Browsing by Subject "Karyotypes"
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Item Automatic segmentation and classification of multiplex-fluorescence in-situ hybridization chromosome images(2006-08-14) Choi, Hyo Hun; Bovik, Alan C. (Alan Conrad), 1958-Multicolor fluorescence in-situ hybridization (M-FISH) techniques provide color karyotyping that allows simultaneous analysis of numerical and structural abnormalities of whole human chromosomes. Chromosomes are stained combinatorially in M-FISH. By analyzing the intensity combinations of each pixel, all chromosome pixels in an image are classified. Often, the intensity distributions between different images are found to be considerably different and the difference becomes the source of misclassifications of the pixels. Improved pixel classification accuracy is the most important task to ensure the success of the M-FISH technique. Along with a reliable pixel classification method, automation of the karyotyping process is another important goal. The automation requires segmentation of chromosomes, which not only involves object/background separation but also involves separating touching and overlapping chromosomes. While automating the segmentation of partially occluded chromosomes is an extremely challenging problem, a pixel classification method that satisfies both high accuracy and minimum human intervention has not been realized. The main contributions of this dissertation include development of a new feature normalization method for M-FISH images that reduces the difference in the feature distributions among different images, and development of a new decomposition method for clusters of overlapping and touching chromosomes. A significant improvement was achieved in pixel classification accuracy after the new feature normalization. The overall pixel classification accuracy improved by 40% after normalization. Given a cluster, a number of hypotheses was formed utilizing the geometry of a cluster, pixel classification results, and chromosome sizes, and a hypotheis that maximized the likelihood function was chosen as the correct decomposition. Superior decomposition results were obtained using the new method compared to the previous methods. Contributions also include development of a color compensation method for combinatorially stained FISH images (including M-FISH images) based on a new signal model for multicolor/multichannel FISH images. The true signal was recovered based on the signal model after color compensation. The resulting true signal does not have color spreading (channel crosstalk) among different color channels. Two new unsupervised nonparametric classification methods for M-FISH images are also introduced in this dissertation: a fuzzy logic classifier and a template matching method (a minimum distance classifier). While both methods produce an equivalent accuracy compared to a supervised classification method, their computation time is significantly less than a Bayes classifier. Highly sophisticated and practical algorithms have been developed through this research. Using the developed methods, the amount of human intervention required will be significantly reduced: chromosomes are reliably and accurately segmented from the background, pixels are accurately classified, and clusters of overlapping and touching chromosomes are automatically decomposed.Item Automatic segmentation and classification of multiplex-fluorescence in-situ hybridization chromosome images(2006-08) Choi, Hyo Hun, 1973-; Bovik, Alan C. (Alan Conrad), 1958-Multicolor fluorescence in-situ hybridization (M-FISH) techniques provide color karyotyping that allows simultaneous analysis of numerical and structural abnormalities of whole human chromosomes. Chromosomes are stained combinatorially in M-FISH. By analyzing the intensity combinations of each pixel, all chromosome pixels in an image are classified. Often, the intensity distributions between different images are found to be considerably different and the difference becomes the source of misclassifications of the pixels. Improved pixel classification accuracy is the most important task to ensure the success of the M-FISH technique. Along with a reliable pixel classification method, automation of the karyotyping process is another important goal. The automation requires segmentation of chromosomes, which not only involves object/background separation but also involves separating touching and overlapping chromosomes. While automating the segmentation of partially occluded chromosomes is an extremely challenging problem, a pixel classification method that satisfies both high accuracy and minimum human intervention has not been realized. The main contributions of this dissertation include development of a new feature normalization method for M-FISH images that reduces the difference in the feature distributions among different images, and development of a new decomposition method for clusters of overlapping and touching chromosomes. A significant improvement was achieved in pixel classification accuracy after the new feature normalization. The overall pixel classification accuracy improved by 40% after normalization. Given a cluster, a number of hypotheses was formed utilizing the geometry of a cluster, pixel classification results, and chromosome sizes, and a hypotheis that maximized the likelihood function was chosen as the correct decomposition. Superior decomposition results were obtained using the new method compared to the previous methods. Contributions also include development of a color compensation method for combinatorially stained FISH images (including M-FISH images) based on a new signal model for multicolor/multichannel FISH images. The true signal was recovered based on the signal model after color compensation. The resulting true signal does not have color spreading (channel crosstalk) among different color channels. Two new unsupervised nonparametric classification methods for M-FISH images are also introduced