowa Districts, the granitic source is evident from their field context. For all others the granitic origin is interpreted by mineralogical and geochemical evidence. All analysed pegmatites belong to either the Rare Element Class or the Miarolitic Class, but they vary in their degree of fractionation. The more evolved pegmatites are more enriched in incompatible elements such as Be, Li, B, and Ta, which resulted in the formation of gem minerals such as beryl, aquamarine, tourmaline and topaz, which may or may not be associated with tantalite. The Rare Element pegmatites can be further subdivided into the REL-Li subclass, beryl type, beryl-columbite subtype, and in the complex type and elbaite subtype. The Miarolitic pegmatites include Mi-Li subclass and beryl-topaz type. Fluid inclusion studies (heating-cooling stage, Raman spectroscopy) identified a variety of fluid compositions that were present at different times and different places, indicating a variety of fluid sources. They range from aqueous-saline to CO2–rich carbonic fluids (CO2 +C3H8+ N2), or aqueous-carbonic fluids (H2O-CO2-CH4 and H2O-CO2-H2-H2S-CH4). The dominant solutes and species for the pegmatites show genetic variations over time and orogen (Paleo-/Meso-/Neoproterozoic). Uniform homogenisation temperatures and salinities in individual samples indicate that the gem-bearing pegmatites contained homogeneous fluids at the time of their capturing in quartz. Based on fluid inclusion data, the estimated trapping conditions of inclusions in quartz for all studied pegmatites except for one pegmatite suggest low pressures between 0.9 to 2.6 kb at temperatures of 400-600 C. The other pegmatite formed at slightly higher pressures of 2.2 to 3.6 kb. However, the pressure range for all the pegmatites is in agreement with the known liquidus conditions of Rare-Element pegmatite crystallisation. The shallow crustal emplacement level (3.4-9.8 km) and the greater depth (8.3 to 13.6 km) favoured the formation of gemstones. , Thesis (PhD) -- Faculty of Science, Geology, 2019
- Full Text: false
Political constellations: an analysis of the use of language in positioning South African political parties in the Daily Sun
- Authors: Siebörger, Ian
- Date: 2019
- Subjects: Knowledge, Theory of , Political culture South Africa , Systemic grammar , Political parties South Africa , Functionalism (Linguistics) , Mass media and language South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/113934 , vital:33846 , http://doi.org/10.21504/10962/113934
- Description: As a young democracy, post-apartheid South Africa has both a complex and rapidly changing political landscape, and a developing system of interconnected public spheres in which ordinary citizens engage in political discourses. In this context, this thesis examines the ways in which language is used to position South Africa's political parties in the Daily Sun, the country's most widely-read tabloid newspaper. It uses a complex, multi-stage method of analysis to develop tools for describing how different policy positions and moral evaluations are associated with political parties. This is accomplished through complementary analyses using Systemic Functional Linguistics (SFL) and Legitimation Code Theory (LCT). The study describes current political discourses in South Africa as the products of a long process of historical development extending through the segregationist and apartheid eras to the post-apartheid present. It also situates the Daily Sun within South Africa's current media landscape and argues that the newspaper is to some extent successful in facilitating a vibrant alternative public sphere in which readers engage with the news. The study's multi-stage method of analysis begins with a corpus analysis of all political news articles from the Daily Sun dating from January to June 2015. This analysis reveals various tendencies in the positioning of South Africa's three largest political parties that are investigated further in later stages of analysis. Three selected individual articles are subjected to _ne-grained analysis in an exploratory analysis stage, and three others in a targeted analysis stage. The exploratory analyses are designed to investigate the contribution of various linguistic and discursive resources to political positioning in the data, while the targeted analyses demonstrate the contribution of these resources to positioning in articles that were carefully selected to reflect as many of the trends found in the corpus analysis as possible. These analyses enact the concept of axiological-semantic density from LCT to show the ways in which political knowledge is condensed in the articles. This condensation produces constellations of people, policy positions and moral evaluations in each article. These constellations, in turn, give indications of the cosmologies, or organizing principles, behind the Daily Sun's political news coverage. On the basis of the exploratory analyses, a multi-level translation device for axiological-semantic density is developed to describe the ways in which this concept is enacted in the analysis. The use of this translation device is then demonstrated using the targeted analyses. This study adapts the