title: Do PhoH2 proteins regulate SigF in mycobacteria?

authors: Rzoska-Smith, Elizabeth

abstract: There is little known about the role of the PhoH2 proteins in biology. PhoH2 consists of two domains, an N-terminal PIN domain with RNase activity and a C-terminal PhoH domain shown to have ATP induced RNA helicase activity. PhoH2 proteins from Mycobacterium tuberculosis and Mycobacterium smegmatis show ATP and magnesium dependent, sequence-specific RNA unwinding and cleavage activity. It is hypothesised based on RNAseq data that PhoH2 from M. smegmatis may be acting as a potential regulator of sigma factor SigF, through its targeted RNA helicase and RNase activity. Regulation may occur directly on the sigF mRNA transcript, or indirectly through regulation of anti-sigma factor antagonists. This thesis used purified PhoH2 proteins to examine the activity of PhoH2 against mRNA substrates designed to span regions of the sigF gene and the genes co-expressed in the sigF operon; rsbW and chaB. Results show that PhoH2 co-purifies with E. coli nucleic acid and that despite this co-purification, activity was observed on sigF mRNA, that was improved with increasing amounts of ATP. qPCR experiments were designed to test expression levels of 12 genes, that showed significant up or down regulation expression in M. smegmatis mc²155 ΔphoH2 compared to wild-type M. smegmatis mc²155. qPCR analysis revealed a significant upregulation of the genes MSMEG_1804 (sigF) and MSMEG_0064 (PPE) in M. smegmatis mc²155 ΔphoH2 compared to M. smegmatis mc²155. These results differ from the gene expression results obtained from RNAseq data, yet results still point towards regulation of SigF by PhoH2. Further experiments using qPCR and activity assays with PhoH2 aim to verify the precise role of PhoH2 in the regulation of SigF.

text: Do PhoH2 proteins regulate SigF in mycobacteria? There is little known about the role of the PhoH2 proteins in biology. PhoH2 consists of two domains, an N-terminal PIN domain with RNase activity and a C-terminal PhoH domain shown to have ATP induced RNA helicase activity. PhoH2 proteins from Mycobacterium tuberculosis and Mycobacterium smegmatis show ATP and magnesium dependent, sequence-specific RNA unwinding and cleavage activity. It is hypothesised based on RNAseq data that PhoH2 from M. smegmatis may be acting as a potential regulator of sigma factor SigF, through its targeted RNA helicase and RNase activity. Regulation may occur directly on the sigF mRNA transcript, or indirectly through regulation of anti-sigma factor antagonists. This thesis used purified PhoH2 proteins to examine the activity of PhoH2 against mRNA substrates designed to span regions of the sigF gene and the genes co-expressed in the sigF operon; rsbW and chaB. Results show that PhoH2 co-purifies with E. coli nucleic acid and that despite this co-purification, activity was observed on sigF mRNA, that was improved with increasing amounts of ATP. qPCR experiments were designed to test expression levels of 12 genes, that showed significant up or down regulation expression in M. smegmatis mc²155 ΔphoH2 compared to wild-type M. smegmatis mc²155. qPCR analysis revealed a significant upregulation of the genes MSMEG_1804 (sigF) and MSMEG_0064 (PPE) in M. smegmatis mc²155 ΔphoH2 compared to M. smegmatis mc²155. These results differ from the gene expression results obtained from RNAseq data, yet results still point towards regulation of SigF by PhoH2. Further experiments using qPCR and activity assays with PhoH2 aim to verify the precise role of PhoH2 in the regulation of SigF.

year: 2018

title: Tephrochronology of last termination sequences in Europe: a protocol for improved analytical precision and robust correlation procedures (a joint SCOTAV–INTIMATE proposal)

authors: Turney, Chris S.M.

subjects: basaltic and rhyolitic tephra

abstract: The precise sequence of events during the Last Termination (18 000–9000 ka 14C yr BP), and the extent to which major environmental changes were synchronous, are difficult to establish using the radiocarbon method alone because of serious distortions of the radiocarbon time-scale, as well as the influences of site-specific errors that can affect the materials dated. Attention has therefore turned to other methods that can provide independent tests of the chronology and correlation of events during the Last Termination. With emphasis on European sequences, we summarise here the potential of tephrostratigraphy and tephrochronology to fulfil this role. Recent advances in the detection and analysis of ‘hidden’ tephra layers (cryptotephra) indicate that some tephras of Last Termination age are much more widespread in Europe than appreciated hitherto, and a number of new tephra deposits have also been identified. There is much potential for developing an integrated tephrochronological framework for Europe, which can help to underpin the overall chronology of events during the Last Termination. For that potential to be realised, however, there needs to be a more systematic and robust analysis of tephra layers than has been the practice in the past. We propose a protocol for improving analytical and reporting procedures, as well as the establishment of a centralised data base of the results, which will provide an important geochronological tool to support a diverse range of stratigraphical studies, including opportunities to reassess volcanic hazards. Although aimed primarily at Europe, the protocol proposed here is of equal relevance to other regions and periods of interest.

