title: Breast cancer talk: A cross-linguistic study of lexical verbs occurring with generic pronoun ‘you’

authors: Malik, Sara

subjects: corpus linguistics

abstract: Breast cancer discourse is increasingly studied within medical humanities, reflecting a broader interest in illness narratives and patient-centered storytelling (DeShazer, 2005; Frank, 1995). Using a cognitive, usage-based approach, we explore how New Zealand (NZ) English and Pakistani (PK) Urdu speakers use language, particularly metaphor, speech acts, pronouns and verbs to express their cancer experiences on YouTube. This paper focuses on one aspect: the use of lexical verbs following generic second-person pronouns, analysing their semantic patterns which offer insight into how speakers construe illness. Drawing on Payne’s (2011) verb categories and expanding Durst-Andersen et al.’s (2013) classification of
state verbs, this study explores the range and types of verbs in both datasets. The data includes 46 narratives from NZ and 36 from PK, posted between 2011 and 2023 by organisations such as the NZ Breast Cancer Foundation and Pink Ribbon Pakistan. These videos were transcribed using Whisper AI and filtered to include only patients’ discourse, then organised into eight narrative topics. A mixed-method approach was used: quantitative analysis with AntConc extracted keyword-in-context (KWIC) instances of you, followed by qualitative analysis to identify generic uses of you and the types of verbs that follow it. The study investigates (a) shared and distinct lexical verbs across datasets, and (b) insights from the most frequent verbs. Preliminary findings show that most verb types are similar across both datasets, with action and state verbs being the most frequently used. Building on Stirling and Manderson’s (2011) findings about the use of generic you pronoun in Australian English, we report that speakers of both NZ English and PK Urdu similarly use generic you, along with state verbs to foster empathy and action verbs to convey credibility and authority in illness narratives. We argue that pronoun-verb pairings function as strategic tools for positioning cancer experiences within speaker narratives.

text: Breast cancer talk: A cross-linguistic study of lexical verbs occurring with generic pronoun ‘you’ Breast cancer discourse is increasingly studied within medical humanities, reflecting a broader interest in illness narratives and patient-centered storytelling (DeShazer, 2005; Frank, 1995). Using a cognitive, usage-based approach, we explore how New Zealand (NZ) English and Pakistani (PK) Urdu speakers use language, particularly metaphor, speech acts, pronouns and verbs to express their cancer experiences on YouTube. This paper focuses on one aspect: the use of lexical verbs following generic second-person pronouns, analysing their semantic patterns which offer insight into how speakers construe illness. Drawing on Payne’s (2011) verb categories and expanding Durst-Andersen et al.’s (2013) classification of
state verbs, this study explores the range and types of verbs in both datasets. The data includes 46 narratives from NZ and 36 from PK, posted between 2011 and 2023 by organisations such as the NZ Breast Cancer Foundation and Pink Ribbon Pakistan. These videos were transcribed using Whisper AI and filtered to include only patients’ discourse, then organised into eight narrative topics. A mixed-method approach was used: quantitative analysis with AntConc extracted keyword-in-context (KWIC) instances of you, followed by qualitative analysis to identify generic uses of you and the types of verbs that follow it. The study investigates (a) shared and distinct lexical verbs across datasets, and (b) insights from the most frequent verbs. Preliminary findings show that most verb types are similar across both datasets, with action and state verbs being the most frequently used. Building on Stirling and Manderson’s (2011) findings about the use of generic you pronoun in Australian English, we report that speakers of both NZ English and PK Urdu similarly use generic you, along with state verbs to foster empathy and action verbs to convey credibility and authority in illness narratives. We argue that pronoun-verb pairings function as strategic tools for positioning cancer experiences within speaker narratives.

year: 2025

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: Surplus Public Works Land: The Crown's Special Duty to Maori

authors: Grayson, Michael Robert

subjects: Maori

abstract: The Crown's obligations to Maori regarding the offer back of surplus Crown land under s40 of the Public Works Act 1981.

text: Surplus Public Works Land: The Crown's Special Duty to Maori The Crown's obligations to Maori regarding the offer back of surplus Crown land under s40 of the Public Works Act 1981.

year: 2017