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    DNA sequence reading by image processing: a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in computer science at Massey University
    (Massey University, 1993) Fan, Baozhen
    The research described in this thesis is the development of the DNA sequence reading system. Macromolecular sequences of DNA are the encoded form of the genetic information of all living organisms. DNA sequencing has therefore played a significant role in the elucidation of biological systems. DNA sequence reading is a part of DNA sequencing. This project is for reading DNA sequences directly from DNA sequencing gel autoradiographs within a general purpose image processing system. The DNA sequence reading software is developed based on the waterfall software development approach combined with exploratory programming. Requirement analysis, software design, detailed design, implementation, system testing and maintenance are the basic development stages. The feedback from implementation and system testing to detailed design is much stronger in image processing than a lot of other software development. After an image is captured from a gel autoradiograph, the background of the image is normalised and the contrast is enhanced. The captured image consists several lane sets of bands. Each of the lane set represents one part of a DNA sequence. The lane sets are separated automatically into subimages to be read individually. The gap lines between the lane sets are detected for separation. The geometric distortions are corrected by finding the boundaries of the lane set in the subimage. The left boundary of the lane set is used to straighten lane set and the right boundary is used to warp the lane set into a standard width. If separation of the lane sets or geometry correction is unsuccessful by automatical processing, manual selection is used. After the band features are enhanced, the individual bands are extracted and the positions of the bands are determined. The band positions are then converted into the order of the DNA sequence. Different part of a sequence from subsequences are merged into a longer sequence. In most of the cases, the individual lane sets in a captured image are able to be separated automatically. Manual processing is necessary to handle the cases where the lane sets are too close. The system may reach an accuracy of 98% if the bands are clear. Manual checking and correcting the detected bands helps to obtain a reliable sequence. If a lane set on the autoradiograph is indistinct or bands are too close it may reduce the accuracy, in extreme cases to the point where it is unreadable. For a 512x512 image captured from a gel autoradiograph, preprocessing takes 90 seconds, processing each subimage takes 40 seconds on a 33Hz 486 PC. If processing a 430x350 mm autoradiograph with 16 lane sets, assuming 6 images are required, it takes about 40 minutes.
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    Ancient DNA analysis of Māori feather cloaks and kete : implications for conservation and culture : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Molecular Biosciences at Massey University, Auckland, New Zealand, 2012
    (Massey University, 2012) Hartnup, Katie
    Feather cloaks (kakahu) and bags (kete), particularly those adorned with kiwi feathers, are treasured items or taonga to the Maori people of New Zealand. They are considered iconic expressions of Maori culture. Despite their status, much of our knowledge of the materials used to construct these artefacts, the provenance of these artefacts and the origins of these traditions, has been lost. We used ancient DNA methods to recover mitochondrial DNA sequences from 849 feather samples taken from 109 kiwi feathered cloaks (kahu kiwi) and 161 feather samples from 55 kiwi feathered kete (kete kiwi). We show that almost all (>99%) of the cloaks and all (100%) of the kete were constructed using feathers from North Island brown kiwi (Apteryx mantelli). Just one cloak was found to have been constructed using feathers from little spotted kiwi (Apteryx owenii). The remaining three species of kiwi (Apteryx haasti, Apteryx rowi and Apteryx australis) were not found in any of the cloaks and kete sampled. Molecular sexing of nuclear DNA from 92 feather cloak samples also revealed that the sex-ratio of birds deviated from a ratio of 1:1 observed in reference populations, with a male skew observed. Additionally, a reference database of 185 North Island brown kiwi mitochondrial control region DNA sequences was constructed, comprising samples collected from 26 North Island locations together with data available from the literature. For contemporary populations, we saw a phylogeographic structuring of haplotypes using both SAMOVA and Nested Clade Analysis into Eastern, Northern and West and Central populations. Utilising this structuring, it was possible to infer the provenance of 847 kiwi feathers from 108 cloaks and 153 kiwi feathers from 52 kete. A surprising proportion of cloaks (15%) and some kete (5.5%) were found to contain feathers from different geographic locations providing evidence of either kiwi trading among Maori tribes (iwi), tribal displacement, or organised hunting trips into other tribal areas. The data also suggests that the east of the North Island was the most prolific of all kiwi cloak and kete making areas, accounting for over 50% of all cloaks analysed and over 58% of all kete. This could indicate that the East of the North Island was the epicentre for this cultural tradition. Also, the structuring observed in the reference database will prove to be useful to conservationists, such as the New Zealand Department of Conservation, when deciding strategies to maintain populations of New Zealand’s most iconic bird. The genetic analysis of these treasured items has been invaluable in enriching our knowledge and rebuilding their lost histories. Additionally, genetic data from historical items can aid our understanding or how populations change overtime, thus aiding conservation of valuable species.
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    DNA barcoding the birds of New Zealand : a thesis presented in fulfillment of the requirements for the degree of Doctor of Philosophy in Molecular BioSciences at Massey University, Auckland, New Zealand
    (Massey University, 2011) Waugh, William John; Waugh, William John
    A comprehensive inventory of the life forms on earth is at the heart of any scientific study of evolution and biodiversity. The international "Barcode of Life" project is an attempt to identify the earth's biodiversity, at the species level, using short signature DNA sequences. The hypothesis underlying DNA barcoding is being comprehensively tested in different taxa. A database was constructed of DNA sequences from part of the mitochondrial gene cytochrome c oxidase subunit 1 for the avian fauna of New Zealand. To date, 833 sequences from 215 species have been added to this database, of which 628 sequences from 126 species are from native or endemic birds. This represents an average of 5 samples per species (minimum 1, maximum 18) for the latter group, which is the central focus of this thesis. Samples of species, from different geographical locations throughout New Zealand, have been collected to highlight any intraspecific nucleotide variation that may occur. Some samples analysed here were from historical specimens housed in museum collections and required specialised DNA extraction and amplification. These techniques were developed as part of the project and provide a means of collecting DNA barcodes where no modern material is available. In general, DNA barcoding proved effective at identifying avian species in New Zealand. However, some species were highlighted that contained distinct DNA barcode clusters, indicative of possible subspecies or cryptic species while in other cases two or more species that appear to be different share very similar DNA barcodes. Remains from aircraft birdstrikes were identified using this technique in order to inform wildlife management at airports around New Zealand. A review of and outlook for the uses of this technique are given.