concepts of iconization, aggregation and technicality from SFL, collectively referred to as 'mass', to show how language works to position political parties. It finds that the use of intertextual references and lexical strings makes a considerable contribution toward political positioning in the data. Repeated couplings of the abovementioned resources in complexes (also known as syndromes) drive the process of political positioning. The Daily Sun is found to report primarily on concrete actions by individual politicians, and contains little to no information on policy decisions. No one political party is favoured, but coverage tends to emphasize accusations against politicians. This may reinforce distrust in politics and a withdrawal from engagement in political processes among readers. By contrast, this study shows that engagement in South Africa's public discourses can be encouraged through stronger promotion of critical language awareness in education, the growth of civil society organizations as vehicles for dialogue and social action on matters of public interest, and a variety of initiatives by the media designed to show the relevance of policy decisions to individuals' lives and increase participation in the news-making process. , Thesis (PhD) -- Faculty of Humanities, English Language and Linguistics, 2019
- Full Text: false
- Authors: Siebörger, Ian
- Date: 2019
- Subjects: Knowledge, Theory of , Political culture South Africa , Systemic grammar , Political parties South Africa , Functionalism (Linguistics) , Mass media and language South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/113934 , vital:33846 , http://doi.org/10.21504/10962/113934
- Description: As a young democracy, post-apartheid South Africa has both a complex and rapidly changing political landscape, and a developing system of interconnected public spheres in which ordinary citizens engage in political discourses. In this context, this thesis examines the ways in which language is used to position South Africa's political parties in the Daily Sun, the country's most widely-read tabloid newspaper. It uses a complex, multi-stage method of analysis to develop tools for describing how different policy positions and moral evaluations are associated with political parties. This is accomplished through complementary analyses using Systemic Functional Linguistics (SFL) and Legitimation Code Theory (LCT). The study describes current political discourses in South Africa as the products of a long process of historical development extending through the segregationist and apartheid eras to the post-apartheid present. It also situates the Daily Sun within South Africa's current media landscape and argues that the newspaper is to some extent successful in facilitating a vibrant alternative public sphere in which readers engage with the news. The study's multi-stage method of analysis begins with a corpus analysis of all political news articles from the Daily Sun dating from January to June 2015. This analysis reveals various tendencies in the positioning of South Africa's three largest political parties that are investigated further in later stages of analysis. Three selected individual articles are subjected to _ne-grained analysis in an exploratory analysis stage, and three others in a targeted analysis stage. The exploratory analyses are designed to investigate the contribution of various linguistic and discursive resources to political positioning in the data, while the targeted analyses demonstrate the contribution of these resources to positioning in articles that were carefully selected to reflect as many of the trends found in the corpus analysis as possible. These analyses enact the concept of axiological-semantic density from LCT to show the ways in which political knowledge is condensed in the articles. This condensation produces constellations of people, policy positions and moral evaluations in each article. These constellations, in turn, give indications of the cosmologies, or organizing principles, behind the Daily Sun's political news coverage. On the basis of the exploratory analyses, a multi-level translation device for axiological-semantic density is developed to describe the ways in which this concept is enacted in the analysis. The use of this translation device is then demonstrated using the targeted analyses. This study adapts the concepts of iconization, aggregation and technicality from SFL, collectively referred to as 'mass', to show how language works to position political parties. It finds that the use of intertextual references and lexical strings makes a considerable contribution toward political positioning in the data. Repeated couplings of the abovementioned resources in complexes (also known as syndromes) drive the process of political positioning. The Daily Sun is found to report primarily on concrete actions by individual politicians, and contains little to no information on policy decisions. No one political party is favoured, but coverage tends to emphasize accusations against politicians. This may reinforce distrust in politics and a withdrawal from engagement in political processes among readers. By contrast, this study shows that engagement in South Africa's public discourses can be encouraged through stronger promotion of critical language awareness in education, the growth of civil society organizations as vehicles for dialogue and social action on matters of public interest, and a variety of initiatives by the media designed to show the relevance of policy decisions to individuals' lives and increase participation in the news-making process. , Thesis (PhD) -- Faculty of Humanities, English Language and Linguistics, 2019
