title: The working life of John McCraw (1925-2014): a remarkable New Zealand pedologist and Earth scientist

authors: Nelson, Campbell S.

abstract: John McCraw was an Earth scientist who began working as a pedologist with Soil Bureau, DSIR, then became the Foundation Professor of Earth Sciences at the University of Waikato in Hamilton, inspiring a new generation to study and work in Earth sciences, a discipline he introduced into the tertiary education system in New Zealand. In retirement, he was an author and historian with a special emphasis on Central Otago as well as the Waikato region. Throughout his career, marked especially by meritorious leadership, accomplished administration, and commitment to his staff and students at the University of Waikato, John McCraw also contributed widely to the communities in which he lived through public service organizations and as a public speaker. He received a number of awards including an MBE, fellowship, and companionship, and, uniquely, is commemorated also with a glacier, a fossil, and a museum-based research room named for him. The Earth sciences programme today as an integral part of the School of Science at the University of Waikato is stronger than ever. In the past few years several new staff have been appointed, both academic and technical, giving the largest-ever Earth sciences team of about 30 staff. As well as research-led teaching, Earth sciences has strong research groups, at the cores of which are doctoral and masterate students, and postdoctoral fellows, to carry on the work envisaged by John McCraw all those years ago. This thriving continuation of our discipline, which has always had strong multidisciplinary linkages with other sciences, is − alongside the countless students he has taught and inspired − surely his greatest legacy.

text: The working life of John McCraw (1925-2014): a remarkable New Zealand pedologist and Earth scientist John McCraw was an Earth scientist who began working as a pedologist with Soil Bureau, DSIR, then became the Foundation Professor of Earth Sciences at the University of Waikato in Hamilton, inspiring a new generation to study and work in Earth sciences, a discipline he introduced into the tertiary education system in New Zealand. In retirement, he was an author and historian with a special emphasis on Central Otago as well as the Waikato region. Throughout his career, marked especially by meritorious leadership, accomplished administration, and commitment to his staff and students at the University of Waikato, John McCraw also contributed widely to the communities in which he lived through public service organizations and as a public speaker. He received a number of awards including an MBE, fellowship, and companionship, and, uniquely, is commemorated also with a glacier, a fossil, and a museum-based research room named for him. The Earth sciences programme today as an integral part of the School of Science at the University of Waikato is stronger than ever. In the past few years several new staff have been appointed, both academic and technical, giving the largest-ever Earth sciences team of about 30 staff. As well as research-led teaching, Earth sciences has strong research groups, at the cores of which are doctoral and masterate students, and postdoctoral fellows, to carry on the work envisaged by John McCraw all those years ago. This thriving continuation of our discipline, which has always had strong multidisciplinary linkages with other sciences, is − alongside the countless students he has taught and inspired − surely his greatest legacy.

year: 2015

title: The structural and mechanistic characterisation of Thermophilic RNA Ligases

