title: Verifying clustered mutation regions inside the newly-completed genome of a clinically-significant New Zealand Mycobacterium tuberculosis strain

authors: Steele, Mackenzie

subjects: Tuberculosis

abstract: In 2019, active infections of Mycobacterium tuberculosis (Mtb) affected 10 million people globally, with 1.4 million deaths, and an additional 1.7-1.9 billion people infected without symptomatic disease (latent Mtb). While Mtb is often associated with Asia and Africa, New Zealand had 360 Mtb infections and 21 deaths in 2019, and roughly 20% of cases were caused by three strains unique to New Zealand. One is CS1 (formerly Rangipo), which is known to be more transmissible than its relatives and has been causing outbreaks in the Waikato region for 30 years. As CS1 has genetic features linked to virulence in unrelated Mtb strains, having a complete and accurate record of genetic features is important, in particular those with the potential to change protein structure (Variable Regions Inside Proteins, VRIPs). Resolving VRIPs would simultaneously remove sequencing mistakes and increase knowledge about Mtb virulence. The aim of this project was to investigate the genetic cause of improved transmissibility in CS1 and produce a closed genome.
Sequencing data from Illumina and PacBio reads was processed, assembled, and checked for quality discrepancies which would require more sequencing to resolve. VRIPs were mapped alongside regions of low-quality data, low data-coverage, and repeat regions. Characteristics of the CS1 genome, such as repeat levels and size, were found by comparing with the reference strain H37Rv.
The read data and assembly were found to be good quality, and the genome is of high enough quality to be considered closed. As expected, some regions of low coverage and poor quality were discovered inside large repeat regions, and more work on these would be valuable. 13 of the 32 VRIPs were verified, all linked with virulence factors. 5 verified VRIPs caused genes to split into domains, accumulating mutations in the non-coding region. Further work resolving the remaining 19 VRIPs is recommended.

text: Verifying clustered mutation regions inside the newly-completed genome of a clinically-significant New Zealand Mycobacterium tuberculosis strain In 2019, active infections of Mycobacterium tuberculosis (Mtb) affected 10 million people globally, with 1.4 million deaths, and an additional 1.7-1.9 billion people infected without symptomatic disease (latent Mtb). While Mtb is often associated with Asia and Africa, New Zealand had 360 Mtb infections and 21 deaths in 2019, and roughly 20% of cases were caused by three strains unique to New Zealand. One is CS1 (formerly Rangipo), which is known to be more transmissible than its relatives and has been causing outbreaks in the Waikato region for 30 years. As CS1 has genetic features linked to virulence in unrelated Mtb strains, having a complete and accurate record of genetic features is important, in particular those with the potential to change protein structure (Variable Regions Inside Proteins, VRIPs). Resolving VRIPs would simultaneously remove sequencing mistakes and increase knowledge about Mtb virulence. The aim of this project was to investigate the genetic cause of improved transmissibility in CS1 and produce a closed genome.
Sequencing data from Illumina and PacBio reads was processed, assembled, and checked for quality discrepancies which would require more sequencing to resolve. VRIPs were mapped alongside regions of low-quality data, low data-coverage, and repeat regions. Characteristics of the CS1 genome, such as repeat levels and size, were found by comparing with the reference strain H37Rv.
The read data and assembly were found to be good quality, and the genome is of high enough quality to be considered closed. As expected, some regions of low coverage and poor quality were discovered inside large repeat regions, and more work on these would be valuable. 13 of the 32 VRIPs were verified, all linked with virulence factors. 5 verified VRIPs caused genes to split into domains, accumulating mutations in the non-coding region. Further work resolving the remaining 19 VRIPs is recommended.

year: 2021

title: Sometimes the Internet reads the question wrong: children’s search strategies & difficulties

authors: Vanderschantz, Nicholas

subjects: computer science

abstract: When children search for information on a given topic, how do they go about searching for and retrieving information? What can their information seeking strategies tell us about the development of search interfaces for children's digital libraries, search engines and information repositories? We interviewed New Zealand (NZ) school children to seek insights into how they are conducting information searches during their education.

text: Sometimes the Internet reads the question wrong: children’s search strategies & difficulties When children search for information on a given topic, how do they go about searching for and retrieving information? What can their information seeking strategies tell us about the development of search interfaces for children's digital libraries, search engines and information repositories? We interviewed New Zealand (NZ) school children to seek insights into how they are conducting information searches during their education.

year: 2014

title: Addressing the context and complexity of indigenous language revitalization

authors: May, Stephen

subjects: revitilization

abstract: This response discusses six key themes that emerge, either explicitly or implicitly, from Nancy Hornberger's exemplary analysis of the challenges facing indigenous language revitalization initiatives, particularly as they are currently expressed and implemented in three key indigenous language education contexts--Quechua in the South American Andes; Guarani in Paraguay and Maori in Aotearoa/New Zealand. These themes include, first, the importance of recognizing the wider social and political contexts within which indigenous revitalization initiatives are invariably situated. Second, it requires a related recognition of the internationalism of these initiatives. Third, any academic analysis of indigenous language revitalization requires, or at least must benefit from, an interdisciplinary approach, as exemplified by Hornberger's own analysis. Fourth, Hornberger's continua of biliteracy provides a sufficiently robust framework to explore the complexities and interrelationships inevitably involved in the articulation of language revitalization efforts, as well as how individuals and groups are situated in relation to those efforts. Fifth, the ongoing challenges and tensions inherent in indigenous language revitalization efforts need to continue to be discussed candidly, in order for them to be seriously addressed and, where possible, resolved. And finally, the importance of recognizing and including the voices of those centrally involved in these initiatives, as Hornberger again does, is a crucial feature, as well as a reflection of the inclusive, emancipatory aims of indigenous language revitalization itself.

text: Addressing the context and complexity of indigenous language revitalization This response discusses six key themes that emerge, either explicitly or implicitly, from Nancy Hornberger's exemplary analysis of the challenges facing indigenous language revitalization initiatives, particularly as they are currently expressed and implemented in three key indigenous language education contexts--Quechua in the South American Andes; Guarani in Paraguay and Maori in Aotearoa/New Zealand. These themes include, first, the importance of recognizing the wider social and political contexts within which indigenous revitalization initiatives are invariably situated. Second, it requires a related recognition of the internationalism of these initiatives. Third, any academic analysis of indigenous language revitalization requires, or at least must benefit from, an interdisciplinary approach, as exemplified by Hornberger's own analysis. Fourth, Hornberger's continua of biliteracy provides a sufficiently robust framework to explore the complexities and interrelationships inevitably involved in the articulation of language revitalization efforts, as well as how individuals and groups are situated in relation to those efforts. Fifth, the ongoing challenges and tensions inherent in indigenous language revitalization efforts need to continue to be discussed candidly, in order for them to be seriously addressed and, where possible, resolved. And finally, the importance of recognizing and including the voices of those centrally involved in these initiatives, as Hornberger again does, is a crucial feature, as well as a reflection of the inclusive, emancipatory aims of indigenous language revitalization itself.

year: 2006-01-01