Towards the bioremediation of the hypertrophic Swartkops Solar Salt-works
- Authors: Difford, Mark
- Date: 2008
- Subjects: Salt industry and trade -- South Africa -- Port Elizabeth , Bioremediation
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10606 , http://hdl.handle.net/10948/1506 , Salt industry and trade -- South Africa -- Port Elizabeth , Bioremediation
- Description: This thesis presents the results of three studies aimed at improving brine-quality at the Swartkops solar salt-works (Swartkops Sea Salt [Pty] Ltd) on the outskirts of Port Elizabeth, South Africa. This is a highly eutrophic salt-works, the management of which has become increasingly difficult in recent years. The fundamental problem is how best to operate the system at maximum capacity while limiting nutrient inputs from the nutrient-rich microtidal Swartkops Estuary. In the first study, brine-quality at several sites along the axis of the Swartkops Estuary, and the extent to which it is affected by a variety of factors, is compared. Sites were sampled on micro- and macrotidal time scales, and were selected by the management of the salt-works as possible locations for a new pump-house (for extracting brine from the estuary) for their salt-work operations at Swartkops and Missionvale. The study showed that there are incremental benefits to be had from moving the site of extraction downstream from its present position to a site closer to the mouth of the estuary, where the concentration of nutrients usually is lower and where salinity usually is higher. There is little to be gained from moving the site of extraction laterally, to the mouth of the Inlet from which brine currently is extracted, so that brine is extracted directly from the estuary itself. A set of models relating the concentrations of NH+ 4 , NO{u100000}3 , and PO34{u100000} to salinity is proposed. These take into account the influences of site and season and may be used to estimate the concentration of these nutrients from a measurement of salinity. The model for PO34{u100000} shows that it would be more damaging to the salt-works’ operations to pump “low”-salinity brine during the early months of summer than during autumn. Evidence is also presented to show that Wylde Bridge has no influence on nutrient concentrations in the estuary, with tidal flushing generally passing beyond the Wylde-Bridge break-point. The exceptionally heavy flooding of the estuary that occurred in September 2002 may, however, have biased this conclusion, because of its scouring effect. The second study concentrated on monitoring the effect of (1) decreasing pond depth and (2) increasing pond salinity—two readily available management tools—on brine quality at the salt-works. Pond depth throughout the salt-works was decreased by 40 cm, and the salinity of Pond 5, a pond in the middle of the system, was increased to 175 S. Both measures were kept in place for the duration of the study (Nov. 2002–Aug. 2004). The pond-depth experiment did not have the expected result, there being no evidence of the increase in microalgal growth in the water column that was predicted based on previous research. There was, however, a significant increase in benthic chlorophyll-a, and there was a general improvement in the condition of the sedimentary system of the salt-works. There was also a substantial decrease in particulate organic matter in the water column, with clear evidence that the remaining fraction was closely associated with living forms of particulate matter rather than with detritus. The pond-salinity experiment proves that there is a flourishing, and resilient, population of brine shrimp (Artemia salina L.) at the salt-works. Restocking the salina, or stocking it with a different strain of brine shrimp, is therefore not necessary. The results of this study show that the brine shrimp population at the salt-works needs salinities of greater than about 65–70 S to survive. As a living force they almost certainly need a protective salinity that is greater than about 120–140 S, perhaps even as great as 160 S. Brine shrimp thrived in the high salinity milieu of the experimental pond for the duration of the study, but dwindled from three other ponds of the system once their salinities fell to below 90 S, eventually to disappear from them, apparently completely, once salinity fell to below 65 S. The third and final study concentrated on establishing whether the products released by decomposing barley straw could be used in a solar salt-works to control macroalgal blooms without detrimentally affecting the benthic-mat. Previous research has shown that these products are effective inhibitors of macroalgal growth and that they remain effective under saline conditions. The results presented here show that the same products, or products released under similar conditions of decomposition, adversely effect both the structure and the function of the mat. Consequently, their use in a solar salt-works cannot be recommended.
