title: DNA repair enzymes in Prochlorococcus marinus strain MIT9312

authors: Kirby, Bronwyn

abstract: Prochlorococcus marinus, a marine cyanobacterium, is one of the most abundant photosynthetic organisms in the ocean. P. marinus contributes towards approximately 8.5% of global ocean primary productivity. P. marinus is of interest because of the cell’s simple and unique photosynthetic system, efficient carbon concentrating mechanism, and streamlined genome. P. marinus strain MIT9312 is a high-light adapted strain that thrives in the upper euphotic zone where there are minimal nutrients and high levels of UV exposure, which would typically put an organism at risk. Understanding the function of repair proteins is significant for being able to identify the DNA repair pathways used by Prochlorococcus to survive under increasingly more harmful conditions. My research, outlined in this thesis, aimed to characterize DNA repair enzymes in Prochlorococcus marinus strain MIT9312 to further our understanding of cyanobacterial growth, survival, and repair.

LigW is an ATP-dependent ligase that is unique to strain MIT9312. It was found to have low ligase activity on nicked DNA compared to other ligases, making its retention in the small Prochlorococcus genome unusual. It is suspected that LigW could achieve higher ligation rates by interacting with other proteins. LigW is in an operon with other proteins that are predicted to promote LigW activity or have their own DNA modifying activities. The three proteins of interest have been annotated as Pmar3, Pmar4, and Pmar5. The
individual function and relationships between each protein were investigated in this thesis.

This thesis focused on recombinantly producing and biochemically characterizing three of the proteins adjacent to LigW and assessing their activities in vitro. Pmar3 was successfully expressed, purified, and characterized as a potential nuclease. Further mutagenesis work will confirm the proposed function of Pmar3. Attempts were made to characterize Pmar4, with further optimization of expression and purification protocols necessary. Pmar5 has been characterized as a pentameric Mg-dependent topoisomerase-like protein, with an inability to re-join DNA. It is likely that these proteins on the LigW operon work together with LigW in a currently unidentified repair pathway. Once the LigW DNA repair system is characterized, then this can be more easily identified and understood in other organisms where it may not be detected at present.

text: DNA repair enzymes in Prochlorococcus marinus strain MIT9312 Prochlorococcus marinus, a marine cyanobacterium, is one of the most abundant photosynthetic organisms in the ocean. P. marinus contributes towards approximately 8.5% of global ocean primary productivity. P. marinus is of interest because of the cell’s simple and unique photosynthetic system, efficient carbon concentrating mechanism, and streamlined genome. P. marinus strain MIT9312 is a high-light adapted strain that thrives in the upper euphotic zone where there are minimal nutrients and high levels of UV exposure, which would typically put an organism at risk. Understanding the function of repair proteins is significant for being able to identify the DNA repair pathways used by Prochlorococcus to survive under increasingly more harmful conditions. My research, outlined in this thesis, aimed to characterize DNA repair enzymes in Prochlorococcus marinus strain MIT9312 to further our understanding of cyanobacterial growth, survival, and repair.

LigW is an ATP-dependent ligase that is unique to strain MIT9312. It was found to have low ligase activity on nicked DNA compared to other ligases, making its retention in the small Prochlorococcus genome unusual. It is suspected that LigW could achieve higher ligation rates by interacting with other proteins. LigW is in an operon with other proteins that are predicted to promote LigW activity or have their own DNA modifying activities. The three proteins of interest have been annotated as Pmar3, Pmar4, and Pmar5. The
individual function and relationships between each protein were investigated in this thesis.

This thesis focused on recombinantly producing and biochemically characterizing three of the proteins adjacent to LigW and assessing their activities in vitro. Pmar3 was successfully expressed, purified, and characterized as a potential nuclease. Further mutagenesis work will confirm the proposed function of Pmar3. Attempts were made to characterize Pmar4, with further optimization of expression and purification protocols necessary. Pmar5 has been characterized as a pentameric Mg-dependent topoisomerase-like protein, with an inability to re-join DNA. It is likely that these proteins on the LigW operon work together with LigW in a currently unidentified repair pathway. Once the LigW DNA repair system is characterized, then this can be more easily identified and understood in other organisms where it may not be detected at present.

