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: A new record of Percursaria percursa (Ulvaceae, Ulvales) on the North Island, New Zealand

authors: Pratt, S.J.

subjects: Percursaria percursa

abstract: The filamentous green alga Percursaria percursa (Ulvaceae, Ulvales) was recorded for the first time on the North Island of New Zealand at mokoroa Estuary, Tauranga Harbour. This species is previously known within New Zealand from only two records, both from the South Island. In Tauranga Harbour, this species was restricted to anoxic estuarine sediments where mangrove forests had been mulched, and mulchate left in situ. Percursaria percursa was found intertwined with Ulva spp. and Rhizoclonium spp. Surveys of other North and South Island estuaries suggest that this alga, although occurring as part of nuisance green algal blooms in Tauranga Harbour, has only colonized human-impacted locations, and has not yet been observed in natural' estuarine ecosystems in New Zealand. As this species was found intertwined with other mat-forming filamentous green algae, it can easily be misidentified in the field, leading to both over- and under-reporting of species occurrence.

text: A new record of Percursaria percursa (Ulvaceae, Ulvales) on the North Island, New Zealand The filamentous green alga Percursaria percursa (Ulvaceae, Ulvales) was recorded for the first time on the North Island of New Zealand at mokoroa Estuary, Tauranga Harbour. This species is previously known within New Zealand from only two records, both from the South Island. In Tauranga Harbour, this species was restricted to anoxic estuarine sediments where mangrove forests had been mulched, and mulchate left in situ. Percursaria percursa was found intertwined with Ulva spp. and Rhizoclonium spp. Surveys of other North and South Island estuaries suggest that this alga, although occurring as part of nuisance green algal blooms in Tauranga Harbour, has only colonized human-impacted locations, and has not yet been observed in natural' estuarine ecosystems in New Zealand. As this species was found intertwined with other mat-forming filamentous green algae, it can easily be misidentified in the field, leading to both over- and under-reporting of species occurrence.

year: 2013

title: Lifting barriers: Leadership, tactical, and strategic issues from, and for, indigenous community development

authors: Murthy, Vikram

subjects: indigenous communities

abstract: This paper uses learnings from a project with indigenous youth to engage with a recurring challenge in indigenous community organisation (ICO) development initiatives: The unwitting detraction from outcome efficacy by charismatic and influential indigenous leadership leading with an out-of-date repertoire. Using material from recent literature in the fields of non-profit management, new leadership, and social enterprise, the paper suggests guides to improved practice for meeting this challenge. It also sets out to effectiveness, will better underwrite sensitivity in entrepreneurial environments with complex cultural and social beliefs and practices. Such a repertoire will energise intraorganisational communal and consensual processes, which would resonate culturally with the ICO's normative behaviours and values, and would thus help the organisation marshall its collective will to frame futures that best capture their stakeholders' hopes and aspirations. Finally, it recommends that future research examine interfaces between these fields and the spiritual frameworks of indigenous world-views.

text: Lifting barriers: Leadership, tactical, and strategic issues from, and for, indigenous community development This paper uses learnings from a project with indigenous youth to engage with a recurring challenge in indigenous community organisation (ICO) development initiatives: The unwitting detraction from outcome efficacy by charismatic and influential indigenous leadership leading with an out-of-date repertoire. Using material from recent literature in the fields of non-profit management, new leadership, and social enterprise, the paper suggests guides to improved practice for meeting this challenge. It also sets out to effectiveness, will better underwrite sensitivity in entrepreneurial environments with complex cultural and social beliefs and practices. Such a repertoire will energise intraorganisational communal and consensual processes, which would resonate culturally with the ICO's normative behaviours and values, and would thus help the organisation marshall its collective will to frame futures that best capture their stakeholders' hopes and aspirations. Finally, it recommends that future research examine interfaces between these fields and the spiritual frameworks of indigenous world-views.

year: 2006