xiv, 196 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / Establishing homologous (evolutionary) relationships among a set of genes allows us to hypothesize about their histories: how are they related, how have they changed over time, and are those changes the source of novel features? Likewise, aggregating related genes into larger, structurally conserved regions of the genome allows us to infer the evolutionary history of the genome itself: how have the chromosomes changed in number, gene content, and gene order over time? Establishing homology between genes is important for the construction of human disease models in other organisms, such as the zebrafish, by identifying and manipulating the zebrafish copies of genes involved in the human disease. To make such inferences, researchers compare the genomes of extant species. However, the dynamic nature of genomes, in gene content and chromosomal architecture, presents a major technical challenge to correctly identify homologous genes. This thesis presents a system to infer ancient homology between genes that takes into account a major but previously overlooked source of architectural change in genomes: whole-genome duplication. Additionally, the system integrates genomic conservation of synteny (gene order on chromosomes), providing a new source of evidence in homology assignment that complements existing methods. The work applied these algorithms to several genomes to infer the evolutionary history of genes, gene families, and chromosomes in several case studies and to study several unique architectural features of post-duplication genomes, such as Ohnologs gone missing. / Committee in charge: John Conery, Chairperson, Computer & Information Science; Virginia Lo, Member, Computer & Information Science; Arthur Farley, Member, Computer & Information Science; John Postlethwait, Member, Biology; William Cresko, Outside Member, Biology

In systems with female heterogamety (e.g. WZ/ZZ; female/male), the Z chromosome has several characteristics that distinguish it from autosomes, such as different effective population size (Ne) and hemizygosity in the heterogametic sex. These characteristics may lead to an accelerated rate of adaptive changes for the Z-linked genes compared to autosomal coding sequences, often referred to as the Fast-Z effect. This work is the first attempt to test the Fast Z effect in Lepidoptera by using two methodological approaches. These included comparative fluorescence in situ hybridizations and comparisons of substitution rates in coding sequences.

Made available in DSpace on 2018-08-01T22:57:30Z (GMT). No. of bitstreams: 1 tese_9189_Dissertação Final Paulo Marcos Amaral Silva20160628-103338.pdf: 832244 bytes, checksum: de4cc3d0c60078e1f76f3d4f95f3b534 (MD5) Previous issue date: 2015-08-14 / The dioecy occurs in 6% of the angiosperms, including all the Myrsine species (Primulaceae) that show male and female individuals distinguishable based in sexual organs and morphology of sepals and petals. The sexual system fixed in this genus, was the motivation in research if the existence of sexual chromosomes culminate in dioecy for Myrsine. Employing tissue culture, flow cytometry and cytogenetic tools, the aimed this study was characterize the karyotype of Myrsine coriacea (Sw.) R.Br. ex Roem & Schult., Myrsine umbellata Mart., Myrsine guianensis (Aubl.) Kuntze and Myrsine parvifolia A.DC. From leaves of male and female individuals collected in the field and leaves and roots of unknown sex obtained of in vitro culture, were found mean values of DNA content statistically identical. These data were attributed to the presence of secondary metabolites reported for the genus. However, an intraspecific variation was observed in cytogenetic analysis in the four Myrsine species. Slides exhibited metaphases with 2n = 45 and 2n = 46 chromosomes in different individuals. These results were observed consistently from different times of exposition to anti-mitotic agent and distinct treatments of enzymatic maceration. Thus, the chromosome number variation found, associated with the sexual system well defined, can be concerning to the sexual chromosomes in Myrsine genus. These data suggest a chromosomal system of sex 9 determination with multiple X and/or Y described in some plant species. The system ZW also is possible, as well as X0 or Z0, systems still not reported in vegetal groups. The present work provided the first data about the nuclear DNA content by flow cytometry in Myrsine and supplied cytogenetics evidences that indicate the existence of sexual chromosomes.

