title: Characterisation of VapBC Toxin-Antitoxins from Mycobacterium tuberculosis

authors: Sharrock, Abigail Victoria

subjects: vapBC

abstract: Toxin-antitoxin (TA) systems were identified more than 20 years ago on the mini F plasmid of Escherichia coli as plasmid stability elements; components responsible for purging bacterial cells that lack the plasmid from the population. More recent discovery of TA systems spanning a wide diversity of prokaryotic chromosomes, including that of Mycobacterium tuberculosis (M. tb), suggests a broader biochemical role. TA systems can be classified into a number of families, with the vapBC systems being by far the largest. The biochemical role of vapBC systems in M. tb remains unclear despite their abundance within the genome. 
This thesis describes the biochemical and functional characterisation of two vapBC systems encoded by operons Rv0065a/c and Rv0617a/c in the M. tb genome. VapCRv0617 overexpression had a bacteriostatic effect on the growth of Mycobacterium smegmatis cultures. Therefore, the biochemistry underlying this phenotype was investigated, along with that of the Rv0065a/c system. VapCRv0065 and VapCRv0617 are Mg2+-dependent, sequence-specific ribonucleases targeting GC rich 4-mers. Ribonuclease assays with in vitro synthesised RNA transcripts suggested an additional layer of target recognition resides in RNA secondary structure, and revealed that both VapC proteins exhibit high activity against isolated M. smegmatis 16S and 23S rRNA. Electrophoretic mobility shift assays with purified VapBC protein and labelled DNA demonstrated an autoregulatory function for the VapBCRv0617a/c complex and not the VapBCRv0065a/c complex. VapBCRv0617a/c bound specifically to a near-perfect inverted repeat in the Rv0617a/c promoter region that overlaps an annotated -10 M. tb promoter element. In contrast, the VapBCRv0065a/c complex exhibited no DNA binding activity against a putative Rv0065a/c promoter region. Individualised vapBC transcriptional regulation mechanisms may help explain the persistence of such an expanded number of these systems in the genome.

Knowledge of the physiological role of vapBC systems in M. tb will enable a better understanding of how they contribute to the pathogenicity of this bacterium. This would serve as the basis for the design of drugs which interfere with vapBC system functioning and in turn the ability of M. tb cells to enter the persistent state.

text: Characterisation of VapBC Toxin-Antitoxins from Mycobacterium tuberculosis Toxin-antitoxin (TA) systems were identified more than 20 years ago on the mini F plasmid of Escherichia coli as plasmid stability elements; components responsible for purging bacterial cells that lack the plasmid from the population. More recent discovery of TA systems spanning a wide diversity of prokaryotic chromosomes, including that of Mycobacterium tuberculosis (M. tb), suggests a broader biochemical role. TA systems can be classified into a number of families, with the vapBC systems being by far the largest. The biochemical role of vapBC systems in M. tb remains unclear despite their abundance within the genome. 
This thesis describes the biochemical and functional characterisation of two vapBC systems encoded by operons Rv0065a/c and Rv0617a/c in the M. tb genome. VapCRv0617 overexpression had a bacteriostatic effect on the growth of Mycobacterium smegmatis cultures. Therefore, the biochemistry underlying this phenotype was investigated, along with that of the Rv0065a/c system. VapCRv0065 and VapCRv0617 are Mg2+-dependent, sequence-specific ribonucleases targeting GC rich 4-mers. Ribonuclease assays with in vitro synthesised RNA transcripts suggested an additional layer of target recognition resides in RNA secondary structure, and revealed that both VapC proteins exhibit high activity against isolated M. smegmatis 16S and 23S rRNA. Electrophoretic mobility shift assays with purified VapBC protein and labelled DNA demonstrated an autoregulatory function for the VapBCRv0617a/c complex and not the VapBCRv0065a/c complex. VapBCRv0617a/c bound specifically to a near-perfect inverted repeat in the Rv0617a/c promoter region that overlaps an annotated -10 M. tb promoter element. In contrast, the VapBCRv0065a/c complex exhibited no DNA binding activity against a putative Rv0065a/c promoter region. Individualised vapBC transcriptional regulation mechanisms may help explain the persistence of such an expanded number of these systems in the genome.