in this dissertation: a fuzzy logic classifier and a template matching method (a minimum distance clasvii sifier). While both methods produce an equivalent accuracy compared to a supervised classification method, their computation time is significantly less than a Bayes classifier. Highly sophisticated and practical algorithms have been developed through this research. Using the developed methods, the amount of human intervention required will be significantly reduced: chromosomes are reliably and accurately segmented from the background, pixels are accurately classified, and clusters of overlapping and touching chromosomes are automatically decomposed.Item Chromosomal banding and phylogenetic relationships of vespertilionid bats(Texas Tech University, 1976-05) Bickham, John WNot availableItem Chromosomal evolution in the rodent family Gerbillidae(Texas Tech University, 1986-05) Qumsiyeh, Mazin Butros HannaNot availableItem Evolution in the family Pteropodidae (Chiroptera: Megachiroptera) as indicated by chromosomal and immunoelectrophoretic analyses(Texas Tech University, 1983-08) Haiduk, Michael WayneNot availableItem Evolutionary genetics and speciation of the tent-making bat Uroderma (Chiroptera: Phyllostomatidae)(Texas Tech University, 1978-05) Greenbaum, Ira F.Not availableItem Evolutionary implications of G- and C-banded chromosomes of 13 species of stenodermine bats(Texas Tech University, 1979-08) Johnson, Martha AnetteNot availableItem Evolutionary Implications of the G-Banded and C-Banded Karyotypes of Phyllostomatoid Bats(Texas Tech University, 1976-08) Patton, John CNot Available.Item Factors that effect chromosomal evolution: repetitive DNA in conservative versus rapidly evolving karyotypes(Texas Tech University, 1991-05) Bradley, Robert D.Chromosomal evolution has been used in many systematic and evolutionary investigations, including speciation mechanisms, rates of speciation, predicting effective long-term population sizes, fixation of chromosomal rearrangements, gene duplication, sex determination, and hybrid zones. However, little is known about the cause and effect relationship of chromosomal evolution. Ideas to explain this relationship include demographic models, negative heterosis, recombinational breakdown, and molecular effects. In a study of equids, considered to be chromosomally the most rapidly evolving group of mammals, the hypothesis that tandemly repeated DNA sequences may be responsible for chromosomal evolution was proposed. Predictions of this hypothesis for rapidly evolving genomes include: 1) an abundance of tandemly repeated sequences, 2) these sequences will have undergone intragenomic movement, and 3) these tandemly repeated sequences will represent multiple classes of elements. In this study, I test this hypothesis by examining repetitive sequences in a bat species (Macrotus waterhousii) which has a conservatively evolving karyotype. If M.- waterhousii has fewer numbers and classes of tandemly repeated sequences and if these sequences are restricted to certain chromosomal fields, then the hypothesis remains viable. A genome library was constructed for M.- waterhousii and 649 clones, representing 0.1% of the genome, were screened using Artibeus jamaicensis as an outgroup. This phylogenetic screening process produced 11 hypervariable clones. These were separated into three classes: a) clones found in either the ingroup or the outgroup but not in both; b) clones which possessed different numbers of hybridizing bands in the ingroup versus the outgroup; and c) clones which possess differences in copy number of the ingroup versus the outgroup. These clones were sorted into two families based on cross-hybridization experiments. One family contained only one clone; whereas, the second family contained the remaining 10 clones. Hybridization of this single clone to genomic DNAs of A- jamaicensis and M.. waterhousii digested with four restriction enzymes showed it to be tandemly repeated in Ajamaicensis. The remaining clones produced smears, indicative of interspersed distribution. In situ hybridization of these clones to chromosomes of R. waterhousii and A- jamaicensis revealed hybridization to four clones. Two clones, produced hybridization to centromeric regions on two pair of chromosomes and slight hybridization to some of the remaining chromosomes in A- jamaicensis but no visible hybridization to M.. waterhousii. Two additional clones showed faint hybridization to most chromosomes in M.- waterhousii and A- jamaicensis indicating high copy number with an interspersed pattern of distribution. Comparison of data from the chromosomally conserved bat species to equids which have rapidly evolving karyotypes (possessing 30 hypervariable clones, seven families, and intragenomic movement of sequences) suggests that the conservatively evolving bat species have fewer copies and types of hypervariable sequences than do equids. It is concluded that the hypothesis that a molecular basis, specifically rapidly evolving repetitive sequences, may play an important role in chromosomal evolution merits further testing.Item Karyotypes and chromosomal evolution in West Texas pocket gophers (Rodentia, geomyidae)(Texas Tech University, 1969-05) Berry, Dale LawrenceNot availableItem Karyotypic megaevolution in species of new world leaf-nosed bats(Texas Tech University, 1981-05) Arnold, Michael LynnNot availableItem Population genetics of Chironomus Stigmaterus Say (Diptera: Chironomidae): cytogenetic and enzyme variability in populations of the southwestern United States(Texas Tech University, 1978-08) Hilburn, Larry RichardNot availableItem Relationships between Peromyscus Maniculatus Oreas and P.M. Austerus as Indicated by Differentially Stained Chromosomes(Texas Tech University, 1983-08) Clark, Cora LeeNot Available.Item Systematics of the Desmodonitinae and Phyllonycterinae (Chiroptera: Phyllostomatidae) based on G-band chromosomal homologies(Texas Tech University, 1978-05) Bass, Rebecca A.Not available