title: Studies on carbon and DNA preservation in allophanic soils and paleosols on Holocene tephras in New Zealand

authors: Huang, Yu-Tuan

abstract: The recovery of ancient DNA (aDNA) and palaeoenvironmental DNA (PalEnDNA) from soils and sediments has enabled detailed paleontological and ecological records to be obtained. Because of the superior ability of allophanic soils and Andisols to adsorb considerable soil organic matter (SOM), and to slow the rate of carbon turnover in such soils, I hypothesised that environmental DNA can be preserved in allophanic soils and Andisols together with SOM, and that such DNA may be able to help reveal past environments. I characterised the preserved SOM in stratigraphic successions of buried paleosols on Holocene tephras of known age in northern New Zealand and attempted to extract and analyse the DNA to search for possible PalEnDNA.

Using synchrotron radiation-based carbon near-edge X-ray absorption fine structure (C NEXAFS) spectroscopy, I found the compositions and proportions of carbon functional groups of SOM in allophanic paleosols on precisely-dated Holocene tephras (c. 12,000 to 1718 calendar [cal] years BP) at four sites in northern New Zealand were similar and dominated by carboxylic functional groups, with subordinate amounts of quinonic, aromatic, and aliphatic groups. Differences in clay and allophane contents, stratigraphic position, age, parenttephra composition (andesitic versus rhyolitic), and mode of soil origin (retardant versus developmental upbuilding pedogenesis) seemed not to affect the structure of SOM over time. The similarity of the SOM in allophanic paleosols of different ages implied its preservation in allophanic soils over a long time, and the presence of quinonic carbon, normally very susceptible to degradation and transformation, shows that the allophanic soils have protected it very effectively. The quinonic carbon in buried horizons is thus indicative of the preservation of biological materials originating from bacteria and plants. The SOM originated through upbuilding pedogenesis: as soil genesis began in a newly-deposited tephra at the soil surface, allophane formed and it sequestered SOM from the modern (surface) organic cycle dominated by inputs from broadleaf-podocarp forest. Ongoing tephra deposition then caused the land surface to rise so that once-surface horizons were buried more deeply and hence became increasingly divorced from the modern organic cycle over time. The SOM adsorbed when the soil horizon was at the land surface was preserved in the buried soils because a fractal pore network of allophane aggregates and nanopores encapsulated and shielded the ‘old’ or relict SOM (including quinonic carbon) derived from past environments of the Holocene.

To provide fundamental knowledge about the interaction of allophane, DNA, and SOM in soils, I examined the adsorption capacity and adsorption mechanisms of salmon-sperm DNA on pure synthetic allophane and humic acidrich synthetic allophane. The pure synthetic allophane was able to adsorb up to 34 μg/mg of salmon-sperm DNA, but the humic acid-rich synthetic allophane adsorbed only 3.5 μg/mg of salmon-sperm DNA. Salmon-sperm DNA was adsorbed chemically through its phosphate group to the aluminol groups of synthetic allophane, and adsorbed chemically through humic acid covering the synthetic allophane spherules, and thus became bound indirectly to synthetic allophane. The chemical adsorption of salmon-sperm DNA on synthetic allophane led to the aggregation of allophane spherules to form nanoaggregates and microaggregates, and ~80% of total adsorbed DNA on allophane was held physically within the interstices (pores) between allophane spherules and nanoaggregates. The encapsulated DNA within the stable allophane-DNA aggregates may not be accessible to enzymes nor microbes, hence enabling DNA protection and preservation in allophanic soils. By implication, organic carbon is therefore likely to be sequestered and protected in allophanic soils (Andisols) in the same way as demonstrated here for DNA − that is, predominantly by encapsulation within a tortuous network of nanopores and submicropores amidst stable nanoaggregates and microaggregates, rather than by chemisorption alone.

A novel two-step method was developed to isolate DNA from allophane, based in part on experiments devised to extract salmon-sperm DNA from synthetic allophane. The two-step method for DNA extraction from allophanic soils is based on (1) chelating DNA and blocking adsorptive sites on allophane using EDTA and phosphate, respectively, and (2) dissolving allophane using acidified ammonium oxalate. The DNA yield from three allophanic paleosols on Holocene tephras was up to 44.5 μg/g soil (oven-dry basis). The extracted DNA was then successfully purified via gel electrophoresis followed by a gel purification kit, and the amplifiable and sequenced DNA extracted from a paleosol (which had been at the land surface for around 4000 years between c. 9423 and c. 5526 calendar years BP) on Rotoma tephra contained New Zealand endemic and exotic plants that differed from the European grasses growing currently on the land surface. The difference in vegetation indicates that the DNA extraction method I (with others) have developed is able to access environmental DNA originating from previous vegetation cover. The DNA extraction method could be used to facilitate the search for possible PalEnDNA in allophanic paleosols for reconstructing the past terrestrial environments as well as to investigate the biodiversity in allophanic soils and the origins of SOM.

