title: Few genetic differences between Victorian and Western Australian blue penguins, Eudyptula minor

authors: Banks, Jonathan C.

subjects: control region

abstract: Blue penguins, Eudyptula minor, breeding on Penguin Island, Western Australia are considerably larger than other blue penguins in Australia. If genetic isolation is the cause, it may have implications for the conservation status of some blue penguin populations. We compared the sequences of two mitochondrial gene regions (cytochrome‐b and the control region) from Western Australian blue penguins with other populations of blue penguins from Australia and New Zealand. We found few differences between sequences from Western Australia, Phillip Island, Victoria and Otago, New Zealand, although all three differed considerably from other New Zealand blue penguins. Sequences for the control region from the Western Australian blue penguins and 30 more birds breeding at various Australasian sites provided further support for two major clades within Eudyptula; an Australian clade (including Otago) and a New Zealand clade.

text: Few genetic differences between Victorian and Western Australian blue penguins, Eudyptula minor Blue penguins, Eudyptula minor, breeding on Penguin Island, Western Australia are considerably larger than other blue penguins in Australia. If genetic isolation is the cause, it may have implications for the conservation status of some blue penguin populations. We compared the sequences of two mitochondrial gene regions (cytochrome‐b and the control region) from Western Australian blue penguins with other populations of blue penguins from Australia and New Zealand. We found few differences between sequences from Western Australia, Phillip Island, Victoria and Otago, New Zealand, although all three differed considerably from other New Zealand blue penguins. Sequences for the control region from the Western Australian blue penguins and 30 more birds breeding at various Australasian sites provided further support for two major clades within Eudyptula; an Australian clade (including Otago) and a New Zealand clade.

year: 2008

title: Clonal cell proliferation in the mammary gland

authors: Jacobson, Gregory M.

abstract: The primary aim of this thesis was to classify the nature of the clonal expansion of cells that gives rise to bovine and murine mammary epithelia. It is generally assumed that the mammary gland is derived from the outgrowth of mammary-determined stem cell progeny, and that this expansion produces a mixture of cellular clones throughout the gland. Molecular techniques that enable the 'visualization' of the size and distribution of these clones will lead to a better appreciation of mammary gland development and architecture. 
In female mammals, the simplest 'mark' of clonality is provided by the inactivation of one or the other of the two X chromosomes. This event occurs early in embryogenesis and gives rise to stem cells that propagate this mark in progeny cells throughout the life of the animal. Two approaches, that utilized X-inactivation as a mark of clonality, were investigated, 1) naturally occurring X-linked gene polymorphisms in cattle, and 2) artificially introduced X-linked transgenes in mice. 
The first part of this thesis deals with the isolation and utilization of polymorphic markers on the bovine X-chromosome as markers of clonality. Such expressed genetic markers are essential if one is to distinguish which of the two X-chromosomes is active in a given cell. Two X-linked bovine genes, glucose-6-phosphate dehydrogenase (g6pd) and the X-inactive specific transcript (Xist) were selected for sequencing and SNP detection. As no specific sequence data was available for these genes, a bovine lambda genomic DNA library was screened. The G6PD clone selected from a lambda library was shown to be a pseudogene and therefore not useful for the present study. Another clone, that hybridized with an Xist gene probe, was shown to actually represent a bovine Huntingtin Associated Protein 1 like (Hap1-like) pseudogene, making it of no utility in this study. However, screening of regions of exon 1 of the Xist gene by direct PCR and sequencing, led to the discovery of an informative G↔T single nucleotide polymorphism (SNP). The variation, which was found in frequencies of 0.8 and 0.2 for 'G' and 'T' variants respectively (32% of females are heterozygous), was used in a number of different ways in order to assess the clonal profile of small 'blocks' of the gland (≤30 mm3). In these preliminary experiments, RT-PCR analysis of Xist expression patterns within each of the small blocks (each comprising around 3 X 107 cells) showed general heterogeneity but the experiments were not conclusive. Limitations of the experimental methods used are discussed and suggestions of alternative approaches, that will offer higher resolution, are presented. 
A second experimental approach, involving mice with a reporter transgene construct introduced into the X-chromosome (H253), was also used. The transgene consisted of 14 tandem repeats of a lacZ nuclear-localized reporter gene coupled with a mouse 3-hydroxyl-3-methylglutaryl coenzyme A reductase (hmgcr) promoter (Tam and Tan, 1992). A number of researchers had already utilized this transgenic model, and had confirmed that the cellular patterns of lacZ expression reflected actual X-inactivation patterns in a number of tissues. While carrying out initial investigations to ascertain the utility of this reporter system in investigations of the mammary gland it was discovered that the usual description of hmgcr as a 'house-keeping' gene is somewhat of a misnomer, as some tissues in the mouse show very strong patterns of lacZ expression while others gave minimal, or no, detectable expression. Furthermore, transgene expression was observed to increase during pregnancy and it was concluded that this effect was almost certainly a response to increased estrogen levels at this time. 
Whole mount analysis of five mouse mammary glands from transgenic animals revealed heterogeneous patterns of lacZ staining, indicating that mammary epithelia is generally polyclonal. In total, 42% of terminal buds and alveoli displayed a single lacZ staining pattern. Analysis of these staining patterns induct termini indicated that the majority of individual alveoli are derived from two or three division competent (stem) cells.