Knowledge of the physiological role of vapBC systems in M. tb will enable a better understanding of how they contribute to the pathogenicity of this bacterium. This would serve as the basis for the design of drugs which interfere with vapBC system functioning and in turn the ability of M. tb cells to enter the persistent state.

year: 2013

title: Quaternary environmental change in New Zealand and its effects on the soil pattern

authors: Lowe, David J.

abstract: NZ is an exceptional place for studying environmental change and soil evolution during the Quaternary: (1) it lies in a climatically sensitive, oceanic location spanning 17 degrees of the mid-latitudes; (2) its active plate boundary setting has produced high mountains lying athwart the prevailing westerlies, active volcanism, and a dynamic landscape; and (3) it has an exceptionally short prehistory (c. 700 years). Consequently, there is a striking diversity of topography - the landscape is characterized by strong relief and youthfulness - and lithology, markedly variable climatic regimes, and a unique, relict 'Gondwana' flora. In this paper, we firstly describe environmental change in NZ during the Quaternary and then examine examples of the effects of such change, chiefly during and since the LG, on the soil pattern in NZ.

text: Quaternary environmental change in New Zealand and its effects on the soil pattern NZ is an exceptional place for studying environmental change and soil evolution during the Quaternary: (1) it lies in a climatically sensitive, oceanic location spanning 17 degrees of the mid-latitudes; (2) its active plate boundary setting has produced high mountains lying athwart the prevailing westerlies, active volcanism, and a dynamic landscape; and (3) it has an exceptionally short prehistory (c. 700 years). Consequently, there is a striking diversity of topography - the landscape is characterized by strong relief and youthfulness - and lithology, markedly variable climatic regimes, and a unique, relict 'Gondwana' flora. In this paper, we firstly describe environmental change in NZ during the Quaternary and then examine examples of the effects of such change, chiefly during and since the LG, on the soil pattern in NZ.

year: 2000

title: Reduplication in Maori

authors: Keegan, Peter J.

subjects: Te reo Māori

abstract: This thesis is a study of reduplication in Māori. The aim of the thesis is to make a thorough study of both the formal and semantic properties of reduplication in Māori. This is done by reviewing the relevant literature on reduplication, and collating reduplication data. Most data are from textual sources. Some data have been provided by native-speaker informants. 
The first chapter looks at previous attempts to describe reduplication in Māori. It begins with some definitions of the term reduplication. This is followed by a review of the attempts made by previous authors to describe reduplication in Māori. Aspects of reduplication not covered by those attempts are noted.
The second chapter looks at reduplication in Māori within a Generative framework. The units of reduplication in Māori are given in prosodic terms. This is followed by an overview of Marantz (1982), and a critique of two very recent attempts to account for reduplication in Māori within Optimality Theory. Aspects of Māori reduplication that poses difficulties for Optimality Theory are noted.
The third chapter describes the semantics of reduplication in Māori. An illustration is given of some of the common meanings of reduplication attested across languages. The various meanings of reduplication in Māori are described. Also, the semantics of reduplication in Māori are compared to the semantics of reduplication in Malayo-Polynesian (Austronesian) languages within the framework suggested by Kiyomi (1995).
The fourth chapter comments on descriptive aspects of reduplication in Māori not covered by the previous three chapters.
The fifth chapter provides statistics on the reduplication data collated in the appendices. Reduplication data are divided according to the number of mora in the stem (or base) of origin. Statistics are given on the occurrence of various patterns of reduplication in Māori.

text: Reduplication in Maori This thesis is a study of reduplication in Māori. The aim of the thesis is to make a thorough study of both the formal and semantic properties of reduplication in Māori. This is done by reviewing the relevant literature on reduplication, and collating reduplication data. Most data are from textual sources. Some data have been provided by native-speaker informants. 
The first chapter looks at previous attempts to describe reduplication in Māori. It begins with some definitions of the term reduplication. This is followed by a review of the attempts made by previous authors to describe reduplication in Māori. Aspects of reduplication not covered by those attempts are noted.
The second chapter looks at reduplication in Māori within a Generative framework. The units of reduplication in Māori are given in prosodic terms. This is followed by an overview of Marantz (1982), and a critique of two very recent attempts to account for reduplication in Māori within Optimality Theory. Aspects of Māori reduplication that poses difficulties for Optimality Theory are noted.
The third chapter describes the semantics of reduplication in Māori. An illustration is given of some of the common meanings of reduplication attested across languages. The various meanings of reduplication in Māori are described. Also, the semantics of reduplication in Māori are compared to the semantics of reduplication in Malayo-Polynesian (Austronesian) languages within the framework suggested by Kiyomi (1995).
The fourth chapter comments on descriptive aspects of reduplication in Māori not covered by the previous three chapters.
The fifth chapter provides statistics on the reduplication data collated in the appendices. Reduplication data are divided according to the number of mora in the stem (or base) of origin. Statistics are given on the occurrence of various patterns of reduplication in Māori.

year: 1996