The zonation of coastal dune plants in relation to sand burial, resource availability and physiological adaptation
- Authors: Gilbert, Matthew Edmund
- Date: 2008
- Subjects: Sand dune conservation -- South Africa -- Eastern Cape Coastal ecology -- South Africa -- Eastern Cape Botany -- South Africa -- Eastern Cape Coastal biology -- South Africa -- Eastern Cape Littoral plants -- South Africa -- Eastern Cape Littoral plants Sand dune plants -- Ecophysiology Sand dune plants -- Geographical distribution
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4195 , http://hdl.handle.net/10962/d1003764
- Description: When considering the large amount of work done on dune ecology, and that a number of the classical ecological theories originate from work on dunes, it is apparent that there remains a need for physiological and mechanistic explanations of dune plant phenomena. This thesis demonstrated that in the extreme coastal environment dune plants must survive both high rates of burial (disturbance), and low nutrient availability (stress). The ability of four species to respond to these two factors corresponded with their position in a vegetation gradient on the dunes. A low stem tissue density was shown to enhance the potential stem elongation rate of buried plants, but reduced the maximum height to which a plant could grow. Such a tradeoff implies that tall light-competitive plants are able to survive only in stable areas, while burial responsive mobile-dune plants are limited to areas of low vegetation height. This stem tissue density tradeoff was suggested as the mechanism determining the zonation that species show within the dune vegetation gradient present at various sites in South Africa. Finally, detailed investigations of dune plant ecophysiology found that: 1) The resources used in the response to burial derive from external sources of carbon and nitrogen, as well as simple physiological and physical mechanisms of resource allocation. 2) The leaves of dune plants were found to be operating at one extreme of the photosynthetic continuum; viz efficient use of leaf nitrogen at the expense of water loss. 3) Contrary to other ecosystems, the environmental characteristics of dunes may allow plants to occupy a high disturbance, high stress niche, through the maintenance of lowered competition. 4) At least two mobile-dune species form steep dunes, and are able to optimise growth, on steeper dunes, such that they have to grow less in response to burial than plants that form more shallow dunes. In this thesis, it was shown that the link between the carbon and nitrogen economies of dune plants was pivotal in determining species distributions and survival under extreme environmental conditions. As vast areas of the world’s surface are covered by sand dunes these observations are not just of passing interest.
- Full Text:
- Authors: Gilbert, Matthew Edmund
- Date: 2008
- Subjects: Sand dune conservation -- South Africa -- Eastern Cape Coastal ecology -- South Africa -- Eastern Cape Botany -- South Africa -- Eastern Cape Coastal biology -- South Africa -- Eastern Cape Littoral plants -- South Africa -- Eastern Cape Littoral plants Sand dune plants -- Ecophysiology Sand dune plants -- Geographical distribution
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4195 , http://hdl.handle.net/10962/d1003764
- Description: When considering the large amount of work done on dune ecology, and that a number of the classical ecological theories originate from work on dunes, it is apparent that there remains a need for physiological and mechanistic explanations of dune plant phenomena. This thesis demonstrated that in the extreme coastal environment dune plants must survive both high rates of burial (disturbance), and low nutrient availability (stress). The ability of four species to respond to these two factors corresponded with their position in a vegetation gradient on the dunes. A low stem tissue density was shown to enhance the potential stem elongation rate of buried plants, but reduced the maximum height to which a plant could grow. Such a tradeoff implies that tall light-competitive plants are able to survive only in stable areas, while burial responsive mobile-dune plants are limited to areas of low vegetation height. This stem tissue density tradeoff was suggested as the mechanism determining the zonation that species show within the dune vegetation gradient present at various sites in South Africa. Finally, detailed investigations of dune plant ecophysiology found that: 1) The resources used in the response to burial derive from external sources of carbon and nitrogen, as well as simple physiological and physical mechanisms of resource allocation. 2) The leaves of dune plants were found to be operating at one extreme of the photosynthetic continuum; viz efficient use of leaf nitrogen at the expense of water loss. 3) Contrary to other ecosystems, the environmental characteristics of dunes may allow plants to occupy a high disturbance, high stress niche, through the maintenance of lowered competition. 4) At least two mobile-dune species form steep dunes, and are able to optimise growth, on steeper dunes, such that they have to grow less in response to burial than plants that form more shallow dunes. In this thesis, it was shown that the link between the carbon and nitrogen economies of dune plants was pivotal in determining species distributions and survival under extreme environmental conditions. As vast areas of the world’s surface are covered by sand dunes these observations are not just of passing interest.