- Full Text:
- Date Issued: 2008
- Authors: Difford, Mark
- Date: 2008
- Subjects: Salt industry and trade -- South Africa -- Port Elizabeth , Bioremediation
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10606 , http://hdl.handle.net/10948/1506 , Salt industry and trade -- South Africa -- Port Elizabeth , Bioremediation
- Description: This thesis presents the results of three studies aimed at improving brine-quality at the Swartkops solar salt-works (Swartkops Sea Salt [Pty] Ltd) on the outskirts of Port Elizabeth, South Africa. This is a highly eutrophic salt-works, the management of which has become increasingly difficult in recent years. The fundamental problem is how best to operate the system at maximum capacity while limiting nutrient inputs from the nutrient-rich microtidal Swartkops Estuary. In the first study, brine-quality at several sites along the axis of the Swartkops Estuary, and the extent to which it is affected by a variety of factors, is compared. Sites were sampled on micro- and macrotidal time scales, and were selected by the management of the salt-works as possible locations for a new pump-house (for extracting brine from the estuary) for their salt-work operations at Swartkops and Missionvale. The study showed that there are incremental benefits to be had from moving the site of extraction downstream from its present position to a site closer to the mouth of the estuary, where the concentration of nutrients usually is lower and where salinity usually is higher. There is little to be gained from moving the site of extraction laterally, to the mouth of the Inlet from which brine currently is extracted, so that brine is extracted directly from the estuary itself. A set of models relating the concentrations of NH+ 4 , NO{u100000}3 , and PO34{u100000} to salinity is proposed. These take into account the influences of site and season and may be used to estimate the concentration of these nutrients from a measurement of salinity. The model for PO34{u100000} shows that it would be more damaging to the salt-works’ operations to pump “low”-salinity brine during the early months of summer than during autumn. Evidence is also presented to show that Wylde Bridge has no influence on nutrient concentrations in the estuary, with tidal flushing generally passing beyond the Wylde-Bridge break-point. The exceptionally heavy flooding of the estuary that occurred in September 2002 may, however, have biased this conclusion, because of its scouring effect. The second study concentrated on monitoring the effect of (1) decreasing pond depth and (2) increasing pond salinity—two readily available management tools—on brine quality at the salt-works. Pond depth throughout the salt-works was decreased by 40 cm, and the salinity of Pond 5, a pond in the middle of the system, was increased to 175 S. Both measures were kept in place for the duration of the study (Nov. 2002–Aug. 2004). The pond-depth experiment did not have the expected result, there being no evidence of the increase in microalgal growth in the water column that was predicted based on previous research. There was, however, a significant increase in benthic chlorophyll-a, and there was a general improvement in the condition of the sedimentary system of the salt-works. There was also a substantial decrease in particulate organic matter in the water column, with clear evidence that the remaining fraction was closely associated with living forms of particulate matter rather than with detritus. The pond-salinity experiment proves that there is a flourishing, and resilient, population of brine shrimp (Artemia salina L.) at the salt-works. Restocking the salina, or stocking it with a different strain of brine shrimp, is therefore not necessary. The results of this study show that the brine shrimp population at the salt-works needs salinities of greater than about 65–70 S to survive. As a living force they almost certainly need a protective salinity that is greater than about 120–140 S, perhaps even as great as 160 S. Brine shrimp thrived in the high salinity milieu of the experimental pond for the duration of the study, but dwindled from three other ponds of the system once their salinities fell to below 90 S, eventually to disappear from them, apparently completely, once salinity fell to below 65 S. The third and final study concentrated on establishing whether the products released by decomposing barley straw could be used in a solar salt-works to control macroalgal blooms without detrimentally affecting the benthic-mat. Previous research has shown that these products are effective inhibitors of macroalgal growth and that they remain effective under saline conditions. The results presented here show that the same products, or products released under similar conditions of decomposition, adversely effect both the structure and the function of the mat. Consequently, their use in a solar salt-works cannot be recommended.
