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Subject: search.filters.subject.DNA Analysis

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    Characterization of a new horse transferrin variant : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry at Massey University
    (Massey University, 1993) Paterson, Geoffrey Reayburn
    Transferrin is a glycoprotein with a molecular weight of approximately 80 kd. Its single polypeptide chain is formed into two lobes and it is able to bind two ferric (Fe III) ions per protein molecule. Horse serum transferrin, like the transferrins of most vertebrate species, exhibits extensive genetic polymorphism. Transferrin is one of several protein systems used for blood-typing horses. During routine blood typing a new band (designated*) was found. This variant originated from a thoroughbred stallion which was of considerable value as a sire and so it was of interest to characterize this new transferrin variant. Thoroughbred horses carry genes for only six of the fourteen known transferrin isoforms; D, Fl, F2, H2, 0 and R. The aim of this project was to characterize, by classical amino acid sequence analysis, the transferrin variant and the parental variants D and Fl, from one of which must have arisen. All three variant forms (D, Fl and*) were purified. Tryptic digests of the variants were analysed by HPLC and those peaks appearing to differ between the HPLC profiles were sequenced by automated protein sequencing. The sequences obtained confirmed that the protein isolated was a transferrin variant. Further sequencing allowed deduction of the parent transferrin variant. Two clear sequence differences between the D and Fl variant have been identified. The Fl variant was found to contain an arginine residue at amino acid position 553, whereas the D variant contains a cysteine residue at this position. At position 418 of the Fl variant a serine residue was found and at the same position in the D variant a proline residue was found. Sequence determination of peptides from the * tryptic digest revealed that a proline residue and a cysteine residue were found at positions 418 and 553 respectively, clearly indicating that the new * phenotype has arisen from the D allele and not the Fl allele.
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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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    The determination of nucleotide arrangement in oligonucleotides derived from deoxyribonucleic acid : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry at Massey University
    (Massey University, 1969) Simes, Lynda Joy
    The importance of DNA sequences The genetic material of all animals, plants bacteria, and of many animal and bacterial viruses has long been established as deoxyribonucleic acid or DNA, and recent studies (1a) have shown that its major function is to carry the genetic information required by a cell for the synthesis of species specific proteins. This information is stored by the nucleic acid macromolecule in the form of a linear code determined by its intrinsic nucleotide sequence or primary structure. The information is carried in such a way that a specific sequence of three nueleotides has the ability to code for one of every type of amino acid found in protein. In recent years the message corresponding to each nucleotide triplet has been established (2). Besides coding for amino acids, nucleotide sequences exist which are known to code for ribosomal transfer RNA's. There are probably other sequences which are involved in a variety of special roles, the more important being regulating and initiating transcription of the genetic message into functional messenger RNA, and the initiation of DNA replication. Because little information is available about the actual arrangement of bases needed to effect these functions, a knowledge of the complete nucleotide sequence of a biologically active DNA molecule may help to elucidate the nature of these extremely important processes. In addition it in hoped that new approaches can be found towards a better understanding of the actual changes to DNA caused by mutagens and carcinogenic agents, and it is also hoped that some knowledge can be obtained of the extent to which degenerate codons exist in genetic material, and the function of these codons when they do occur.