- Full Text:
Thermal, spectroscopic and x-ray diffraction studies of copper(II) 1,2,4,5-Benzenetetracarboxylates and copper(II) oxalate a study of metal-organic frameworks
- Authors: Lamprecht, Emmanuel
- Date: 2008
- Subjects: Organometallic compounds Copper Oxalates -- Thermal properties Organic compounds -- Synthesis Spectrum analysis X-rays -- Diffraction
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4389 , http://hdl.handle.net/10962/d1005054
- Description: Novel and known metal organic frameworks with copper(II), sodium and 1,2,4,5-benzenetetracarboxylate were prepared by ambient precipitation, solvothermal and gel-synthesis methods, and characterized by single-crystal X-ray diffraction, X-ray powder diffraction, infrared spectroscopy, differential scanning calorimetry, and thermogravimetry with FTIR evolved-gas analysis. Some of these complexes were investigated for guest inclusion properties with water (the original guest species), methanol, ethanol and pyridine. The gel-synthesis products were the most interesting. The novel threedimensional metal-organic framework complex Cu₂ Na(OH)L·7H₂O (where L=1,2,4,5-benzenetetracarboxylate) -formed by gel-synthesis- is a covalent three-dimensional metal organic framework polymer with open channels containing both guest water molecules and water molecules coordinated to sodium. The structure collapsed on dehydration, but was essentially restored to the original structure on rehydration in moist air. On exposure of the dehydrated material to methanol and ethanol vapour, significant uptake of these solvents was observed, and the resolvated structures closely resembled that of the parent material. On heating in dry nitrogen, small amounts of methanol and ethanol remained until about 280 °C, when loss of the remaining guest triggered decomposition of the framework. The related complex, Cu₂¼(OH)½ L·7½H₂O (or possibly Cu₂⅓ (OH)⅔L·8H₂O) -formed by gel-synthesis- had a different physical appearance to Cu₂Na(OH)L·7H₂O above, but had nearly identical X-ray diffraction pattern, mid-infrared spectrum and thermal behaviour. The novel complex Cu₄Na₄L₃·14H₂O -formed by gel-synthesis- is a covalent three-dimensional metal-organic framework with small channels containing both guest water molecules and water coordinated to sodium and copper. Upon dehydration the structure collapsed, but on rehydration in moist air the original structure was partly restored. The dehydrated material did not absorb methanol. Known two-dimensional polymeric complexes [Cu₂L·6H₂O]·4H₂O and [Cu₂L·4H₂O]·2H₂O were also obtained by gel-synthesis, and were characterized and investigated for guest inclusion properties. The structures of these complexes collapsed on dehydration, and were only partly restored on rehydration in saturated water vapour. The dehydrated materials did not absorb methanol. The two-dimensional polymeric mixed-ligand complex Cu₂(pyridine)₄·6H₂O -formed very slowly by gel-synthesis- was characterized by TG-FTIR, and was shown to undergo a complicated decomposition involving the loss of water and pyridine, carbon dioxide and carbon monoxide in various stages. Solvothermal synthesis did not yield materials suitable for single-crystal X-ray diffraction studies or inclusion studies, producing only an anhydrous or hemihydrate complex with the formula Cu₂L·0.65H2O. Ambient precipitation syntheses did not yield materials suitable for singlecrystal diffraction studies, forming products approximately equivalent to the complexes [Cu₂L·6H₂O]·4H₂O and Cu₂¼(OH)½L·7 ½H₂O above. During the course of the above study it was discovered that, on changing the DSC purge from nitrogen to argon, the normally exothermic carboxylate decompositions appeared to become endothermic. The effects of the supposedly inert atmospheres of argon and nitrogen on the decomposition-mechanism of copper(II) oxalate -a well-studied copper carboxylate- were therefore studied by DSC, TG, TG-FTIR and XRPD. DSC experiments were performed in nitrogen and argon at different flow-rates, in various mixtures of nitrogen and argon, and at various heating rates. Regardless of the proportions of nitrogen and argon, the DSC residues consisted mainly of copper metal, a small amount of copper(I) oxide (cuprite) and, in some circumstances, traces of copper(II) oxide (tenorite). Also, regardless of whether TG-FTIR experiments were performed under argon or nitrogen, the gaseous decomposition products consisted mainly of carbon dioxide, with traces of carbon monoxide being detected over part of the decomposition period. Various explanations for the thermal behaviour are discussed, and it is possible that small amounts of O2 or monatomic oxygen were given off during the decomposition under argon. The design and implementation of a low-cost prototype X-ray proportional counter detector system, consisting of a hybrid analog-digital computer built using commonly available electronic components, is presented. This system was designed to replace ageing discrete-transistor designs still in use in earlier X-ray diffractometers. The prototype performs the functions of pulse-shaping, pulseheight discrimination, counting and scaling, and provides both digital and scaled analog outputs.