- Full Text:
- Date Issued: 2008
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:
- Date Issued: 2008
- 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:
- Date Issued: 2008
Utility of the cognitive assessment system (CAS) to predict reading proficiency in grade 1
- Authors: Hüttenrauch, Maria Eleonore
- Date: 2008
- Subjects: Das-Naglieri Cognitive Assessment System , Intelligence tests for preliterates , Cognition in children , Reading disability
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: vital:9839 , http://hdl.handle.net/10948/965 , Das-Naglieri Cognitive Assessment System , Intelligence tests for preliterates , Cognition in children , Reading disability
- Description: Reading disability, as the most commonly diagnosed learning disability, continues to pose a tenacious problem to teachers, practitioners and researchers. In an effort to understand the causes of reading disability, voluminous research has been undertaken over the past decades to pinpoint its causes or developmental stumbling blocks. One approach, the Planning, Attention, Simultaneous, and Successive processing (PASS) model, combines neuropsychological theory with elements from cognitive psychology. Based on this model, the Cognitive Assessment System (CAS), as well as methods of intervention for reading disability were developed. Although many studies have been conducted that investigated reading disability in terms of PASS cognitive processes, the final version of the CAS and its predictive utility with respect to reading disability has not been explored to date. The present study aimed to investigate the utility of the CAS, administered at the beginning of grade 1, to predict reading proficiency at the end of grade 1. The sample was comprised of 119 “average” (i.e., belonging to the general population) grade 1 students from schools of the Calgary Board of Education (CBE). The Basic Battery of the CAS was administered to the children in the sample at the beginning of grade 1, as well as four reading subtests of the Woodcock-Johnson Tests of Achievement – Third Edition (WJ-III ACH) at the end of grade 1. The WJ-III ACH yielded a cluster score for basic reading and one for reading comprehension. Correlational and regression analyses were used to address the first aim of this study, namely to explore the relationship between students’ scores on the CAS and their later reading proficiency. To this end, the children’s CAS Full Scale scores and WJ-III ACH cluster scores were subjected to a hierarchical regression analysis, whereby age, gender, and - xviii - SES were kept constant by entering them first in the equation. Next, the relationship between students’ PASS scale scores and the CAS subtest scores respectively and scores on the WJ-III ACH Basic Reading and Reading Comprehension Cluster scores was explored by means of stepwise regression analysis. To improve on the generalizability of results, the regression analyses were conducted on a randomly drawn analysis sample consisting of 80% of the sample, and cross-validated on the remaining 20% of the sample. The second aim of the present study was to ascertain whether clusters could be identified on the basis of CAS performance as well as levels of reading proficiency. To this end, the children’s CAS FS scores, PASS scale scores, and CAS subtest scores were subjected to cluster analyses. The investigation of aim 1 yielded some encouraging results, in that it was found that, together with the covariates: • The CAS FS emerged as a moderately strong predictor of both basic reading and reading comprehension; • Successive processing, in particular the Word Series subtest, significantly predicted basic reading skills; • Successive and simultaneous processing, particularly the Nonverbal Matrices and Sentence Repetition subtests, were significant predictors of reading comprehension; The second aim, which explored the relationship between patterns of CAS cognitive processes and their relationship with reading proficiency, yielded: • Two clusters with distinctly different PASS scale scores and with significant differences between their levels of reading proficiency. Higher PASS scales scores, particularly on the Attention and Planning scales, were associated with higher reading proficiency scores. • Four clusters with distinctly different CAS subtest scores that were also associated with distinctly different levels of reading performance. Good - xix - reading proficiency was associated with good CAS performance, whereas weaker reading proficiency was linked to weaker CAS performance. Biographical variables, such as age and SES were found to be related to performance on the CAS and reading proficiency, while gender did not emerge as an important predictor variable. The present study demonstrated the usefulness of the CAS, particularly its Successive and Simultaneous scales, as potential early predictor of reading disability. An exploration of the relationship between patterns of CAS cognitive processes and later reading proficiency also yielded encouraging and interesting results.
