title: Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

authors: Campbell, Barbara J.

subjects: 16S rRNA

abstract: Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

text: Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

year: 2013

title: Investigating bioinformatic pipelines for De novo variant identification in New Zealand dairy cattle

authors: Erika, Duerre

subjects: Bioinformatic pipelines

abstract: New Zealand is the biggest single entity for milk and milk product export in the world and being the country’s main industry, keeping track of bovine mutations allows influence of the national herd’s health and the ability to breed cattle better suited to the current farming and climate needs. With advances in next-generation sequencing of whole genomes, research understanding and tracking germline de novo mutations (DNMs) is attainable. However, current techniques being used to identify and study candidate DNMs are unvetted and experimental. Some of these techniques include bioinformatic software packages such as DenovoCNN, DenovoGear, PedFilter, and RUFUS.
This thesis aimed to investigate and test two of these identification pipelines, DenovoGear and PedFilter using next-generation sequencing data from bovine trios. Output data was generated by writing scripts and extracting data from six trios into Excel workbooks or manual IGV validation of selected candidate DNMs. Of the total 714,393 candidates identified across PedFilter and DenovoGear, only 161 of them were identified by both programs. After Integrative Genomic Viewer validation, 50% of these candidates were deemed to be true positives while only 12% were deemed false positives. Data analysis shows neither technique is 100% accurate and they both should be used with secondary filtering and confirmation of the identified DNM candidates. It was also apparent that the different techniques would be better suited to different study situations. For example, (1) For smaller studies (e.g., 3–15 trios), with limited data available to them, using DenovoGear with a secondary software program for filtering would be best (2) If sufficient samples are available to provide a simulated population data set, PedFilter has higher accuracy than DenovoGear on its own (3) For fast analysis without requiring heavy filtering of the output data use a combination of both PedFilter and DenovoGear. 
Lastly, it is clear that further developments and more testing is required in this area of research before a set standard of practice or guidelines can be recommended and implemented. It is suggested to testing DenovoCNN and Rufus or branching out to other packages to trial like SynthDNM, DNMFilter_INDELs or HAPDeNovo.

text: Investigating bioinformatic pipelines for De novo variant identification in New Zealand dairy cattle New Zealand is the biggest single entity for milk and milk product export in the world and being the country’s main industry, keeping track of bovine mutations allows influence of the national herd’s health and the ability to breed cattle better suited to the current farming and climate needs. With advances in next-generation sequencing of whole genomes, research understanding and tracking germline de novo mutations (DNMs) is attainable. However, current techniques being used to identify and study candidate DNMs are unvetted and experimental. Some of these techniques include bioinformatic software packages such as DenovoCNN, DenovoGear, PedFilter, and RUFUS.
This thesis aimed to investigate and test two of these identification pipelines, DenovoGear and PedFilter using next-generation sequencing data from bovine trios. Output data was generated by writing scripts and extracting data from six trios into Excel workbooks or manual IGV validation of selected candidate DNMs. Of the total 714,393 candidates identified across PedFilter and DenovoGear, only 161 of them were identified by both programs. After Integrative Genomic Viewer validation, 50% of these candidates were deemed to be true positives while only 12% were deemed false positives. Data analysis shows neither technique is 100% accurate and they both should be used with secondary filtering and confirmation of the identified DNM candidates. It was also apparent that the different techniques would be better suited to different study situations. For example, (1) For smaller studies (e.g., 3–15 trios), with limited data available to them, using DenovoGear with a secondary software program for filtering would be best (2) If sufficient samples are available to provide a simulated population data set, PedFilter has higher accuracy than DenovoGear on its own (3) For fast analysis without requiring heavy filtering of the output data use a combination of both PedFilter and DenovoGear. 
Lastly, it is clear that further developments and more testing is required in this area of research before a set standard of practice or guidelines can be recommended and implemented. It is suggested to testing DenovoCNN and Rufus or branching out to other packages to trial like SynthDNM, DNMFilter_INDELs or HAPDeNovo.

year: 2023

title: Health reform and the impact on Mäori 1983-1997

authors: Ferguson, Lisa Arleen.

abstract: This study investigates the New Zealand health sector reforms from 1983 to 1997and examines whether the reform process has been consistent with the principles of the Treaty of Waitangi. It evaluates the impact of the reforms on Mäori from that perspective. 

The study introduces the health sector reforms generally and then their specific effects on Mäori. It draws on two research exercises undertaken by the author, being research for the Wai 692 Napier Hospital and Health Services claim to the Waitangi Tribunal and on improving Mäori Health outcomes for the National Health Committee. The methodologies used are those from the discipline of history.