text: Tephrochronology of last termination sequences in Europe: a protocol for improved analytical precision and robust correlation procedures (a joint SCOTAV–INTIMATE proposal) The precise sequence of events during the Last Termination (18 000–9000 ka 14C yr BP), and the extent to which major environmental changes were synchronous, are difficult to establish using the radiocarbon method alone because of serious distortions of the radiocarbon time-scale, as well as the influences of site-specific errors that can affect the materials dated. Attention has therefore turned to other methods that can provide independent tests of the chronology and correlation of events during the Last Termination. With emphasis on European sequences, we summarise here the potential of tephrostratigraphy and tephrochronology to fulfil this role. Recent advances in the detection and analysis of ‘hidden’ tephra layers (cryptotephra) indicate that some tephras of Last Termination age are much more widespread in Europe than appreciated hitherto, and a number of new tephra deposits have also been identified. There is much potential for developing an integrated tephrochronological framework for Europe, which can help to underpin the overall chronology of events during the Last Termination. For that potential to be realised, however, there needs to be a more systematic and robust analysis of tephra layers than has been the practice in the past. We propose a protocol for improving analytical and reporting procedures, as well as the establishment of a centralised data base of the results, which will provide an important geochronological tool to support a diverse range of stratigraphical studies, including opportunities to reassess volcanic hazards. Although aimed primarily at Europe, the protocol proposed here is of equal relevance to other regions and periods of interest.

year: 2004

title: Child poverty and mental health: A literature review (Commissioned for New Zealand Psychological Society and Child Poverty Action Group)

authors: Gibson, Kerry

abstract: Large numbers of children in New Zealand suffer from mental health problems, and large numbers of children suffer from poverty and hardship. This literature review provides information on the relationship between poverty experienced during childhood and the impact that poverty may have on the mental health of a child or young person, or later in their adulthood. It was found that:
• There is an accepted relationship between poverty experienced in childhood and a greater likelihood of mental health problems through the life span.
• Child poverty and its associated problems such as poor nutrition, inadequate housing, increased likelihood of adverse events and living in poor neighbourhoods put children at higher risk of having mental health problems.
• The evidence strongly suggests that the incidence of mental health conditions among children and adolescents can be reduced by addressing severe and persistent poverty, particularly during the early years of a child’s life.
• Intervention to address poverty and the effects of poverty on children is likely to prevent the perpetuation of inter-generational cycles of poverty and poor mental health.
• The prevalence of child poverty and mental health issues is likely to be higher for Māori and Pasifika than for other children and young people.
• While many Māori and Pasifika children are subject to inequities in material and socio-economic circumstances as well as institutional racism, they also experience the benefits of a rich cultural life and sense of belonging that is seldom accounted for in research reports that focus on deprivation.
The evidence strongly suggests that the incidence of mental health problems throughout the lifespan could be reduced through addressing the causes of child poverty and associated factors. Any mental health strategy for children should sit alongside a comprehensive programme to alleviate poverty.
Strategies aimed at addressing child poverty in Māori and Pasifika communities are more likely to be effective if these are well-resourced at an early stage and developed in a genuine partnership with local communities.

text: Child poverty and mental health: A literature review (Commissioned for New Zealand Psychological Society and Child Poverty Action Group) Large numbers of children in New Zealand suffer from mental health problems, and large numbers of children suffer from poverty and hardship. This literature review provides information on the relationship between poverty experienced during childhood and the impact that poverty may have on the mental health of a child or young person, or later in their adulthood. It was found that:
• There is an accepted relationship between poverty experienced in childhood and a greater likelihood of mental health problems through the life span.
• Child poverty and its associated problems such as poor nutrition, inadequate housing, increased likelihood of adverse events and living in poor neighbourhoods put children at higher risk of having mental health problems.
• The evidence strongly suggests that the incidence of mental health conditions among children and adolescents can be reduced by addressing severe and persistent poverty, particularly during the early years of a child’s life.
• Intervention to address poverty and the effects of poverty on children is likely to prevent the perpetuation of inter-generational cycles of poverty and poor mental health.
• The prevalence of child poverty and mental health issues is likely to be higher for Māori and Pasifika than for other children and young people.
• While many Māori and Pasifika children are subject to inequities in material and socio-economic circumstances as well as institutional racism, they also experience the benefits of a rich cultural life and sense of belonging that is seldom accounted for in research reports that focus on deprivation.
The evidence strongly suggests that the incidence of mental health problems throughout the lifespan could be reduced through addressing the causes of child poverty and associated factors. Any mental health strategy for children should sit alongside a comprehensive programme to alleviate poverty.
Strategies aimed at addressing child poverty in Māori and Pasifika communities are more likely to be effective if these are well-resourced at an early stage and developed in a genuine partnership with local communities.

year: 2017