title: Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

authors: Lear, Gavin

subjects: Science & Technology

abstract: Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

text: Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

year: 2018

title: Professional Development for a New Curriculum for a Developing Country: The Example of Technology Education in the Solomon Islands

authors: Sade, David

subjects: teacher professional development

abstract: This thesis explores the impact of a specially designed technology education
professional development programme for traditional technical education secondary
teachers to assist with the implementation of technology education in the Solomon
Islands. Technology education is a new development for the teachers in Solomon
Islands who are used to a more prescribed technical education. The technology
education in the Solomon Islands is in the process of change with the curriculum
being developed into a broader technological literacy approach comprising of
technological knowledge, technological process, and technological and societal
values. Thus, the development of teacher knowledge of technology and technology
education and their technology education practices are crucial for the successful
implementation of the new technology curriculum proposal.
The theoretical framework of this thesis is based on the interpretivist paradigm with a
qualitative case study approach. A two-year study with eight secondary technology
education teachers in the Solomon Islands was undertaken in 2005 and 2006. The
teachers existing perceptions of technology and technology education, classroom
practices and student learning in 2005 are described. The professional development
programme undertaken in 2006 and its impact on the secondary school teachers'
perceptions of technology and technology education, classroom practices, and student
learning in technology education are also examined.
The preliminary inquiry in 2005 showed that the technology teachers in the Solomon
Islands held narrow perspectives of technology and technology education, with views
centring on narrow technical aspects. The teachers' 2005 classroom practices were
very conservative with technical skills focussed teaching approaches fostered mainly
rote learning, and their assessment was dominated by summative assessment foci. The
2005 findings were used as a basis for a professional development to prepare teachers
to become more effective when teaching the proposed technology curriculum. A
professional development intervention programme was undertaken in 2006. It was
based on key professional development principles of teacher support and teacher
reflection and sharing. It was on-going and was undertaken over time. A social
constructivist learning model was used by the professiosnal development provider to
iii
help bring about teacher change. This programme built on the localised context and
was crafted around best practices from other professional developemnt models.
The study provides empirical evidence that the professional development intervention
programme had a positive impact on the teachers' perceptions of technology and
technology education, and teachers' teaching practices which changed from having a
technical education focus to a technology education focus. There were strong links
between teachers' perceptions and their classroom practices. When teachers
developed robust knowledge about technology and technology education, and used
appropriate technology education specific pedagogies they were able to successfully
implement the new Solomon Island technology education curriculum. The positive
impact of the professional development programme on teachers' understandings of
the nature of technology and technology education, their classroom practices, and
student learning demonstrate its effectiveness. The success of the professional
development model justifies the recommendation for its wider use in other developing
countries with similar contexts and situations to the Solomon Islands.

text: Professional Development for a New Curriculum for a Developing Country: The Example of Technology Education in the Solomon Islands This thesis explores the impact of a specially designed technology education
professional development programme for traditional technical education secondary
teachers to assist with the implementation of technology education in the Solomon
Islands. Technology education is a new development for the teachers in Solomon
Islands who are used to a more prescribed technical education. The technology
education in the Solomon Islands is in the process of change with the curriculum
being developed into a broader technological literacy approach comprising of
technological knowledge, technological process, and technological and societal
values. Thus, the development of teacher knowledge of technology and technology
education and their technology education practices are crucial for the successful
implementation of the new technology curriculum proposal.
The theoretical framework of this thesis is based on the interpretivist paradigm with a
qualitative case study approach. A two-year study with eight secondary technology
education teachers in the Solomon Islands was undertaken in 2005 and 2006. The
teachers existing perceptions of technology and technology education, classroom
practices and student learning in 2005 are described. The professional development
programme undertaken in 2006 and its impact on the secondary school teachers'
perceptions of technology and technology education, classroom practices, and student
learning in technology education are also examined.
The preliminary inquiry in 2005 showed that the technology teachers in the Solomon
Islands held narrow perspectives of technology and technology education, with views
centring on narrow technical aspects. The teachers' 2005 classroom practices were
very conservative with technical skills focussed teaching approaches fostered mainly
rote learning, and their assessment was dominated by summative assessment foci. The
2005 findings were used as a basis for a professional development to prepare teachers
to become more effective when teaching the proposed technology curriculum. A
professional development intervention programme was undertaken in 2006. It was
based on key professional development principles of teacher support and teacher
reflection and sharing. It was on-going and was undertaken over time. A social
constructivist learning model was used by the professiosnal development provider to
iii
help bring about teacher change. This programme built on the localised context and
was crafted around best practices from other professional developemnt models.
The study provides empirical evidence that the professional development intervention
programme had a positive impact on the teachers' perceptions of technology and
technology education, and teachers' teaching practices which changed from having a
technical education focus to a technology education focus. There were strong links
between teachers' perceptions and their classroom practices. When teachers
developed robust knowledge about technology and technology education, and used
appropriate technology education specific pedagogies they were able to successfully
implement the new Solomon Island technology education curriculum. The positive
impact of the professional development programme on teachers' understandings of
the nature of technology and technology education, their classroom practices, and
student learning demonstrate its effectiveness. The success of the professional
development model justifies the recommendation for its wider use in other developing
countries with similar contexts and situations to the Solomon Islands.

year: 2009

title: Ko ētehi waiata tangi o Pare Hauraki

authors: Ngāpō, Korohere

subjects: Waiata tangi

abstract: Inā hiahia ai te tangata kia mōhio ngā momo mōteatea o Pare Hauraki i ngā wā o mua me huri atu rātou ki ngā wāhi kohinga waiata pērā i Ngā Mōteatea a Ngata. Ka mutu kua tuhia tēnei pitopito kōrero hei tautoko atu i te hui waiata tawhito i whakatūria i Te Whare Wānanga o Waikato i te 2008. He tirohanga tēnei tuhinga ki te momo o ngā waiata e rua kāore i āta waiatahia, i āta rangona i runga i ngā marae o Hauraki ā mohoa nei. Ka mutu mā te waihape atu anō ki tētehi waiata i titoa e Pua ki Tawhiti mō tōna tungāne tae noa atu ki te waiata tangi i titoa e Wetea rāua ko Tūkehu, tēnā pea, ka ara ake anō te whakaaro me hoki anō ngā iwi o Pare Hauraki ki te waiata atu anō i ēnei waiata.

text: Ko ētehi waiata tangi o Pare Hauraki Inā hiahia ai te tangata kia mōhio ngā momo mōteatea o Pare Hauraki i ngā wā o mua me huri atu rātou ki ngā wāhi kohinga waiata pērā i Ngā Mōteatea a Ngata. Ka mutu kua tuhia tēnei pitopito kōrero hei tautoko atu i te hui waiata tawhito i whakatūria i Te Whare Wānanga o Waikato i te 2008. He tirohanga tēnei tuhinga ki te momo o ngā waiata e rua kāore i āta waiatahia, i āta rangona i runga i ngā marae o Hauraki ā mohoa nei. Ka mutu mā te waihape atu anō ki tētehi waiata i titoa e Pua ki Tawhiti mō tōna tungāne tae noa atu ki te waiata tangi i titoa e Wetea rāua ko Tūkehu, tēnā pea, ka ara ake anō te whakaaro me hoki anō ngā iwi o Pare Hauraki ki te waiata atu anō i ēnei waiata.

year: 2011