Allophanic soils are demonstrably able to protect environmental DNA from degradation for a long period of time, and such DNA is able to reveal past environments. However, the duration over which that environmental DNA can be preserved in allophanic soils needs to be resolved, and additional investigations of gene diversity in allophanic paleosols of different ages using high-throughput sequencing (HTS) are required to determine the taxonomic profiles recovered in paleosols and to rule out contamination of modern DNA.

text: Studies on carbon and DNA preservation in allophanic soils and paleosols on Holocene tephras in New Zealand The recovery of ancient DNA (aDNA) and palaeoenvironmental DNA (PalEnDNA) from soils and sediments has enabled detailed paleontological and ecological records to be obtained. Because of the superior ability of allophanic soils and Andisols to adsorb considerable soil organic matter (SOM), and to slow the rate of carbon turnover in such soils, I hypothesised that environmental DNA can be preserved in allophanic soils and Andisols together with SOM, and that such DNA may be able to help reveal past environments. I characterised the preserved SOM in stratigraphic successions of buried paleosols on Holocene tephras of known age in northern New Zealand and attempted to extract and analyse the DNA to search for possible PalEnDNA.

Using synchrotron radiation-based carbon near-edge X-ray absorption fine structure (C NEXAFS) spectroscopy, I found the compositions and proportions of carbon functional groups of SOM in allophanic paleosols on precisely-dated Holocene tephras (c. 12,000 to 1718 calendar [cal] years BP) at four sites in northern New Zealand were similar and dominated by carboxylic functional groups, with subordinate amounts of quinonic, aromatic, and aliphatic groups. Differences in clay and allophane contents, stratigraphic position, age, parenttephra composition (andesitic versus rhyolitic), and mode of soil origin (retardant versus developmental upbuilding pedogenesis) seemed not to affect the structure of SOM over time. The similarity of the SOM in allophanic paleosols of different ages implied its preservation in allophanic soils over a long time, and the presence of quinonic carbon, normally very susceptible to degradation and transformation, shows that the allophanic soils have protected it very effectively. The quinonic carbon in buried horizons is thus indicative of the preservation of biological materials originating from bacteria and plants. The SOM originated through upbuilding pedogenesis: as soil genesis began in a newly-deposited tephra at the soil surface, allophane formed and it sequestered SOM from the modern (surface) organic cycle dominated by inputs from broadleaf-podocarp forest. Ongoing tephra deposition then caused the land surface to rise so that once-surface horizons were buried more deeply and hence became increasingly divorced from the modern organic cycle over time. The SOM adsorbed when the soil horizon was at the land surface was preserved in the buried soils because a fractal pore network of allophane aggregates and nanopores encapsulated and shielded the ‘old’ or relict SOM (including quinonic carbon) derived from past environments of the Holocene.

To provide fundamental knowledge about the interaction of allophane, DNA, and SOM in soils, I examined the adsorption capacity and adsorption mechanisms of salmon-sperm DNA on pure synthetic allophane and humic acidrich synthetic allophane. The pure synthetic allophane was able to adsorb up to 34 μg/mg of salmon-sperm DNA, but the humic acid-rich synthetic allophane adsorbed only 3.5 μg/mg of salmon-sperm DNA. Salmon-sperm DNA was adsorbed chemically through its phosphate group to the aluminol groups of synthetic allophane, and adsorbed chemically through humic acid covering the synthetic allophane spherules, and thus became bound indirectly to synthetic allophane. The chemical adsorption of salmon-sperm DNA on synthetic allophane led to the aggregation of allophane spherules to form nanoaggregates and microaggregates, and ~80% of total adsorbed DNA on allophane was held physically within the interstices (pores) between allophane spherules and nanoaggregates. The encapsulated DNA within the stable allophane-DNA aggregates may not be accessible to enzymes nor microbes, hence enabling DNA protection and preservation in allophanic soils. By implication, organic carbon is therefore likely to be sequestered and protected in allophanic soils (Andisols) in the same way as demonstrated here for DNA − that is, predominantly by encapsulation within a tortuous network of nanopores and submicropores amidst stable nanoaggregates and microaggregates, rather than by chemisorption alone.

