title: The PIN-domain ribonucleases and the prokaryotic VapBC toxin–antitoxin array

authors: Arcus, Vickery L.

subjects: growth regulation

abstract: The PIN-domains are small proteins of ∼130 amino acids that are found in bacteria, archaea and eukaryotes and are defined by a group of three strictly conserved acidic amino acids. The conserved three-dimensional structures of the PIN-domains cluster these acidic residues in an enzymatic active site. PIN-domains cleave single-stranded RNA in a sequence-specific, Mg²⁺- or Mg²⁺- dependent manner. These ribonucleases are toxic to the cells which express them and to offset this toxicity, they are co-expressed with tight binding protein inhibitors. The genes encoding these two proteins are adjacent in the genome of all prokaryotic organisms where they are found. This sequential arrangement of inhibitor-RNAse genes conforms to that of the so-called toxin–antitoxin (TA) modules and the PIN-domain TAs have been named VapBC TAs (virulence associated proteins, VapB is the inhibitor which contains a transcription factor domain and VapC is the PIN-domain ribonuclease). The presence of large numbers of vapBC loci in disparate prokaryotes has motivated many researchers to investigate their biochemical and biological functions. For example, the devastating human pathogen Mycobacterium tuberculosis has 45 vapBC loci encoded in its genome whereas its non-pathogenic relative, Mycobacterium smegmatis has just one vapBC operon. On another branch of the prokaryotic tree, the nitrogen-fixing symbiont of legumes, Sinorhizobium meliloti has 21 vapBC loci and at least one of these loci have been implicated in the regulation of growth in the plant nodule. A range of biological functions has been suggested for these operons and this review sets out to survey the PIN-domains and summarise the current knowledge about the vapBC TA systems and their roles in diverse bacteria.

text: The PIN-domain ribonucleases and the prokaryotic VapBC toxin–antitoxin array The PIN-domains are small proteins of ∼130 amino acids that are found in bacteria, archaea and eukaryotes and are defined by a group of three strictly conserved acidic amino acids. The conserved three-dimensional structures of the PIN-domains cluster these acidic residues in an enzymatic active site. PIN-domains cleave single-stranded RNA in a sequence-specific, Mg²⁺- or Mg²⁺- dependent manner. These ribonucleases are toxic to the cells which express them and to offset this toxicity, they are co-expressed with tight binding protein inhibitors. The genes encoding these two proteins are adjacent in the genome of all prokaryotic organisms where they are found. This sequential arrangement of inhibitor-RNAse genes conforms to that of the so-called toxin–antitoxin (TA) modules and the PIN-domain TAs have been named VapBC TAs (virulence associated proteins, VapB is the inhibitor which contains a transcription factor domain and VapC is the PIN-domain ribonuclease). The presence of large numbers of vapBC loci in disparate prokaryotes has motivated many researchers to investigate their biochemical and biological functions. For example, the devastating human pathogen Mycobacterium tuberculosis has 45 vapBC loci encoded in its genome whereas its non-pathogenic relative, Mycobacterium smegmatis has just one vapBC operon. On another branch of the prokaryotic tree, the nitrogen-fixing symbiont of legumes, Sinorhizobium meliloti has 21 vapBC loci and at least one of these loci have been implicated in the regulation of growth in the plant nodule. A range of biological functions has been suggested for these operons and this review sets out to survey the PIN-domains and summarise the current knowledge about the vapBC TA systems and their roles in diverse bacteria.

year: 2010

title: Waitangi Soda Springs alum dosing – bioavailability of aluminium 2015

authors: Ling, Nicholas

abstract: Continuous alum dosing of the Waitangi Soda Springs at Lake Rotoehu commenced in 2010 to reduce inflows of dissolved reactive phosphorus to Lake Rotoehu. Analyses of bioaccumulation in the tissues of kōura and goldfish from Lake Rotoehu were undertaken on animals collected in November 2015 to determine the bioavailability and bioaccumulation of aluminium to satisfy annual resource consent conditions 11.7 and 11.8 of resource consent 65966. Comparative analyses were undertaken on goldfish collected from Lake Rotorua and compared to values obtained from goldfish and kōura collected from Lakes Rotoehu, Rotorua and Rotoiti in 2013. Lake Rotoehu kōura and goldfish showed slightly elevated aluminium concentrations in the gills indicating enhanced exposure to aluminium as a result of alum discharge from the Waitangi Soda Springs but little evidence for significant bioaccumulation in tissues.

text: Waitangi Soda Springs alum dosing – bioavailability of aluminium 2015 Continuous alum dosing of the Waitangi Soda Springs at Lake Rotoehu commenced in 2010 to reduce inflows of dissolved reactive phosphorus to Lake Rotoehu. Analyses of bioaccumulation in the tissues of kōura and goldfish from Lake Rotoehu were undertaken on animals collected in November 2015 to determine the bioavailability and bioaccumulation of aluminium to satisfy annual resource consent conditions 11.7 and 11.8 of resource consent 65966. Comparative analyses were undertaken on goldfish collected from Lake Rotorua and compared to values obtained from goldfish and kōura collected from Lakes Rotoehu, Rotorua and Rotoiti in 2013. Lake Rotoehu kōura and goldfish showed slightly elevated aluminium concentrations in the gills indicating enhanced exposure to aluminium as a result of alum discharge from the Waitangi Soda Springs but little evidence for significant bioaccumulation in tissues.

year: 2016

title: What’s in a name? The sense of reference, the rigidity of designators and the history of causes when determining the names of the two main islands of Aotearoa/New Zealand

authors: Parker, Martin

subjects: New Zealand

abstract: The New Zealand Geographic Board recently revealed that the two main islands of Aotearoa/New Zealand have never been officially named. The revelation made both national and international news and led to a large number of publicly aired comments on the matter, suggesting that something so fundamental and seemingly innocuous as naming is in fact likely to generate a good deal of controversy, no more so than in a bicultural/bilingual context. This paper will examine the phenomenon of naming from a number of angles. After discussing a layperson’s idea of what is meant by the meaning of names, we shall attempt to apply a number of theoretical models from the field of Language Philosophy to the case of the main islands of Aotearoa/New Zealand: the Descriptivist approach of Frege and Russell, Kripke’s Rigid Designators, and Causal Grounding theory. We shall conclude that, in the case of applying the first two of these, there is a question mark over whether any of the current names for the two islands, both Māori and Pākehā, are in fact names at all; in terms of applying the theory of Causal Grounding, we are drawn to the conclusion that in history lies the key to the future.

text: What’s in a name? The sense of reference, the rigidity of designators and the history of causes when determining the names of the two main islands of Aotearoa/New Zealand The New Zealand Geographic Board recently revealed that the two main islands of Aotearoa/New Zealand have never been officially named. The revelation made both national and international news and led to a large number of publicly aired comments on the matter, suggesting that something so fundamental and seemingly innocuous as naming is in fact likely to generate a good deal of controversy, no more so than in a bicultural/bilingual context. This paper will examine the phenomenon of naming from a number of angles. After discussing a layperson’s idea of what is meant by the meaning of names, we shall attempt to apply a number of theoretical models from the field of Language Philosophy to the case of the main islands of Aotearoa/New Zealand: the Descriptivist approach of Frege and Russell, Kripke’s Rigid Designators, and Causal Grounding theory. We shall conclude that, in the case of applying the first two of these, there is a question mark over whether any of the current names for the two islands, both Māori and Pākehā, are in fact names at all; in terms of applying the theory of Causal Grounding, we are drawn to the conclusion that in history lies the key to the future.

year: 2010-02