authors: Kamal, Aliyah

subjects: RNA Ligase

abstract: MicroRNAs (miRNAs) are short regulatory RNAs that play critical roles in post-transcriptional gene regulation. Dysregulation of miRNA expression can be implicated in numerous diseases, including cancer, making miRNAs valuable diagnostic and prognostic biomarkers. Next-generation sequencing (NGS) enables quantitative profiling of miRNA populations, but a key limitation lies in the adapter ligation step required for library preparation. Current commercial RNA ligases, typically active between 14-37 ℃, display strong biases based on RNA sequence and secondary structure resulting in a skewed representation of miRNA populations. At low temperatures, miRNA secondary structures can obscure 5’-phosphate, and 3’-hydroxyl ends, preventing efficient ligation. Thermophilic RNA ligases with high thermostability and distinct substrate preferences may therefore reduce ligation bias and improve NGS accuracy. The archaeal Paleococcus pacificus RNA ligase (PpaRnl) represents a valuable model for exploring the structural and mechanistic features of thermophilic RNA ligases. 
This study aimed to further investigate the substrate preference of a PpaRnl mutant; K238G, a point mutation of lysine at position 238, a key residue in the coordination of the AMP and in turn the binding of the Mg2+ ions in PpaRnl. Alongside the structural and mechanistic characterisation of several PpaRnl mutants to explore the role of a newly identified Mg2+ binding site (Mg2+ B) close to the active site. Key residues for coordinating the Mg2+B ion were mutated in the PpaRnl enzyme (D94A, D248A, E155A, and the double mutant D94A-D248A) as characterisation of these mutants would allow for a deeper understanding of this mechanism. 
Mutants were expressed in Escherichia coli and purified using a combination of immobilised metal affinity chromatography (IMAC) and gel-filtration chromatography. Expression and purification outcomes varied significantly between constructs, while some mutants were successfully obtained in sufficient yields, others demonstrated poor or inconsistent expression, often not even seeing improvement after optimisation of growth conditions and large-scale culture volumes. In particular, the E155A mutant displayed extremely slow growth, while the D94A-D248A double mutant produced negligible results across expression trials. Further characterisation of the mutants, K238G, D94A, and D248A, had shown that these enzymes retain robust activity between 60-65 ℃, with measurable activity extending up to 80 ℃.  Distinct sequence and cofactor preferences were observed. When combined with adapters, these mutants efficiently produced RNA ligation products with minimal side reactions and, in several cases, displayed improved activity compared to the wild-type enzyme. 
The structures of PpaRnl D94A and D248A were solved via X-ray crystallography and although there was similarity in the structures compared to that of the wild-type enzyme and K238G, it was found that a number of the residues coordinating the ligands present within the active-site had changed their orientation. This resulted in the Mg2+B ion not being present in D94A, and no AMP cofactor, Mg2+A or Mg2+B present within the D248A mutant.
Overall, this work highlighted the variability in expression and crystallisation outcomes among the second Mg2+ binding site mutants of PpaRnl with notable differences observed in expression, activity, and structure, highlighting that the Mg2+B ion and its coordination have an impact of the efficiency of the enzyme. This unique mechanism is still not fully understood but its importance and impact has been highlighted within this research, reiterating the importance of construct specific optimisation in structural studies and the potential utility of engineered thermophilic RNA ligases, as tools to reduce ligation bias in NGS based miRNA sequencing. Allowing for the possible discovery of biomarkers within viral diseases, and cancer.