- Full Text:
- Authors: Lamprecht, Emmanuel
- Date: 2008
- Subjects: Organometallic compounds Copper Oxalates -- Thermal properties Organic compounds -- Synthesis Spectrum analysis X-rays -- Diffraction
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4389 , http://hdl.handle.net/10962/d1005054
- Description: Novel and known metal organic frameworks with copper(II), sodium and 1,2,4,5-benzenetetracarboxylate were prepared by ambient precipitation, solvothermal and gel-synthesis methods, and characterized by single-crystal X-ray diffraction, X-ray powder diffraction, infrared spectroscopy, differential scanning calorimetry, and thermogravimetry with FTIR evolved-gas analysis. Some of these complexes were investigated for guest inclusion properties with water (the original guest species), methanol, ethanol and pyridine. The gel-synthesis products were the most interesting. The novel threedimensional metal-organic framework complex Cu₂ Na(OH)L·7H₂O (where L=1,2,4,5-benzenetetracarboxylate) -formed by gel-synthesis- is a covalent three-dimensional metal organic framework polymer with open channels containing both guest water molecules and water molecules coordinated to sodium. The structure collapsed on dehydration, but was essentially restored to the original structure on rehydration in moist air. On exposure of the dehydrated material to methanol and ethanol vapour, significant uptake of these solvents was observed, and the resolvated structures closely resembled that of the parent material. On heating in dry nitrogen, small amounts of methanol and ethanol remained until about 280 °C, when loss of the remaining guest triggered decomposition of the framework. The related complex, Cu₂¼(OH)½ L·7½H₂O (or possibly Cu₂⅓ (OH)⅔L·8H₂O) -formed by gel-synthesis- had a different physical appearance to Cu₂Na(OH)L·7H₂O above, but had nearly identical X-ray diffraction pattern, mid-infrared spectrum and thermal behaviour. The novel complex Cu₄Na₄L₃·14H₂O -formed by gel-synthesis- is a covalent three-dimensional metal-organic framework with small channels containing both guest water molecules and water coordinated to sodium and copper. Upon dehydration the structure collapsed, but on rehydration in moist air the original structure was partly restored. The dehydrated material did not absorb methanol. Known two-dimensional polymeric complexes [Cu₂L·6H₂O]·4H₂O and [Cu₂L·4H₂O]·2H₂O were also obtained by gel-synthesis, and were characterized and investigated for guest inclusion properties. The structures of these complexes collapsed on dehydration, and were only partly restored on rehydration in saturated water vapour. The dehydrated materials did not absorb methanol. The two-dimensional polymeric mixed-ligand complex Cu₂(pyridine)₄·6H₂O -formed very slowly by gel-synthesis- was characterized by TG-FTIR, and was shown to undergo a complicated decomposition involving the loss of water and pyridine, carbon dioxide and carbon monoxide in various stages. Solvothermal synthesis did not yield materials suitable for single-crystal X-ray diffraction studies or inclusion studies, producing only an anhydrous or hemihydrate complex with the formula Cu₂L·0.65H2O. Ambient precipitation syntheses did not yield materials suitable for singlecrystal diffraction studies, forming products approximately equivalent to the complexes [Cu₂L·6H₂O]·4H₂O and Cu₂¼(OH)½L·7 ½H₂O above. During the course of the above study it was discovered that, on changing the DSC purge from nitrogen to argon, the normally exothermic carboxylate decompositions appeared to become endothermic. The effects of the supposedly inert atmospheres of argon and nitrogen on the decomposition-mechanism of copper(II) oxalate -a well-studied copper carboxylate- were therefore studied by DSC, TG, TG-FTIR and XRPD. DSC experiments were performed in nitrogen and argon at different flow-rates, in various mixtures of nitrogen and argon, and at various heating rates. Regardless of the proportions of nitrogen and argon, the DSC residues consisted mainly of copper metal, a small amount of copper(I) oxide (cuprite) and, in some circumstances, traces of copper(II) oxide (tenorite). Also, regardless of whether TG-FTIR experiments were performed under argon or nitrogen, the gaseous decomposition products consisted mainly of carbon dioxide, with traces of carbon monoxide being detected over part of the decomposition period. Various explanations for the thermal behaviour are discussed, and it is possible that small amounts of O2 or monatomic oxygen were given off during the decomposition under argon. The design and implementation of a low-cost prototype X-ray proportional counter detector system, consisting of a hybrid analog-digital computer built using commonly available electronic components, is presented. This system was designed to replace ageing discrete-transistor designs still in use in earlier X-ray diffractometers. The prototype performs the functions of pulse-shaping, pulseheight discrimination, counting and scaling, and provides both digital and scaled analog outputs.