- Full Text: false
Towards a biological profile for South African perinatal remains: osteological and genetic perspectives
- Authors: Thornton, Roxanne
- Date: 2019
- Subjects: Identification , Forensic osteology , Methylation , RNA , Autopsy
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/68102 , vital:29198 , DOI 10.21504/10962/68102
- Description: Forensic identification of abandoned and suspected infanticide cases admitted to the South African Forensic Pathology Services is often impossible due to decomposition of the remains. In these cases, investigation of suspected criminal activity is almost never pursued. Ancillary tests in the form of anthropological and molecular analyses can assist with the forensic identification of perinatal remains. To provide fundamental information about bone development of perinatal skeleton, osteological and genetic techniques focusing on the pars basilaris, pars lateralis, sternal rib and left femur were used. Samples were obtained from unidentified and unclaimed remains originating from the Johannesburg Forensic Pathology Service (JFPS). To provide a biological age to individuals in the collection, dental aging was used to categorize remains for comparisons with anthropological and molecular data. A molecular protocol was designed to sex individuals using the X-linked G6PD and Y-linked SRY genes. Bone development was studied using osteometric and morphological data of dry bone remains coupled with bone mineral density analysis (Micro-CT). The methylation levels of CpG rich sites within the promoter region of selected bone-associated genes were incorporated to examine silencing of genes during development. Osteological results support the use of the pars basilaris, pars lateralis and femur for age-at-death estimations as well as provide the foundation for dry bone aging criteria for South African individuals. Data compared with established skeletal aging standards indicated developmental differences between populations. Through the use of animal models and the perinatal sternal rib tissue, insights and precautions into the use of post mortem bone derived RNA for forensic applications is communicated. The methylation status of CpG rich sites within the promoter regions support the hypothesis for interdependent machinery involving selected genes during early bone development. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
- Authors: Thornton, Roxanne
- Date: 2019
- Subjects: Identification , Forensic osteology , Methylation , RNA , Autopsy
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/68102 , vital:29198 , DOI 10.21504/10962/68102
- Description: Forensic identification of abandoned and suspected infanticide cases admitted to the South African Forensic Pathology Services is often impossible due to decomposition of the remains. In these cases, investigation of suspected criminal activity is almost never pursued. Ancillary tests in the form of anthropological and molecular analyses can assist with the forensic identification of perinatal remains. To provide fundamental information about bone development of perinatal skeleton, osteological and genetic techniques focusing on the pars basilaris, pars lateralis, sternal rib and left femur were used. Samples were obtained from unidentified and unclaimed remains originating from the Johannesburg Forensic Pathology Service (JFPS). To provide a biological age to individuals in the collection, dental aging was used to categorize remains for comparisons with anthropological and molecular data. A molecular protocol was designed to sex individuals using the X-linked G6PD and Y-linked SRY genes. Bone development was studied using osteometric and morphological data of dry bone remains coupled with bone mineral density analysis (Micro-CT). The methylation levels of CpG rich sites within the promoter region of selected bone-associated genes were incorporated to examine silencing of genes during development. Osteological results support the use of the pars basilaris, pars lateralis and femur for age-at-death estimations as well as provide the foundation for dry bone aging criteria for South African individuals. Data compared with established skeletal aging standards indicated developmental differences between populations. Through the use of animal models and the perinatal sternal rib tissue, insights and precautions into the use of post mortem bone derived RNA for forensic applications is communicated. The methylation status of CpG rich sites within the promoter regions support the hypothesis for interdependent machinery involving selected genes during early bone development. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2019
- Full Text:
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