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: ‘No rugby—no fear’: collective stories, masculinities and transformative possibilities in schools

authors: Pringle, Richard

subjects: masculinities

abstract: This paper contributes to the development of a critical pedagogy in physical education (PE) by illustrating how ‘collective stories’ can be used within schools to help raise awareness of the relationships between sport, PE and gendered identities. A collective story, a concept developed by Laurel Richardson, aims to give voice to those silenced or marginalised by dominant cultural narratives and promote transformative possibilities. Within this paper I present a collective story of eight men's school experiences of rugby union to illustrate the difficulty of negotiating comforting stories of self in the face of rugby's cultural dominance within New Zealand. I detail the representational issues associated with constructing the story and my experience of presenting it to school students to assess whether it encouraged an empathetic response and disrupted romanticised ways of conceptualising the links between sport and masculinities. I conclude by discussing how I used the collective story, as a pedagogical tool, to examine the viability of introducing Foucauldian strategies to help students think critically.

text: ‘No rugby—no fear’: collective stories, masculinities and transformative possibilities in schools This paper contributes to the development of a critical pedagogy in physical education (PE) by illustrating how ‘collective stories’ can be used within schools to help raise awareness of the relationships between sport, PE and gendered identities. A collective story, a concept developed by Laurel Richardson, aims to give voice to those silenced or marginalised by dominant cultural narratives and promote transformative possibilities. Within this paper I present a collective story of eight men's school experiences of rugby union to illustrate the difficulty of negotiating comforting stories of self in the face of rugby's cultural dominance within New Zealand. I detail the representational issues associated with constructing the story and my experience of presenting it to school students to assess whether it encouraged an empathetic response and disrupted romanticised ways of conceptualising the links between sport and masculinities. I conclude by discussing how I used the collective story, as a pedagogical tool, to examine the viability of introducing Foucauldian strategies to help students think critically.

year: 2008

title: Te Pae Mahutonga and the measurement of community capital in regional Aotearoa New Zealand

authors: Ryks, John

abstract: Regionally, iwi and hapū have limited influence over structural changes such as population decline, proximity to labour markets and ageing, and to some extent economic cycles. However, there is still considerable value in thinking about how relevant indicators might point to the regeneration and overall well-being of Māori communities. In this paper we present an exploratory framework that links Durie’s Te Pae Mahutonga model of Māori well-being to the measurement of community capital. We use Te Pae Mahutonga as the basis for developing a number of key indicators for understanding Māori well-being in the regions and apply the framework and indicators to three regional settlements in Aotearoa New Zealand: Pōkeno, Huntly and Ōpōtiki.

text: Te Pae Mahutonga and the measurement of community capital in regional Aotearoa New Zealand Regionally, iwi and hapū have limited influence over structural changes such as population decline, proximity to labour markets and ageing, and to some extent economic cycles. However, there is still considerable value in thinking about how relevant indicators might point to the regeneration and overall well-being of Māori communities. In this paper we present an exploratory framework that links Durie’s Te Pae Mahutonga model of Māori well-being to the measurement of community capital. We use Te Pae Mahutonga as the basis for developing a number of key indicators for understanding Māori well-being in the regions and apply the framework and indicators to three regional settlements in Aotearoa New Zealand: Pōkeno, Huntly and Ōpōtiki.

year: 2018