title: The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains

authors: Summers, Emma Louise

abstract: Glycoside hydrolase (GH) family 29 consists solely of α-l-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29-0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family proteins. GH29-0940 is a monomer and its overall structure consists of an N-terminal TIM-barrel-like domain, a central β-sandwich domain and a C-terminal β-sandwich domain. The TIM-barrel-like catalytic domain exhibits a (β/α)8/7 arrangement in the core instead of the typical (β/α)8 topology, with the 'missing' α-helix replaced by a long meandering loop that 'closes' the barrel structure and suggests a high degree of structural flexibility in the catalytic core. This feature was also noted in all six other structures of GH29 enzymes that have been deposited in the PDB. Based on sequence and structural similarity, the residues Asp162 and Glu220 are proposed to serve as the catalytic nucleophile and the proton donor, respectively. Like other GH29 enzymes, the GH29-0940 structure shows five strictly conserved residues in the catalytic pocket. The structure shows two glycerol molecules in the active site, which have also been observed in other GH29 structures, suggesting that the enzyme catalyses the hydrolysis of small carbohydrates. The two binding domains are classed as family 32 carbohydrate-binding modules (CBM32). These domains have residues involved in ligand binding in the loop regions at the edge of the β-sandwich. The predicted substrate-binding residues differ between the modules, suggesting that different modules bind to different groups on the substrate(s). Enzymes that possess multiple copies of CBMs are thought to have a complex mechanism of ligand recognition. Defined electron density identifying a long 20-amino-acid hydrophilic loop separating the two CBMs was observed. This suggests that the additional C-terminal domain may have a dynamic range of movement enabled by the loop, allowing a unique mode of action for a GH29 enzyme that has not been identified previously.A high-resolution crystal structure of an unknown glycoside hydrolase enzyme from the rumen of B. taurus is presented. Unique dual carbohydrate-binding domains are revealed.

text: The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains Glycoside hydrolase (GH) family 29 consists solely of α-l-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29-0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family proteins. GH29-0940 is a monomer and its overall structure consists of an N-terminal TIM-barrel-like domain, a central β-sandwich domain and a C-terminal β-sandwich domain. The TIM-barrel-like catalytic domain exhibits a (β/α)8/7 arrangement in the core instead of the typical (β/α)8 topology, with the 'missing' α-helix replaced by a long meandering loop that 'closes' the barrel structure and suggests a high degree of structural flexibility in the catalytic core. This feature was also noted in all six other structures of GH29 enzymes that have been deposited in the PDB. Based on sequence and structural similarity, the residues Asp162 and Glu220 are proposed to serve as the catalytic nucleophile and the proton donor, respectively. Like other GH29 enzymes, the GH29-0940 structure shows five strictly conserved residues in the catalytic pocket. The structure shows two glycerol molecules in the active site, which have also been observed in other GH29 structures, suggesting that the enzyme catalyses the hydrolysis of small carbohydrates. The two binding domains are classed as family 32 carbohydrate-binding modules (CBM32). These domains have residues involved in ligand binding in the loop regions at the edge of the β-sandwich. The predicted substrate-binding residues differ between the modules, suggesting that different modules bind to different groups on the substrate(s). Enzymes that possess multiple copies of CBMs are thought to have a complex mechanism of ligand recognition. Defined electron density identifying a long 20-amino-acid hydrophilic loop separating the two CBMs was observed. This suggests that the additional C-terminal domain may have a dynamic range of movement enabled by the loop, allowing a unique mode of action for a GH29 enzyme that has not been identified previously.A high-resolution crystal structure of an unknown glycoside hydrolase enzyme from the rumen of B. taurus is presented. Unique dual carbohydrate-binding domains are revealed.

year: 2016-10-01

title: Knowledge, Experience and Attitudes towards sharks: A case for species-specific environmental education

authors: Broadhead, Kathy A.

subjects: Environmental Education

abstract: Sharks are under threat from human exploitation and their numbers are declining, which has ecosystem consequences. Furthermore, sharks have suffered from a negative public image that has worked to reduce their populations, rather than conserve them. 

This research sought to determine people’s knowledge, experience and attitudes towards sharks. It explored the link between people’s knowledge and experience with sharks and the attitudes held toward them. Research has shown that attitudes regarding the marine environment and wildlife are shaped by several factors including formal education and personal experience, which have been found to influence the development of environmental attitudes and conservation behaviour. 