year: 2021

title: The Accountability of New Zealand's Charities: Meeting the Needs of Charity Stakeholders through Information Disclosure

authors: Dimitrov, Dara

subjects: New Zealand charity

abstract: For decades, New Zealand’s charity sector has been able to operate, unfettered by regulation and with low levels of accountability.  For this reason, gaining any information from charities about the work they do has been historically difficult, because charities have not been required to provide any reports.  The New Zealand government sought to increase the accountability from the charity sector with the introduction of the Charities Act (2005) and basic reporting requirements, but ultimately, the accountability from the sector continues to be an issue.  With limited charity disclosure literature in the New Zealand context, and no information disclosure practice model to guide New Zealand’s charities, the current provision and the quality of the information disclosures from charities are low, leaving the information needs of charity stakeholders unmet.
The overall aim of this investigation is to improve the accountability from New Zealand’s charities by developing a charity information disclosure practice model from a charity stakeholder perspective.  This was achieved by three main objectives:
1.	To develop a qualitative disclosure index from the perspective of charity stakeholders 
2.	To assess the extent and quality of the information disclosure made by thirty registered charities 
3.	To make recommendations to improve the accountability  by New Zealand’s charity sector
To achieve this purpose, a disclosure index, which contained  136 information items was created with the assistance of 86 charity stakeholders. The index was then applied to three publications from thirty charities that were randomly selected from the Charity register. The three publications used in this investigation are the Charity register, the charity’s website and the charity’s annual report/annual review. The collected data was then quantified and analysed to determine the extent and the quality of the information disclosures from the charities.  
The investigation findings indicated that the current level of charity disclosures was poor both in extent and quality and that there was an information gap between the expectations of charity stakeholders and the actual disclosure practices of the charities.  It was found that the top-performing information items were the mandated and the best-practice information items were either missing or inadequately disclosed.  No charity within the sample managed to achieve an index score of 50%.
The annual return summary found on the Charity register was the best disclosure document for both financial and non-financial information items from a charity stakeholder perspective.  However, this document, along with the other publications still lacked sufficient detail to be useful for a charity stakeholder.  To improve the accountability of the New Zealand’s sector, it is recommended that the New Zealand Parliament look at expanding the current annual return summary to include information items more relevant to charity stakeholders.  Finally, it is recommended that the charities should be compelled to produce an annual report and use the disclosure index created by the charity stakeholders in this investigation to improve their current information disclosures.

text: The Accountability of New Zealand's Charities: Meeting the Needs of Charity Stakeholders through Information Disclosure For decades, New Zealand’s charity sector has been able to operate, unfettered by regulation and with low levels of accountability.  For this reason, gaining any information from charities about the work they do has been historically difficult, because charities have not been required to provide any reports.  The New Zealand government sought to increase the accountability from the charity sector with the introduction of the Charities Act (2005) and basic reporting requirements, but ultimately, the accountability from the sector continues to be an issue.  With limited charity disclosure literature in the New Zealand context, and no information disclosure practice model to guide New Zealand’s charities, the current provision and the quality of the information disclosures from charities are low, leaving the information needs of charity stakeholders unmet.
The overall aim of this investigation is to improve the accountability from New Zealand’s charities by developing a charity information disclosure practice model from a charity stakeholder perspective.  This was achieved by three main objectives:
1.	To develop a qualitative disclosure index from the perspective of charity stakeholders 
2.	To assess the extent and quality of the information disclosure made by thirty registered charities 
3.	To make recommendations to improve the accountability  by New Zealand’s charity sector
To achieve this purpose, a disclosure index, which contained  136 information items was created with the assistance of 86 charity stakeholders. The index was then applied to three publications from thirty charities that were randomly selected from the Charity register. The three publications used in this investigation are the Charity register, the charity’s website and the charity’s annual report/annual review. The collected data was then quantified and analysed to determine the extent and the quality of the information disclosures from the charities.  
The investigation findings indicated that the current level of charity disclosures was poor both in extent and quality and that there was an information gap between the expectations of charity stakeholders and the actual disclosure practices of the charities.  It was found that the top-performing information items were the mandated and the best-practice information items were either missing or inadequately disclosed.  No charity within the sample managed to achieve an index score of 50%.
The annual return summary found on the Charity register was the best disclosure document for both financial and non-financial information items from a charity stakeholder perspective.  However, this document, along with the other publications still lacked sufficient detail to be useful for a charity stakeholder.  To improve the accountability of the New Zealand’s sector, it is recommended that the New Zealand Parliament look at expanding the current annual return summary to include information items more relevant to charity stakeholders.  Finally, it is recommended that the charities should be compelled to produce an annual report and use the disclosure index created by the charity stakeholders in this investigation to improve their current information disclosures.

year: 2017

title: An Interactive User Management System for Multilingual Documents: A case study of the Pei Jones collection

authors: Cader, Papitha

subjects: Greenstone Digital Library

abstract: Can general purpose DL software architecture be designed to provide a flexible environment that supports both the management and end-user roles through a single unified web interface? In particular we take the collected correspondence of the Māori scholar Dr. Pei Jones and undertake case study of how this approach can be applied in a practical way.

text: An Interactive User Management System for Multilingual Documents: A case study of the Pei Jones collection Can general purpose DL software architecture be designed to provide a flexible environment that supports both the management and end-user roles through a single unified web interface? In particular we take the collected correspondence of the Māori scholar Dr. Pei Jones and undertake case study of how this approach can be applied in a practical way.

year: 2012