text: Clonal cell proliferation in the mammary gland The primary aim of this thesis was to classify the nature of the clonal expansion of cells that gives rise to bovine and murine mammary epithelia. It is generally assumed that the mammary gland is derived from the outgrowth of mammary-determined stem cell progeny, and that this expansion produces a mixture of cellular clones throughout the gland. Molecular techniques that enable the 'visualization' of the size and distribution of these clones will lead to a better appreciation of mammary gland development and architecture. 
In female mammals, the simplest 'mark' of clonality is provided by the inactivation of one or the other of the two X chromosomes. This event occurs early in embryogenesis and gives rise to stem cells that propagate this mark in progeny cells throughout the life of the animal. Two approaches, that utilized X-inactivation as a mark of clonality, were investigated, 1) naturally occurring X-linked gene polymorphisms in cattle, and 2) artificially introduced X-linked transgenes in mice. 
The first part of this thesis deals with the isolation and utilization of polymorphic markers on the bovine X-chromosome as markers of clonality. Such expressed genetic markers are essential if one is to distinguish which of the two X-chromosomes is active in a given cell. Two X-linked bovine genes, glucose-6-phosphate dehydrogenase (g6pd) and the X-inactive specific transcript (Xist) were selected for sequencing and SNP detection. As no specific sequence data was available for these genes, a bovine lambda genomic DNA library was screened. The G6PD clone selected from a lambda library was shown to be a pseudogene and therefore not useful for the present study. Another clone, that hybridized with an Xist gene probe, was shown to actually represent a bovine Huntingtin Associated Protein 1 like (Hap1-like) pseudogene, making it of no utility in this study. However, screening of regions of exon 1 of the Xist gene by direct PCR and sequencing, led to the discovery of an informative G↔T single nucleotide polymorphism (SNP). The variation, which was found in frequencies of 0.8 and 0.2 for 'G' and 'T' variants respectively (32% of females are heterozygous), was used in a number of different ways in order to assess the clonal profile of small 'blocks' of the gland (≤30 mm3). In these preliminary experiments, RT-PCR analysis of Xist expression patterns within each of the small blocks (each comprising around 3 X 107 cells) showed general heterogeneity but the experiments were not conclusive. Limitations of the experimental methods used are discussed and suggestions of alternative approaches, that will offer higher resolution, are presented. 
A second experimental approach, involving mice with a reporter transgene construct introduced into the X-chromosome (H253), was also used. The transgene consisted of 14 tandem repeats of a lacZ nuclear-localized reporter gene coupled with a mouse 3-hydroxyl-3-methylglutaryl coenzyme A reductase (hmgcr) promoter (Tam and Tan, 1992). A number of researchers had already utilized this transgenic model, and had confirmed that the cellular patterns of lacZ expression reflected actual X-inactivation patterns in a number of tissues. While carrying out initial investigations to ascertain the utility of this reporter system in investigations of the mammary gland it was discovered that the usual description of hmgcr as a 'house-keeping' gene is somewhat of a misnomer, as some tissues in the mouse show very strong patterns of lacZ expression while others gave minimal, or no, detectable expression. Furthermore, transgene expression was observed to increase during pregnancy and it was concluded that this effect was almost certainly a response to increased estrogen levels at this time. 
Whole mount analysis of five mouse mammary glands from transgenic animals revealed heterogeneous patterns of lacZ staining, indicating that mammary epithelia is generally polyclonal. In total, 42% of terminal buds and alveoli displayed a single lacZ staining pattern. Analysis of these staining patterns induct termini indicated that the majority of individual alveoli are derived from two or three division competent (stem) cells.

year: 2004

title: Indigenous knowledge, methodology and mayhem: What is the role of methodology in producing indigenous insights? A discussion from Mātauranga Māori

authors: Smith, Linda Tuhiwai

abstract: The emergence of an academic discourse called Indigenous knowledge internationally, and mātauranga Māori in Aotearoa New Zealand, presents some substantive challenges to concepts of knowing and being, of knowledge creation, knowledge work and the making of meaning. These challenges engage us across philosophical, disciplinary, institutional, inter-generational, territorial and community boundaries, presenting an opportunity to imagine this field anew, and the theories and methodologies that inform contemporary Māori or Indigenous Studies. This article raises some discussion about ‘research methodologies’ being used when discussing mātauranga Māori and Indigenous knowledge (hereafter referred to as IK mātauranga). Research methodologies are often associated with specific disciplines of knowledge and viewed as the primary if not singular way in which knowledge is generated. Arguably, IK mātauranga occupies a different knowledge space from traditional academic disciplines, including their transdisciplinary interstices. This article speaks to a gnawing sense that mayhem is at play, as the academic work around IK mātauranga begins to consolidate and become institutionalised away from its indigenous communities and contexts, where it began and where it still informs identities, ways of living and being.

text: Indigenous knowledge, methodology and mayhem: What is the role of methodology in producing indigenous insights? A discussion from Mātauranga Māori The emergence of an academic discourse called Indigenous knowledge internationally, and mātauranga Māori in Aotearoa New Zealand, presents some substantive challenges to concepts of knowing and being, of knowledge creation, knowledge work and the making of meaning. These challenges engage us across philosophical, disciplinary, institutional, inter-generational, territorial and community boundaries, presenting an opportunity to imagine this field anew, and the theories and methodologies that inform contemporary Māori or Indigenous Studies. This article raises some discussion about ‘research methodologies’ being used when discussing mātauranga Māori and Indigenous knowledge (hereafter referred to as IK mātauranga). Research methodologies are often associated with specific disciplines of knowledge and viewed as the primary if not singular way in which knowledge is generated. Arguably, IK mātauranga occupies a different knowledge space from traditional academic disciplines, including their transdisciplinary interstices. This article speaks to a gnawing sense that mayhem is at play, as the academic work around IK mātauranga begins to consolidate and become institutionalised away from its indigenous communities and contexts, where it began and where it still informs identities, ways of living and being.

year: 2016