- Full Text:
Towards understanding the mechanism of dimerisation of Saccharomyces cerevisiae eukaryotic translation initiation factor 5A
- Authors: Gentz, Petra Monika
- Date: 2008
- Subjects: Cytology Molecular biology Biochemistry Proteins -- Analysis Proteomics Polypeptides Amino acids -- Synthesis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3992 , http://hdl.handle.net/10962/d1004052
- Description: Eukaryotic translation initiation factor 5A (eIF5A) is the only known protein to contain hypusine, formed by post-translational modification of a highly conserved lysine residue. Hypusination is essential for eIF5A function, being required for binding of a specific subset of mRNAs necessary for progression of eukaryotic cells through the G1-S checkpoint. Little structural information is available for eIF5A other than that derived from archaeal homologues. The aim of this study was to conduct structure-function studies on Saccharomyces cerevisiae (yeast) eIF5A, encoded by TIF51A. Homology models of eIF5A were generated from the Methanococcus jannaschii archaeal homologue (aIF5A) and two Leishmania eIF5As. The models, along with secondary structure predictions identified an a-helix on the C-terminal domain, unique to eukaryote eIF5A. The Neurospora crassa structural analogue, HEX-1, which dimerises in three configurations, was used to generate similar dimeric model configurations of eIF5A. A biochemical and functional analysis was used to validate the homology models of eIF5A.Since the crystal structures of aIF5A and eIF5A were solved from unhypusinated protein produced in Escherichia coli, 6 x His-tagged eIF5A (His-eIF5A) was used for biochemical analysis. This analysis revealed that eIF5A existed as a dimer in solution, dependent on the presence of the highly conserved Cys 39 residue. A yeast TIF51A/TIF51B null yeast strain, with a chromosomal copy of TIF51A under control of PGAL1, was used to confirm that HiseIF5A and selected eIF5A mutants were functional in vivo. Biochemical analysis showed that hypusinated His-eIF5A also exists as a dimer, but neither the dimerisation, nor the function of eIF5A are dependent on the presence of Cys 39. Rather they depend on the presence of hypusine (Hpu) 51 and the presence of RNA leading to the conclusion that RNA and hypusine are required for dimerisation and hence function, of native eIF5A in vivo. In contrast, a Lys 51 to Arg 51 substitution or RNase treatment of His-eIF5A produced in E. coli did not destabilize the dimeric form, suggesting different folding/dimerisation mechanisms in E. coli and yeast cells. The information obtained from the initial homology models, together with the results of the biochemical analysis was used to propose a mechanism for dimerisation of yeast eIF5A involving both hypusine and RNA.
- Full Text:
- Authors: Gentz, Petra Monika
- Date: 2008
- Subjects: Cytology Molecular biology Biochemistry Proteins -- Analysis Proteomics Polypeptides Amino acids -- Synthesis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3992 , http://hdl.handle.net/10962/d1004052
- Description: Eukaryotic translation initiation factor 5A (eIF5A) is the only known protein to contain hypusine, formed by post-translational modification of a highly conserved lysine residue. Hypusination is essential for eIF5A function, being required for binding of a specific subset of mRNAs necessary for progression of eukaryotic cells through the G1-S checkpoint. Little structural information is available for eIF5A other than that derived from archaeal homologues. The aim of this study was to conduct structure-function studies on Saccharomyces cerevisiae (yeast) eIF5A, encoded by TIF51A. Homology models of eIF5A were generated from the Methanococcus jannaschii archaeal homologue (aIF5A) and two Leishmania eIF5As. The models, along with secondary structure predictions identified an a-helix on the C-terminal domain, unique to eukaryote eIF5A. The Neurospora crassa structural analogue, HEX-1, which dimerises in three configurations, was used to generate similar dimeric model configurations of eIF5A. A biochemical and functional analysis was used to validate the homology models of eIF5A.Since the crystal structures of aIF5A and eIF5A were solved from unhypusinated protein produced in Escherichia coli, 6 x His-tagged eIF5A (His-eIF5A) was used for biochemical analysis. This analysis revealed that eIF5A existed as a dimer in solution, dependent on the presence of the highly conserved Cys 39 residue. A yeast TIF51A/TIF51B null yeast strain, with a chromosomal copy of TIF51A under control of PGAL1, was used to confirm that HiseIF5A and selected eIF5A mutants were functional in vivo. Biochemical analysis showed that hypusinated His-eIF5A also exists as a dimer, but neither the dimerisation, nor the function of eIF5A are dependent on the presence of Cys 39. Rather they depend on the presence of hypusine (Hpu) 51 and the presence of RNA leading to the conclusion that RNA and hypusine are required for dimerisation and hence function, of native eIF5A in vivo. In contrast, a Lys 51 to Arg 51 substitution or RNase treatment of His-eIF5A produced in E. coli did not destabilize the dimeric form, suggesting different folding/dimerisation mechanisms in E. coli and yeast cells. The information obtained from the initial homology models, together with the results of the biochemical analysis was used to propose a mechanism for dimerisation of yeast eIF5A involving both hypusine and RNA.
- Full Text: