title: Characterisation of VapC in Mycobacterium smegmatis

authors: Willcock, Duncan Mark Koorey

abstract: Members of the VapC family of proteins cleave RNA at specific sites in order to regulate biological processes with a cell. Characterization of the sites targeted by a specific protein using conventional biochemical techniques is resource intensive. This study explores the potential use of computational models to characterize the sites targeted by VapC in Mycobacterium smegmatis. Previous work has reported the impact of VapC upon each gene in the M. smegmatis genome and produced a hypothesis model for the specific motif targeted by the enzyme. However, this model has been shown to be insufficient for the differentiation of sites cleaved by VapC from those not cleaved. This study aims to extend this model to accurately describe the features which influence VapC activity at a site. A model capable of accurately predicting the VapC target sites could supplement the existing biochemical techniques. Furthermore, a process developed to train such a model could potentially be generalized and applied to other proteins and species.
This thesis explores increasingly complex representations of RNA sites and a suite of supervised learning techniques to train models that predict the efficiency with which sites are cleaved by VapC. The simplest representations of RNA sites consider only the RNA sequence. More detail is added to the representation in the form of secondary structures and the potential influences of tertiary structures are discussed. No model is produced that is capable of accurate, meaningful predictions. This suggests that the construction of a successful model requires significant alterations to the representation of RNA sites or that the data available is insufficient for training an accurate model.

text: Characterisation of VapC in Mycobacterium smegmatis Members of the VapC family of proteins cleave RNA at specific sites in order to regulate biological processes with a cell. Characterization of the sites targeted by a specific protein using conventional biochemical techniques is resource intensive. This study explores the potential use of computational models to characterize the sites targeted by VapC in Mycobacterium smegmatis. Previous work has reported the impact of VapC upon each gene in the M. smegmatis genome and produced a hypothesis model for the specific motif targeted by the enzyme. However, this model has been shown to be insufficient for the differentiation of sites cleaved by VapC from those not cleaved. This study aims to extend this model to accurately describe the features which influence VapC activity at a site. A model capable of accurately predicting the VapC target sites could supplement the existing biochemical techniques. Furthermore, a process developed to train such a model could potentially be generalized and applied to other proteins and species.
This thesis explores increasingly complex representations of RNA sites and a suite of supervised learning techniques to train models that predict the efficiency with which sites are cleaved by VapC. The simplest representations of RNA sites consider only the RNA sequence. More detail is added to the representation in the form of secondary structures and the potential influences of tertiary structures are discussed. No model is produced that is capable of accurate, meaningful predictions. This suggests that the construction of a successful model requires significant alterations to the representation of RNA sites or that the data available is insufficient for training an accurate model.

year: 2016

title: Seeing the wood for the trees: empire, nation-making and forest management

authors: Beattie, James John

abstract: Seemingly operating in an inverse relationship to the declining area of actual forest, the vast wood of publications on the topic continues to grow (thereby likely adding to the deforestation of the books’ subject). The reader can consult global surveys of world forestry, thanks to the outstanding efforts of Michael Williams and Stephen Pyne. National and micro studies also abound for those wanting information about a particular geographical area. All such studies displaying an array of different perspectives on forests: their symbolism, exchange, arrangement in gardens, art, cities—even their biological espionage (the cinchona’s ‘abduction’ from South America to South Asia, for instance)—are all covered. For some scholars, forests are objects of ecological imperialism; for others, tokens of enlightened colonialism, precursors to environmentalism.

text: Seeing the wood for the trees: empire, nation-making and forest management Seemingly operating in an inverse relationship to the declining area of actual forest, the vast wood of publications on the topic continues to grow (thereby likely adding to the deforestation of the books’ subject). The reader can consult global surveys of world forestry, thanks to the outstanding efforts of Michael Williams and Stephen Pyne. National and micro studies also abound for those wanting information about a particular geographical area. All such studies displaying an array of different perspectives on forests: their symbolism, exchange, arrangement in gardens, art, cities—even their biological espionage (the cinchona’s ‘abduction’ from South America to South Asia, for instance)—are all covered. For some scholars, forests are objects of ecological imperialism; for others, tokens of enlightened colonialism, precursors to environmentalism.

year: 2008

title: Positive Ageing in Place: Older Māori in Traditional and Non-traditional Place

authors: Williams, Cassandra

subjects: Māori

abstract: This thesis examines the role of place in experiences of ageing for older Māori, and the extent to which places of choice facilitate a sense of positive ageing. Particular attention is given to multiple experiences of home and the complexities surrounding Māori affiliations to place. Participants were older whānau members over the age of 55 who whakapapa to, and have lived, or currently live in Manaia in the Coromandel. Two participants still reside in Manaia to this day, and two have moved into urban areas in Paeroa and Taupo. Two semi-structured interviews were conducted with participants in their own homes. The first interview focused on housing experiences, personal background and support. The second interview incorporated Māori relationship principles relating to the importance of turangawaewae, whānaungatanga, wairua and manaakitanga. My analysis was informed by a narrative approach, and the relevance of Māori principles to participants’ positive ageing experiences.

I found that Māori relationships with places of ancestral connection are complex and do not exclude other places becoming equally, if not as important to individuals. Experiences of home for participants were multiple and extended to places with which they had forged memories, relationships and positive attachments. Findings indicate that the ability to age positively within particular places is largely reliant on the supports available for older Māori. Wairua was acknowledged by participants as being significant in aiding their positive ageing experiences. Strong connections to non-living objects such as places, nature and tupuna were expressed as being a crucial part of their philosophies on life and death. This feeling of knowing ancestors were part of everyday life alleviated feelings of loneliness and reiterated the never-ending connections between whānau. Everyday contact with whānau provided practical social support as well as a chance for reciprocal relationships to be fostered. When whānau support was not readily available due to geographical distances, technological means of relationship building were used to enable ageing at a distance, allowing home to be played out across physical localities. Health issues were expressed by participants, both historical and reoccurring, and appropriate health care services were regarded as playing an active role in participants’ ageing experiences. Three out of four participants accessed a Māori health provider. By accessing a health care service that was financially inexpensive, where the doctors built a rapport with patients and took advice, participants felt culturally safe and reported positive relationships with their provider. Finances were reported as being a support that needed to be strengthened and a lack of income had a negative effect on participants ageing experiences. Participants’ everyday lives were impacted by financial instability, with a lack of finances standing in the way of fully interacting with the community, negotiating place and being able to age in places of choice.
This thesis argues that ageing in place facilitates positive ageing by allowing older Māori to remain in their places of choice with firm attachments where they can maintain control over their affairs and maintain a sense of continuity. Māori ageing needs to be viewed within a history of colonisation, urbanisation, experiences, relationships and spiritual connectedness to human and non-human entities. It is within this context that ageing in place can be truly explored. Recommendations are made to aid positive ageing in place for older Māori. These include further research into supports, a review of the age of eligibility for state pensions, subsidised transport initiatives, and making Māori health services more accessible.

text: Positive Ageing in Place: Older Māori in Traditional and Non-traditional Place This thesis examines the role of place in experiences of ageing for older Māori, and the extent to which places of choice facilitate a sense of positive ageing. Particular attention is given to multiple experiences of home and the complexities surrounding Māori affiliations to place. Participants were older whānau members over the age of 55 who whakapapa to, and have lived, or currently live in Manaia in the Coromandel. Two participants still reside in Manaia to this day, and two have moved into urban areas in Paeroa and Taupo. Two semi-structured interviews were conducted with participants in their own homes. The first interview focused on housing experiences, personal background and support. The second interview incorporated Māori relationship principles relating to the importance of turangawaewae, whānaungatanga, wairua and manaakitanga. My analysis was informed by a narrative approach, and the relevance of Māori principles to participants’ positive ageing experiences.

I found that Māori relationships with places of ancestral connection are complex and do not exclude other places becoming equally, if not as important to individuals. Experiences of home for participants were multiple and extended to places with which they had forged memories, relationships and positive attachments. Findings indicate that the ability to age positively within particular places is largely reliant on the supports available for older Māori. Wairua was acknowledged by participants as being significant in aiding their positive ageing experiences. Strong connections to non-living objects such as places, nature and tupuna were expressed as being a crucial part of their philosophies on life and death. This feeling of knowing ancestors were part of everyday life alleviated feelings of loneliness and reiterated the never-ending connections between whānau. Everyday contact with whānau provided practical social support as well as a chance for reciprocal relationships to be fostered. When whānau support was not readily available due to geographical distances, technological means of relationship building were used to enable ageing at a distance, allowing home to be played out across physical localities. Health issues were expressed by participants, both historical and reoccurring, and appropriate health care services were regarded as playing an active role in participants’ ageing experiences. Three out of four participants accessed a Māori health provider. By accessing a health care service that was financially inexpensive, where the doctors built a rapport with patients and took advice, participants felt culturally safe and reported positive relationships with their provider. Finances were reported as being a support that needed to be strengthened and a lack of income had a negative effect on participants ageing experiences. Participants’ everyday lives were impacted by financial instability, with a lack of finances standing in the way of fully interacting with the community, negotiating place and being able to age in places of choice.
This thesis argues that ageing in place facilitates positive ageing by allowing older Māori to remain in their places of choice with firm attachments where they can maintain control over their affairs and maintain a sense of continuity. Māori ageing needs to be viewed within a history of colonisation, urbanisation, experiences, relationships and spiritual connectedness to human and non-human entities. It is within this context that ageing in place can be truly explored. Recommendations are made to aid positive ageing in place for older Māori. These include further research into supports, a review of the age of eligibility for state pensions, subsidised transport initiatives, and making Māori health services more accessible.

year: 2012