title: Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola

authors: Campbell, Barbara J.

subjects: hydrothermal environment

abstract: Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment—some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20uC increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere—anaerobic, sulfur, H₂- and CO₂-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.

text: Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment—some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20uC increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere—anaerobic, sulfur, H₂- and CO₂-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.

year: 2009

title: Mining Domain-Specific Thesauri from Wikipedia: A case study

authors: Milne, David N.

subjects: computer science

abstract: Domain-specific thesauri are high-cost, high-maintenance, high-value knowledge structures. We show how the classic thesaurus structure of terms and links can be mined automatically from Wikipedia. In a comparison with a professional thesaurus for agriculture we find that Wikipedia contains a substantial proportion of its concepts and semantic relations; furthermore it has impressive coverage of contemporary documents in the domain. Thesauri derived using our techniques capitalize on existing public efforts and tend to reflect contemporary language usage better than their costly, painstakingly-constructed manual counterparts.

text: Mining Domain-Specific Thesauri from Wikipedia: A case study Domain-specific thesauri are high-cost, high-maintenance, high-value knowledge structures. We show how the classic thesaurus structure of terms and links can be mined automatically from Wikipedia. In a comparison with a professional thesaurus for agriculture we find that Wikipedia contains a substantial proportion of its concepts and semantic relations; furthermore it has impressive coverage of contemporary documents in the domain. Thesauri derived using our techniques capitalize on existing public efforts and tend to reflect contemporary language usage better than their costly, painstakingly-constructed manual counterparts.

year: 2006

title: Student belonging: critical relationships and responsibilities

authors: Berryman, Mere

subjects: Belonging

abstract: In this paper, we consider New Zealand’s education system to understand what can happen when we focus only on excellence and students reaching their potential, without simultaneously investing in their sense of belonging and wellbeing. National statistics suggest we are alienating and shortchanging an increasing number of students and, for disproportionate numbers of Indigenous students, these statistics are part of a world trend. The literature, and the students themselves, highlight the need to overturn the underlying racism that persistently disadvantages clearly identifiable groups of students over others. Until we do, using equity and excellence as the most powerful drivers for reform, will continue to promote conditions where our students’ sense of belonging and wellbeing are undermined throughout their education and we will risk, failing to address the ensuing negative statistics. We conclude with a response that we have learned from working with these same students.

text: Student belonging: critical relationships and responsibilities In this paper, we consider New Zealand’s education system to understand what can happen when we focus only on excellence and students reaching their potential, without simultaneously investing in their sense of belonging and wellbeing. National statistics suggest we are alienating and shortchanging an increasing number of students and, for disproportionate numbers of Indigenous students, these statistics are part of a world trend. The literature, and the students themselves, highlight the need to overturn the underlying racism that persistently disadvantages clearly identifiable groups of students over others. Until we do, using equity and excellence as the most powerful drivers for reform, will continue to promote conditions where our students’ sense of belonging and wellbeing are undermined throughout their education and we will risk, failing to address the ensuing negative statistics. We conclude with a response that we have learned from working with these same students.

year: 2019