title: Hypsometry of New Zealand estuaries

authors: Dejeans, Bérengère S.

subjects: hypsometry

abstract: Estuarine morphology is constantly changing because of continual sediment transport mainly driven by tidal asymmetry and wind waves. For modelling purposes, intertidal areas have often been simplified to relatively semi-circular basins. Although suitable for providing a preliminary understanding of processes, this approach does not take into account the real curvature of natural basins. One way of studying the morphology of an estuary is to use its hypsometry. This quantity, often represented as a curve, describes the area-weighted distribution of depth and therefore includes the uneven form of a basin. Overseas studies have shown that the shape of the hypsometric curve of an estuary can be used as a measure of its state of infilling.
	The present study focuses on the morphology of New Zealand estuaries by comparing their hypsometric curves and examining the relative contribution of various forcing factors towards the shape of these curves and consequently towards the development of the morphology. I applied the hypsometric relationship defined by Boon & Byrne (1981) in order to assess how well it describes New Zealand estuaries and what factors influence the shape of the hypsometric curve. Their equation introduces the empirical parameter   which controls the concavity of the curve. Area-depth curves were computed using bathymetric data for the 22 studied estuaries. The best fitting curves relative to Boon & Byrne’s relationship were determined by minimising the error between the modelled and observed curves and provided a measure of   for each site. This relationship appeared to be relatively satisfactory (error of less than 5%) for most estuaries. A database was created where the tidal range, the length of the longest fetch, the length of the fetch along the direction of most common winds, the wind speed and the significant wave height were stored for each study estuary. The impact of each parameter was estimated using statistical clustering analysis. No clear correlation could be identified. Conversely the results suggest that estuaries with the same environmental conditions could present very different values of γ. Current data, sedimentation accumulation rates and proportion of intertidal area at high water were also collected which enabled to observe that for some study sites the value of   seems to be a reasonable indicator of the degree of infilling. However there were exceptions and some sites with higher γ were in an advanced state of infilling. This suggests that even though Boon & Byrne’s relationship provides a reasonable representation of the hypsometry of New Zealand estuaries, the parameter   does not seem to be a satisfactory measure of infilling of New Zealand estuaries. The present study also showed that when comparing with studies conducted in the United Kingdom and in the United Stated it appeared that the values of   estimated for New Zealand estuaries are in the whole higher than overseas. This could be attributed to the fact that New Zealand basins are relatively young systems but also could be due to other specificities of those basins such as the influence of the geology.

text: Hypsometry of New Zealand estuaries Estuarine morphology is constantly changing because of continual sediment transport mainly driven by tidal asymmetry and wind waves. For modelling purposes, intertidal areas have often been simplified to relatively semi-circular basins. Although suitable for providing a preliminary understanding of processes, this approach does not take into account the real curvature of natural basins. One way of studying the morphology of an estuary is to use its hypsometry. This quantity, often represented as a curve, describes the area-weighted distribution of depth and therefore includes the uneven form of a basin. Overseas studies have shown that the shape of the hypsometric curve of an estuary can be used as a measure of its state of infilling.
	The present study focuses on the morphology of New Zealand estuaries by comparing their hypsometric curves and examining the relative contribution of various forcing factors towards the shape of these curves and consequently towards the development of the morphology. I applied the hypsometric relationship defined by Boon & Byrne (1981) in order to assess how well it describes New Zealand estuaries and what factors influence the shape of the hypsometric curve. Their equation introduces the empirical parameter   which controls the concavity of the curve. Area-depth curves were computed using bathymetric data for the 22 studied estuaries. The best fitting curves relative to Boon & Byrne’s relationship were determined by minimising the error between the modelled and observed curves and provided a measure of   for each site. This relationship appeared to be relatively satisfactory (error of less than 5%) for most estuaries. A database was created where the tidal range, the length of the longest fetch, the length of the fetch along the direction of most common winds, the wind speed and the significant wave height were stored for each study estuary. The impact of each parameter was estimated using statistical clustering analysis. No clear correlation could be identified. Conversely the results suggest that estuaries with the same environmental conditions could present very different values of γ. Current data, sedimentation accumulation rates and proportion of intertidal area at high water were also collected which enabled to observe that for some study sites the value of   seems to be a reasonable indicator of the degree of infilling. However there were exceptions and some sites with higher γ were in an advanced state of infilling. This suggests that even though Boon & Byrne’s relationship provides a reasonable representation of the hypsometry of New Zealand estuaries, the parameter   does not seem to be a satisfactory measure of infilling of New Zealand estuaries. The present study also showed that when comparing with studies conducted in the United Kingdom and in the United Stated it appeared that the values of   estimated for New Zealand estuaries are in the whole higher than overseas. This could be attributed to the fact that New Zealand basins are relatively young systems but also could be due to other specificities of those basins such as the influence of the geology.

year: 2015

title: Structural and biochemical characterisation of O-acetylserine  sulphydrylase (CysK) from Neisseria gonorrhoeae

