title: Time-evolving data science and artificial intelligence for Advanced Open Environmental Science (TAIAO) programme

authors: Koh, Yun Sing

subjects: computer science

abstract: New Zealand's unique ecosystems face increasing threats from climate change, impacting biodiversity and posing challenges to safety, livelihoods, and well-being. To tackle these complex issues,  advanced data science and artificial intelligence techniques can provide unique solutions. Currently, in its fourth year of a seven-year program, TAIAO focuses on methods for analyzing environmental datasets. Recognizing this urgency, the open-source TAIAO platform was developed. This platform enables new artificial intelligence research for environmental data and offers an open-access repository to enhance reproducibility in the field. This paper will showcase four environmental case studies, artificial intelligence research, platform implementation details, and future development plans.

text: Time-evolving data science and artificial intelligence for Advanced Open Environmental Science (TAIAO) programme New Zealand's unique ecosystems face increasing threats from climate change, impacting biodiversity and posing challenges to safety, livelihoods, and well-being. To tackle these complex issues,  advanced data science and artificial intelligence techniques can provide unique solutions. Currently, in its fourth year of a seven-year program, TAIAO focuses on methods for analyzing environmental datasets. Recognizing this urgency, the open-source TAIAO platform was developed. This platform enables new artificial intelligence research for environmental data and offers an open-access repository to enhance reproducibility in the field. This paper will showcase four environmental case studies, artificial intelligence research, platform implementation details, and future development plans.

year: 2024

title: The Structure of the Oligomerization Domain of Lsr2 from Mycobacterium tuberculosis Reveals a Mechanism for Chromosome Organization and Protection

authors: Summers, Emma Louise

subjects: biology

abstract: Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNA-binding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal cross-linking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 Å resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß-ß-a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel β-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated.

text: The Structure of the Oligomerization Domain of Lsr2 from Mycobacterium tuberculosis Reveals a Mechanism for Chromosome Organization and Protection Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNA-binding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal cross-linking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 Å resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß-ß-a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel β-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated.

year: 2012

title: Maori & Psychology Research Unit annual report 2006

authors: Rua, Mohi

subjects: Maori and Psychology Research Unit

abstract: Annual report of the Maori and Psychology Research Unit (MPRU) 2006. The unit was established in August of 1997. The unit is designed to provide a catalyst and support network for enhancing research concerning the psychological needs, aspirations, and priorities of Maori people. The MPRU is well situated to draw together skilled and experienced interdisciplinary research groups by networking and establishing working relationships with staff and students within the Faculty of Arts and Social Sciences, the University, and the wider community.

text: Maori & Psychology Research Unit annual report 2006 Annual report of the Maori and Psychology Research Unit (MPRU) 2006. The unit was established in August of 1997. The unit is designed to provide a catalyst and support network for enhancing research concerning the psychological needs, aspirations, and priorities of Maori people. The MPRU is well situated to draw together skilled and experienced interdisciplinary research groups by networking and establishing working relationships with staff and students within the Faculty of Arts and Social Sciences, the University, and the wider community.

year: 2006