The study outlines the argument for Crown responsibilities under the Treaty and draws out the distinctions between Article 2 and Article 3 of the Treaty. It provides a historical background to the place of the Treaty in the health sector, and forms the basis for a Treaty based analysis of the health reforms and their impact. 

The New Zealand health sector has undergone massive government initiated structural change throughout the period under study. During this time the neo-liberal reforms have had a key role in reshaping health service structures. The process of change, the international influences on the changes, and the resulting entities are described. An example from Tainui Iwi of the effect of structural health reform illustrates the changes in Mäori health service provision by Mäori.
Since 1983 successive governments have produced copious Mäori health policy. The key policy documents, and their recommendations, are identified, as is the degree to which they were implemented. The cyclical nature of such policy making suggests that it is not always followed by policy implementation. While Mäori are identified as a health gain priority, the evidence reviewed shows that the responsibility to implement and monitor the policy is diffuse and ineffective.

The Wai 692 claim provides a detailed look at the impact of the 1990s health reform for Mäori. The claim was precipitated by the threatened closure of Napier Hospital, but was broadened to include a wide-ranging look at the impact of health reform on Mäori. As a case study it provides a specific example of one Iwi’s experience of the reality of policy implementation at that time versus policy making.

Crown evaluation of the effectiveness of its own policies, and the extent to which its own agencies breach those policies is explored. The lack of control and accountability measures, plus the inability of the Crown to monitor (let alone sanction) success or failure, is highlighted. A contrast is drawn between the health and local government sectors, using the operation of the Resource Management Act (1991). 

The latest health sector reforms consequent on the 1999 Labour/Alliance coalition government are briefly considered, together with an overview of the Crown’s effectiveness in delivering improved Mäori health outcomes. The study suggests that the use of the Treaty as a cornerstone for Maori health policy formation and delivery may lead to more effective engagement between the Crown and Mäori in addressing Mäori health issues. The study concludes by asking the question, has the health sector reform process of the 1980s and 1990s itself been a Treaty breach?

A brief postscript considers the further reform of the health sector beyond the period of study.

text: Health reform and the impact on Mäori 1983-1997 This study investigates the New Zealand health sector reforms from 1983 to 1997and examines whether the reform process has been consistent with the principles of the Treaty of Waitangi. It evaluates the impact of the reforms on Mäori from that perspective. 

The study introduces the health sector reforms generally and then their specific effects on Mäori. It draws on two research exercises undertaken by the author, being research for the Wai 692 Napier Hospital and Health Services claim to the Waitangi Tribunal and on improving Mäori Health outcomes for the National Health Committee. The methodologies used are those from the discipline of history.

The study outlines the argument for Crown responsibilities under the Treaty and draws out the distinctions between Article 2 and Article 3 of the Treaty. It provides a historical background to the place of the Treaty in the health sector, and forms the basis for a Treaty based analysis of the health reforms and their impact. 

The New Zealand health sector has undergone massive government initiated structural change throughout the period under study. During this time the neo-liberal reforms have had a key role in reshaping health service structures. The process of change, the international influences on the changes, and the resulting entities are described. An example from Tainui Iwi of the effect of structural health reform illustrates the changes in Mäori health service provision by Mäori.
Since 1983 successive governments have produced copious Mäori health policy. The key policy documents, and their recommendations, are identified, as is the degree to which they were implemented. The cyclical nature of such policy making suggests that it is not always followed by policy implementation. While Mäori are identified as a health gain priority, the evidence reviewed shows that the responsibility to implement and monitor the policy is diffuse and ineffective.

The Wai 692 claim provides a detailed look at the impact of the 1990s health reform for Mäori. The claim was precipitated by the threatened closure of Napier Hospital, but was broadened to include a wide-ranging look at the impact of health reform on Mäori. As a case study it provides a specific example of one Iwi’s experience of the reality of policy implementation at that time versus policy making.

Crown evaluation of the effectiveness of its own policies, and the extent to which its own agencies breach those policies is explored. The lack of control and accountability measures, plus the inability of the Crown to monitor (let alone sanction) success or failure, is highlighted. A contrast is drawn between the health and local government sectors, using the operation of the Resource Management Act (1991). 

The latest health sector reforms consequent on the 1999 Labour/Alliance coalition government are briefly considered, together with an overview of the Crown’s effectiveness in delivering improved Mäori health outcomes. The study suggests that the use of the Treaty as a cornerstone for Maori health policy formation and delivery may lead to more effective engagement between the Crown and Mäori in addressing Mäori health issues. The study concludes by asking the question, has the health sector reform process of the 1980s and 1990s itself been a Treaty breach?

A brief postscript considers the further reform of the health sector beyond the period of study.

year: 2002