text: The structural and mechanistic characterisation of Thermophilic RNA Ligases MicroRNAs (miRNAs) are short regulatory RNAs that play critical roles in post-transcriptional gene regulation. Dysregulation of miRNA expression can be implicated in numerous diseases, including cancer, making miRNAs valuable diagnostic and prognostic biomarkers. Next-generation sequencing (NGS) enables quantitative profiling of miRNA populations, but a key limitation lies in the adapter ligation step required for library preparation. Current commercial RNA ligases, typically active between 14-37 ℃, display strong biases based on RNA sequence and secondary structure resulting in a skewed representation of miRNA populations. At low temperatures, miRNA secondary structures can obscure 5’-phosphate, and 3’-hydroxyl ends, preventing efficient ligation. Thermophilic RNA ligases with high thermostability and distinct substrate preferences may therefore reduce ligation bias and improve NGS accuracy. The archaeal Paleococcus pacificus RNA ligase (PpaRnl) represents a valuable model for exploring the structural and mechanistic features of thermophilic RNA ligases. 
This study aimed to further investigate the substrate preference of a PpaRnl mutant; K238G, a point mutation of lysine at position 238, a key residue in the coordination of the AMP and in turn the binding of the Mg2+ ions in PpaRnl. Alongside the structural and mechanistic characterisation of several PpaRnl mutants to explore the role of a newly identified Mg2+ binding site (Mg2+ B) close to the active site. Key residues for coordinating the Mg2+B ion were mutated in the PpaRnl enzyme (D94A, D248A, E155A, and the double mutant D94A-D248A) as characterisation of these mutants would allow for a deeper understanding of this mechanism. 
Mutants were expressed in Escherichia coli and purified using a combination of immobilised metal affinity chromatography (IMAC) and gel-filtration chromatography. Expression and purification outcomes varied significantly between constructs, while some mutants were successfully obtained in sufficient yields, others demonstrated poor or inconsistent expression, often not even seeing improvement after optimisation of growth conditions and large-scale culture volumes. In particular, the E155A mutant displayed extremely slow growth, while the D94A-D248A double mutant produced negligible results across expression trials. Further characterisation of the mutants, K238G, D94A, and D248A, had shown that these enzymes retain robust activity between 60-65 ℃, with measurable activity extending up to 80 ℃.  Distinct sequence and cofactor preferences were observed. When combined with adapters, these mutants efficiently produced RNA ligation products with minimal side reactions and, in several cases, displayed improved activity compared to the wild-type enzyme. 
The structures of PpaRnl D94A and D248A were solved via X-ray crystallography and although there was similarity in the structures compared to that of the wild-type enzyme and K238G, it was found that a number of the residues coordinating the ligands present within the active-site had changed their orientation. This resulted in the Mg2+B ion not being present in D94A, and no AMP cofactor, Mg2+A or Mg2+B present within the D248A mutant.
Overall, this work highlighted the variability in expression and crystallisation outcomes among the second Mg2+ binding site mutants of PpaRnl with notable differences observed in expression, activity, and structure, highlighting that the Mg2+B ion and its coordination have an impact of the efficiency of the enzyme. This unique mechanism is still not fully understood but its importance and impact has been highlighted within this research, reiterating the importance of construct specific optimisation in structural studies and the potential utility of engineered thermophilic RNA ligases, as tools to reduce ligation bias in NGS based miRNA sequencing. Allowing for the possible discovery of biomarkers within viral diseases, and cancer.

year: 2025-09-14

title: The source, composition and typology of ‘Limestone’ Adzes from Eastern North Island, New Zealand

authors: Nelson, Campbell S.

subjects: adzes

abstract: Collections of stone adzes (toki) from the eastern North Island of New Zealand include a number of typologically early (Archaic) forms made from what has been previously described as ‘siliceous or silicified limestone’. Seventy five finished adzes and preforms of this material were recorded in the present study. Their geographic distribution is primarily restricted to southern Hawkes Bay – Wairarapa, and they apparently originated from a single manufacturing centre at Owahanga, on the northern Wairarapa coast. Chemical and mineralogical analyses (by X-ray fluorescence, portable XRF, vacuum gasometry and X-ray diffraction) of two artefacts from Owahanga show they contain about 20–30 per cent CaCO3 (as calcite), while samples of the presumed local source rock have a slightly higher carbonate content but comparable silica (quartz) and Rb concentrations. The rock type used in the manufacture of adzes was therefore not a true limestone but calcareous mudstone, compositionally distinct from siliceous limestones in southern Wairarapa and probably derived from the Whangai Formation. Possible reasons for the use of this stone material are discussed.

text: The source, composition and typology of ‘Limestone’ Adzes from Eastern North Island, New Zealand Collections of stone adzes (toki) from the eastern North Island of New Zealand include a number of typologically early (Archaic) forms made from what has been previously described as ‘siliceous or silicified limestone’. Seventy five finished adzes and preforms of this material were recorded in the present study. Their geographic distribution is primarily restricted to southern Hawkes Bay – Wairarapa, and they apparently originated from a single manufacturing centre at Owahanga, on the northern Wairarapa coast. Chemical and mineralogical analyses (by X-ray fluorescence, portable XRF, vacuum gasometry and X-ray diffraction) of two artefacts from Owahanga show they contain about 20–30 per cent CaCO3 (as calcite), while samples of the presumed local source rock have a slightly higher carbonate content but comparable silica (quartz) and Rb concentrations. The rock type used in the manufacture of adzes was therefore not a true limestone but calcareous mudstone, compositionally distinct from siliceous limestones in southern Wairarapa and probably derived from the Whangai Formation. Possible reasons for the use of this stone material are discussed.

year: 2016