- Full Text:
- Date Issued: 2008
- Authors: Hüttenrauch, Maria Eleonore
- Date: 2008
- Subjects: Das-Naglieri Cognitive Assessment System , Intelligence tests for preliterates , Cognition in children , Reading disability
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: vital:9839 , http://hdl.handle.net/10948/965 , Das-Naglieri Cognitive Assessment System , Intelligence tests for preliterates , Cognition in children , Reading disability
- Description: Reading disability, as the most commonly diagnosed learning disability, continues to pose a tenacious problem to teachers, practitioners and researchers. In an effort to understand the causes of reading disability, voluminous research has been undertaken over the past decades to pinpoint its causes or developmental stumbling blocks. One approach, the Planning, Attention, Simultaneous, and Successive processing (PASS) model, combines neuropsychological theory with elements from cognitive psychology. Based on this model, the Cognitive Assessment System (CAS), as well as methods of intervention for reading disability were developed. Although many studies have been conducted that investigated reading disability in terms of PASS cognitive processes, the final version of the CAS and its predictive utility with respect to reading disability has not been explored to date. The present study aimed to investigate the utility of the CAS, administered at the beginning of grade 1, to predict reading proficiency at the end of grade 1. The sample was comprised of 119 “average” (i.e., belonging to the general population) grade 1 students from schools of the Calgary Board of Education (CBE). The Basic Battery of the CAS was administered to the children in the sample at the beginning of grade 1, as well as four reading subtests of the Woodcock-Johnson Tests of Achievement – Third Edition (WJ-III ACH) at the end of grade 1. The WJ-III ACH yielded a cluster score for basic reading and one for reading comprehension. Correlational and regression analyses were used to address the first aim of this study, namely to explore the relationship between students’ scores on the CAS and their later reading proficiency. To this end, the children’s CAS Full Scale scores and WJ-III ACH cluster scores were subjected to a hierarchical regression analysis, whereby age, gender, and - xviii - SES were kept constant by entering them first in the equation. Next, the relationship between students’ PASS scale scores and the CAS subtest scores respectively and scores on the WJ-III ACH Basic Reading and Reading Comprehension Cluster scores was explored by means of stepwise regression analysis. To improve on the generalizability of results, the regression analyses were conducted on a randomly drawn analysis sample consisting of 80% of the sample, and cross-validated on the remaining 20% of the sample. The second aim of the present study was to ascertain whether clusters could be identified on the basis of CAS performance as well as levels of reading proficiency. To this end, the children’s CAS FS scores, PASS scale scores, and CAS subtest scores were subjected to cluster analyses. The investigation of aim 1 yielded some encouraging results, in that it was found that, together with the covariates: • The CAS FS emerged as a moderately strong predictor of both basic reading and reading comprehension; • Successive processing, in particular the Word Series subtest, significantly predicted basic reading skills; • Successive and simultaneous processing, particularly the Nonverbal Matrices and Sentence Repetition subtests, were significant predictors of reading comprehension; The second aim, which explored the relationship between patterns of CAS cognitive processes and their relationship with reading proficiency, yielded: • Two clusters with distinctly different PASS scale scores and with significant differences between their levels of reading proficiency. Higher PASS scales scores, particularly on the Attention and Planning scales, were associated with higher reading proficiency scores. • Four clusters with distinctly different CAS subtest scores that were also associated with distinctly different levels of reading performance. Good - xix - reading proficiency was associated with good CAS performance, whereas weaker reading proficiency was linked to weaker CAS performance. Biographical variables, such as age and SES were found to be related to performance on the CAS and reading proficiency, while gender did not emerge as an important predictor variable. The present study demonstrated the usefulness of the CAS, particularly its Successive and Simultaneous scales, as potential early predictor of reading disability. An exploration of the relationship between patterns of CAS cognitive processes and later reading proficiency also yielded encouraging and interesting results.
- Full Text:
- Date Issued: 2008