A novel two-step method was developed to isolate DNA from allophane, based in part on experiments devised to extract salmon-sperm DNA from synthetic allophane. The two-step method for DNA extraction from allophanic soils is based on (1) chelating DNA and blocking adsorptive sites on allophane using EDTA and phosphate, respectively, and (2) dissolving allophane using acidified ammonium oxalate. The DNA yield from three allophanic paleosols on Holocene tephras was up to 44.5 μg/g soil (oven-dry basis). The extracted DNA was then successfully purified via gel electrophoresis followed by a gel purification kit, and the amplifiable and sequenced DNA extracted from a paleosol (which had been at the land surface for around 4000 years between c. 9423 and c. 5526 calendar years BP) on Rotoma tephra contained New Zealand endemic and exotic plants that differed from the European grasses growing currently on the land surface. The difference in vegetation indicates that the DNA extraction method I (with others) have developed is able to access environmental DNA originating from previous vegetation cover. The DNA extraction method could be used to facilitate the search for possible PalEnDNA in allophanic paleosols for reconstructing the past terrestrial environments as well as to investigate the biodiversity in allophanic soils and the origins of SOM.

Allophanic soils are demonstrably able to protect environmental DNA from degradation for a long period of time, and such DNA is able to reveal past environments. However, the duration over which that environmental DNA can be preserved in allophanic soils needs to be resolved, and additional investigations of gene diversity in allophanic paleosols of different ages using high-throughput sequencing (HTS) are required to determine the taxonomic profiles recovered in paleosols and to rule out contamination of modern DNA.

year: 2016

title: Mortality, morbidity and population health dynamics

authors: Cheung, Jit

abstract: This thesis is concerned with the dynamics of the health of populations with low levels of mortality, using the non-Maori population in New Zealand as a case study. The primary objective is to study patterns and trends in mortality and morbidity, their interactions, and their implications for the future. 

The key questions addressed in this thesis are central to the future evolution of population health. Given the significant declines in mortality, especially those at older ages that have occurred over the last two decades, will mortality declines at advanced ages continue much longer? Or will mortality become increasingly compressed into a narrow range of ages at death? Moreover, what are the implications for morbidity trends and any indications at present of future trends in population health? Will increased survivorship be accompanied by long periods in ill-health, or will morbidity move in tandem with mortality, or will durations surviving but in ill-health actually decrease? 

The thesis first establishes a theoretical platform by reviewing and synthesising transition theories and empirical observations into a general framework to guide the understanding of population health dynamics. It also forges a theoretical linkage between variations in the individual senescence process, which underpin the validity of demographic models of mortality and morbidity, and their population level manifestations. These theoretical extensions provide the context for an evaluation of contemporary theories on mortality trends and changes in morbidity in relation to mortality. 

In addition to using long term historical data spanning over a century and complemented by a population-based true cohort approach, this thesis also makes methodological advancements by adapting and developing a tool, known as health expectancy, for the analysis of population health. In particular, a new measure termed “hospitalisation expectancy” is developed. It integrates data on hospital utilisation and mortality to yield a summary measure of population health.

The empirical study documents the shift in the forces of mortality of non-Maori, from younger to older ages, and from communicable causes of death to chronic degenerative diseases. Results of the mortality analysis by cohorts show that while there may be some indications of a future trend towards mortality compression, further increases in life expectancy at birth can be realistically expected. Empirical evidence of compression of morbidity is found in the trends of hospitalisation and the patterns of severe forms of disability. The causes of morbidity are becoming more diversified, dominated by non-lethal conditions; whereas the causes of mortality are becoming increasingly compressed into a few chronic conditions, namely cancers and cardiovascular diseases. It is also established in this thesis that the older population represents a heterogeneous group in terms of levels of susceptibility to ill-health. An empirical method for identifying heterogeneity is developed to show non-Maori inter-cohort differences in this property. 

Later in the thesis, a cohort based mortality projection of non-Maori at adult ages is undertaken. Various scenarios of morbidity responses to the projected mortality changes, incorporating the leading theories on future morbidity changes, are then modelled. To conclude the thesis, the implications for policy of further mortality declines at older age among an increasingly heterogeneous population are discussed.

text: Mortality, morbidity and population health dynamics This thesis is concerned with the dynamics of the health of populations with low levels of mortality, using the non-Maori population in New Zealand as a case study. The primary objective is to study patterns and trends in mortality and morbidity, their interactions, and their implications for the future. 

The key questions addressed in this thesis are central to the future evolution of population health. Given the significant declines in mortality, especially those at older ages that have occurred over the last two decades, will mortality declines at advanced ages continue much longer? Or will mortality become increasingly compressed into a narrow range of ages at death? Moreover, what are the implications for morbidity trends and any indications at present of future trends in population health? Will increased survivorship be accompanied by long periods in ill-health, or will morbidity move in tandem with mortality, or will durations surviving but in ill-health actually decrease? 

The thesis first establishes a theoretical platform by reviewing and synthesising transition theories and empirical observations into a general framework to guide the understanding of population health dynamics. It also forges a theoretical linkage between variations in the individual senescence process, which underpin the validity of demographic models of mortality and morbidity, and their population level manifestations. These theoretical extensions provide the context for an evaluation of contemporary theories on mortality trends and changes in morbidity in relation to mortality. 