authors: McGarvie, Jack

subjects: Biochemistry

abstract: Neisseria gonorrhoeae is the causative bacteria of the sexually transmitted infection (STI), gonorrhoea. Rapid emergence of antibiotic resistant strains of N. gonorrhoeae has given rise to almost untreatable gonorrhoea over the last few decades. There is an urgent need for development of new antimicrobial treatments for gonorrhoea infection. Synthesis of the amino acid cysteine is a promising new target for the development of new antimicrobials. Cysteine plays a vital role in protein folding and function, and synthesis of glutathione for protection against oxidative stress during infection. 
The final step of the two-step cysteine biosynthesis pathway is catalysed by the enzyme O-acetylserine sulphydrylase (OASS). Most bacteria have two isoforms of OASS, OASS-A/CysK that utilises sulphide and O-acetylserine for the synthesis of cysteine and OASS-B/CysM that utilises thiosulphate. N. gonorrhoeae has just one OASS isoform (annotated as CysK) in its genome. N. gonorrhoeae displays unique differences in its sulphate acquisition pathway for cysteine biosynthesis, yet little is known about these pathways in N. gonorrhoeae. We propose CysK is a potential antimicrobial target. This 
thesis biochemically characterises the structure and function of CysK to determine its role in cysteine biosynthesis. Kinetic characterisation demonstrates that CysK has O-acetylserine sulphydrylase activity and displays positive cooperativity with respect to substrates, O-acetylserine and sulphide. Sulphide shows partial allosteric inhibition, and the enzyme does not use thiosulphate as a substrate. The structure of CysK was solved to 2.49 Å by X-ray crystallography and shows CysK belongs to the tryptophan synthase β superfamily and adopts a homodimeric structure consisting of two monomers. The structure supports positive cooperativity as co-factor binding residues are in inactive and active conformations in each monomer of the dimer, respectively. Many CysK enzymes form complexes with the first enzyme in the two-step cysteine synthesis pathway, CysE. It appears CysE and CysK from N. gonorrhoeae are unable to form a complex, indicating an alternate pathway for regulation of sulphur flux and cysteine production. Attempts to investigate the in vivo role of CysK were inconclusive.
The research presented in this thesis represents a major leap in our understanding of the  uncharacterised cysteine biosynthesis pathway in N. gonorrhoeae. Data presented here is the basis for future work using the kinetics and structure of CysK to guide computational inhibitor design, to identify lead compounds for CysK inhibition, and thereby development of new antimicrobials for treatment of extensively drug resistant gonorrhoea.

text: Structural and biochemical characterisation of O-acetylserine  sulphydrylase (CysK) from Neisseria gonorrhoeae Neisseria gonorrhoeae is the causative bacteria of the sexually transmitted infection (STI), gonorrhoea. Rapid emergence of antibiotic resistant strains of N. gonorrhoeae has given rise to almost untreatable gonorrhoea over the last few decades. There is an urgent need for development of new antimicrobial treatments for gonorrhoea infection. Synthesis of the amino acid cysteine is a promising new target for the development of new antimicrobials. Cysteine plays a vital role in protein folding and function, and synthesis of glutathione for protection against oxidative stress during infection. 
The final step of the two-step cysteine biosynthesis pathway is catalysed by the enzyme O-acetylserine sulphydrylase (OASS). Most bacteria have two isoforms of OASS, OASS-A/CysK that utilises sulphide and O-acetylserine for the synthesis of cysteine and OASS-B/CysM that utilises thiosulphate. N. gonorrhoeae has just one OASS isoform (annotated as CysK) in its genome. N. gonorrhoeae displays unique differences in its sulphate acquisition pathway for cysteine biosynthesis, yet little is known about these pathways in N. gonorrhoeae. We propose CysK is a potential antimicrobial target. This 
thesis biochemically characterises the structure and function of CysK to determine its role in cysteine biosynthesis. Kinetic characterisation demonstrates that CysK has O-acetylserine sulphydrylase activity and displays positive cooperativity with respect to substrates, O-acetylserine and sulphide. Sulphide shows partial allosteric inhibition, and the enzyme does not use thiosulphate as a substrate. The structure of CysK was solved to 2.49 Å by X-ray crystallography and shows CysK belongs to the tryptophan synthase β superfamily and adopts a homodimeric structure consisting of two monomers. The structure supports positive cooperativity as co-factor binding residues are in inactive and active conformations in each monomer of the dimer, respectively. Many CysK enzymes form complexes with the first enzyme in the two-step cysteine synthesis pathway, CysE. It appears CysE and CysK from N. gonorrhoeae are unable to form a complex, indicating an alternate pathway for regulation of sulphur flux and cysteine production. Attempts to investigate the in vivo role of CysK were inconclusive.
The research presented in this thesis represents a major leap in our understanding of the  uncharacterised cysteine biosynthesis pathway in N. gonorrhoeae. Data presented here is the basis for future work using the kinetics and structure of CysK to guide computational inhibitor design, to identify lead compounds for CysK inhibition, and thereby development of new antimicrobials for treatment of extensively drug resistant gonorrhoea.

year: 2021

title: Indigenous Rights Hollow Rights?

authors: Toki, Valmaine

abstract: The Declaration on the Rights of Indigenous Peoples (“the Declaration”) was the initiative of the Working Group on Indigenous Populations (“WGIP”). Established in 1982, the mandate of the WGIP was to develop international standards concerning Indigenous peoples’ rights. The Declaration was a manifestation of this mandate and a clear articulation of international standards on the rights of Indigenous peoples. It was not until 25 years later, in September 2007, that the final text was adopted by the General Assembly with a majority of 143 states in favour. Eleven states offered abstentions. Four states opposed adoption: Australia, Canada, the United States of America (“the United States”) and New Zealand.

text: Indigenous Rights Hollow Rights? The Declaration on the Rights of Indigenous Peoples (“the Declaration”) was the initiative of the Working Group on Indigenous Populations (“WGIP”). Established in 1982, the mandate of the WGIP was to develop international standards concerning Indigenous peoples’ rights. The Declaration was a manifestation of this mandate and a clear articulation of international standards on the rights of Indigenous peoples. It was not until 25 years later, in September 2007, that the final text was adopted by the General Assembly with a majority of 143 states in favour. Eleven states offered abstentions. Four states opposed adoption: Australia, Canada, the United States of America (“the United States”) and New Zealand.

year: 2011