In this research a questionnaire was used to gather data from a cross section of the Mount Maunganui community using a convenience sampling method. Sixty community members and one class of 25 primary students completed the questionnaire. The questionnaire asked participants about their knowledge and attitudes about sharks, their experience with sharks and their general environmental behaviours. Data were either statistically analysed for closed questions, or thematically analysed for open questions. Correlations between knowledge, attitudes and behaviour were explored, as it has previously been found that individuals with high levels of knowledge and positive attitudes towards animals such as sharks are more likely to support their conservation.

Findings indicate mostly fear-based attitudes in first thoughts about sharks, influenced often by exposure to entertainment and news media. However, responses to more considered attitude orientation questions tended to be largely positive, and naturalistic in nature. Findings further indicate that good levels of knowledge, experience and mostly positive attitudes towards sharks do not always translate to support for their conservation. Recommendations are made for possible ways to develop people’s knowledge, experience and attitudes towards sharks through environmental education for conservation.

text: Knowledge, Experience and Attitudes towards sharks: A case for species-specific environmental education Sharks are under threat from human exploitation and their numbers are declining, which has ecosystem consequences. Furthermore, sharks have suffered from a negative public image that has worked to reduce their populations, rather than conserve them. 

This research sought to determine people’s knowledge, experience and attitudes towards sharks. It explored the link between people’s knowledge and experience with sharks and the attitudes held toward them. Research has shown that attitudes regarding the marine environment and wildlife are shaped by several factors including formal education and personal experience, which have been found to influence the development of environmental attitudes and conservation behaviour. 

In this research a questionnaire was used to gather data from a cross section of the Mount Maunganui community using a convenience sampling method. Sixty community members and one class of 25 primary students completed the questionnaire. The questionnaire asked participants about their knowledge and attitudes about sharks, their experience with sharks and their general environmental behaviours. Data were either statistically analysed for closed questions, or thematically analysed for open questions. Correlations between knowledge, attitudes and behaviour were explored, as it has previously been found that individuals with high levels of knowledge and positive attitudes towards animals such as sharks are more likely to support their conservation.

Findings indicate mostly fear-based attitudes in first thoughts about sharks, influenced often by exposure to entertainment and news media. However, responses to more considered attitude orientation questions tended to be largely positive, and naturalistic in nature. Findings further indicate that good levels of knowledge, experience and mostly positive attitudes towards sharks do not always translate to support for their conservation. Recommendations are made for possible ways to develop people’s knowledge, experience and attitudes towards sharks through environmental education for conservation.

year: 2016

title: Hā Ora: Reflecting on a Kaupapa Māori community engaged co-design approach to lung cancer research

authors: Kidd, Jacquie

abstract: Co-designed research is gaining prominence within the health care space. Community engagement is a key premise of co-design and is also particularly vital when carrying out kaupapa Māori research. Kaupapa Māori describes a “by Māori, for Māori” approach to research in Aotearoa/New Zealand. This article discusses the research process of Hā Ora: a co-design project underpinned by a kaupapa Māori approach. The objective was to explore the barriers to early presentation and diagnosis of lung cancer, barriers identified by Māori. The team worked with four rural Māori communities, with whom we aimed to co-design local interventions that would promote earlier diagnosis of lung cancer. This article highlights and unpacks the complexities of carrying out community- engaged co-design with Māori who live in rural communities. In particular, we draw attention to the importance of flexibility and adaptability in the research process. We highlight issues pertaining to timelines and budgets, and also the intricacies of involving co-governance and advisory groups. Overall, through this article, we argue that health researchers need to prioritise working with and for participants, rather than on them, especially when working with Māori communities.

text: Hā Ora: Reflecting on a Kaupapa Māori community engaged co-design approach to lung cancer research Co-designed research is gaining prominence within the health care space. Community engagement is a key premise of co-design and is also particularly vital when carrying out kaupapa Māori research. Kaupapa Māori describes a “by Māori, for Māori” approach to research in Aotearoa/New Zealand. This article discusses the research process of Hā Ora: a co-design project underpinned by a kaupapa Māori approach. The objective was to explore the barriers to early presentation and diagnosis of lung cancer, barriers identified by Māori. The team worked with four rural Māori communities, with whom we aimed to co-design local interventions that would promote earlier diagnosis of lung cancer. This article highlights and unpacks the complexities of carrying out community- engaged co-design with Māori who live in rural communities. In particular, we draw attention to the importance of flexibility and adaptability in the research process. We highlight issues pertaining to timelines and budgets, and also the intricacies of involving co-governance and advisory groups. Overall, through this article, we argue that health researchers need to prioritise working with and for participants, rather than on them, especially when working with Māori communities.

year: 2021