In addition to using long term historical data spanning over a century and complemented by a population-based true cohort approach, this thesis also makes methodological advancements by adapting and developing a tool, known as health expectancy, for the analysis of population health. In particular, a new measure termed “hospitalisation expectancy” is developed. It integrates data on hospital utilisation and mortality to yield a summary measure of population health.

The empirical study documents the shift in the forces of mortality of non-Maori, from younger to older ages, and from communicable causes of death to chronic degenerative diseases. Results of the mortality analysis by cohorts show that while there may be some indications of a future trend towards mortality compression, further increases in life expectancy at birth can be realistically expected. Empirical evidence of compression of morbidity is found in the trends of hospitalisation and the patterns of severe forms of disability. The causes of morbidity are becoming more diversified, dominated by non-lethal conditions; whereas the causes of mortality are becoming increasingly compressed into a few chronic conditions, namely cancers and cardiovascular diseases. It is also established in this thesis that the older population represents a heterogeneous group in terms of levels of susceptibility to ill-health. An empirical method for identifying heterogeneity is developed to show non-Maori inter-cohort differences in this property. 

Later in the thesis, a cohort based mortality projection of non-Maori at adult ages is undertaken. Various scenarios of morbidity responses to the projected mortality changes, incorporating the leading theories on future morbidity changes, are then modelled. To conclude the thesis, the implications for policy of further mortality declines at older age among an increasingly heterogeneous population are discussed.

year: 1999

title: What is the difference? What factors contribute to the variation of achievement for Year 7 and 8 Māori students in high decile, full primary schools?

authors: McLocklan, Sue

subjects: Maori student achievement

abstract: The educational disparity between indigenous Māori students and those of the majority continue to be a major issue in New Zealand. Attempting to bridge the gap for Māori students has generated focus on Māori student engagement in the classroom, the actions and understanding of the teacher and the relationship and interactions between the teacher and students in their learning environment. Elements of culturally responsive pedagogy have been identified as positive contributing factors to accelerating academic achievement for secondary Māori mainstream students. 
This small-scale cross-cultural exploratory qualitative research project seeks to identify the factors that contribute to student achievement variation for Year 7 and 8 students in high decile full primary schools and the integration of teacher’s cultural competencies in high quality learning opportunities. Within a kaupapa Māori research process, this study uses empirical data collected from a purposive sample through a semi-structured individual interview and a for self-assessment. Voluntary research participants were twelve students and six teachers in three schools in the Bay of Plenty, Waikato and Wellington regions. This research examines the engagement of student and teacher in pedagogical practice, learning variables, cultural knowledge and practices attributable to positive academic achievement for Māori. 
The findings reveal that when teachers place themselves in an agentic position; adopt a professional commitment and willingness to engage in effective relations, interactions and reciprocal practices to support Māori learners, high levels of relational trust and expectations prevail through mutual respect and interdependence to attain successful educational outcomes.
Further teacher professional learning is essential to enlighten and deepen teachers' understanding of culturally responsive pedagogy to enable Māori learners to reach their potential to participate and contribute in their world of choice.

text: What is the difference? What factors contribute to the variation of achievement for Year 7 and 8 Māori students in high decile, full primary schools? The educational disparity between indigenous Māori students and those of the majority continue to be a major issue in New Zealand. Attempting to bridge the gap for Māori students has generated focus on Māori student engagement in the classroom, the actions and understanding of the teacher and the relationship and interactions between the teacher and students in their learning environment. Elements of culturally responsive pedagogy have been identified as positive contributing factors to accelerating academic achievement for secondary Māori mainstream students. 
This small-scale cross-cultural exploratory qualitative research project seeks to identify the factors that contribute to student achievement variation for Year 7 and 8 students in high decile full primary schools and the integration of teacher’s cultural competencies in high quality learning opportunities. Within a kaupapa Māori research process, this study uses empirical data collected from a purposive sample through a semi-structured individual interview and a for self-assessment. Voluntary research participants were twelve students and six teachers in three schools in the Bay of Plenty, Waikato and Wellington regions. This research examines the engagement of student and teacher in pedagogical practice, learning variables, cultural knowledge and practices attributable to positive academic achievement for Māori. 
The findings reveal that when teachers place themselves in an agentic position; adopt a professional commitment and willingness to engage in effective relations, interactions and reciprocal practices to support Māori learners, high levels of relational trust and expectations prevail through mutual respect and interdependence to attain successful educational outcomes.
Further teacher professional learning is essential to enlighten and deepen teachers' understanding of culturally responsive pedagogy to enable Māori learners to reach their potential to participate and contribute in their world of choice.

year: 2013