Cells exposed to DNA damaging agents activate a network of mechanisms called DNA damage response, including telomere length regulation. Telomeres are specialized structures that protect chromosome ends from degrading and being fused together. Mouse-knockout experiments revealed that cell lines deficient of DNA-PKcs or Ku70/80 resulted in high amount of telomere end-to-end fusion. Numerous other studies have shown a functional interplay between DNA damage response and telomere maintenance. The aim of this project is to examine this interplay further by investigating mechanisms of DNA damage response, using cell lines from X-linked homozygous recessive form of Dyskeratosis Congenita (DC) patients, which have dysfunctional telomere maintenance. DC is a multi-system disorder characterised by abnormalities of the bone marrow, immune deficiency and a predisposition to cancer. In this work we have shown that cells with defective DKC1 (the gene implicated in the X- linked homozygous recessive form of DC) exhibit a defective DNA damage response by examining two types of cells: fibroblast and lymphoblastoid cell lines. By using various biomarkers (H2AX, TIF assay etc) we analysed the DNA damage response by exposing DC cell lines to ionizing radiation. Our results demonstrated that DC cell lines have an abnormal DNA damage response and as a result show radiosensitivity. We have also knocked down the DKC1 gene in normal cell lines using siRNA oligonucleotides and demonstrated that this knock-down causes radiosensitivity. Therefore our results conclusively show an abnormal DNA damage response in cells derived from DC patients. Finally we used TA-65, a novel telomerase activator derived from the plant Astragalus membranaceus and showed radioprotective effects of this compound in normal lymphoblastoid cell lines. Taken together our results potentiate further the link between telomere maintenance and DNA damage response.

Philosophiae Doctor - PhD / The pattern of inactivation in the DXS8237E-UBE1-PCTK1 region is of particular interest, since the mechanisms of X chromosome inactivation and the escape from inactivation are, as yet, not fully understood. The inactivation status of the DXS8237E and PCTKl gene differ: the first undergoes normal inactivation and the second escapes this process. The status of the UBEl gene has been controversial, although it is widely excepted that it does escape X chromosome inactivation. Physical mapping of the region employing YACs and subsequently P ACs has been undertaken, but was restricted in scope by the high frequency of rearrangements occurring. DNA sequences between DXS8237E, UBE1, PCTKl and the distal gene, UHX1, have been investigated with regard to LINEI elements, which are thought to playa role in X-inactivation. The results obtained strongly suggest a link between LINE1 elements and X chromosome inactivation. Sequence analysis results also contributed to the understanding of difficulties with restriction mapping of the region. Further, this work includes the first reported establishment of the UBEl exonintron boundaries. Additionally, genomic sequence analysis showed that only 46kb separate DXS8237E from UHX1, which confirms that this region is extremely gene rich. / South Africa

Magister Scientiae - MSc (Biochemistry) / Alternative RNA splicing is one of the leading mechanisms contributing towards transcript and protein diversity. Several alternative splicing surveys have confirmed the frequent occurrence of exon skipping in human genes. However, the occurrence of exon skipping in mouse genes has not yet been extensively examined. Recent improvements in mouse genome sequencing have permitted the current study to explore the occurrence of exon skipping in mouse genes orthologous to human genes on chromosome 22. A low number (5/72 multi-exon genes) of mouse exon-skipped genes were captured through alignments of mouse ESTs to mouse genomic contigs. Exon-skipping events in two mouse exon-skipped genes (GNB1L, SMARCB1) appear to affect biological processes such as electron and protein transport. All mouse, skipped exons were observed to have ubiquitous tissue expression. Comparison of our mouse exon-skipping events to previously detected human exon-skipping events on chromosome 22 by Hide et al.2001, has revealed that mouse and human exon-skipping events were never observed together within an orthologous gene-pair. Although the transcript identity between mouse and human orthologous transcripts were high (greater than 80% sequence identity), the exon order in these gene-pairs may be different between mouse and human orthologous genes. Main factors contributing towards the low detection of mouse exon-skipping events include the lack of mouse transcripts matching to mouse genomic sequences and the under-prediction of mouse exons. These factors resulted in a large number (112/269) of mouse transcripts lacking matches to mouse genomic contigs and nearly half (12/25) of the mouse multi-exon genes, which have matching Ensembl transcript identifiers, have under-predicted exons. The low frequency of mouse exon skipping on chromosome 22 cannot be extrapolated to represent a genome-wide estimate due to the small number of observed mouse exon-skipping events. However, when compared to a higher estimate (52/347) of exon skipping in human genes for chromosome 22 produced under similar conditions by Hide et al.2001, it is possible that our mouse exon-skipping frequency may be lower than the human frequency. Our hypothesis contradicts with a previous study by Brett et al.2002, in which the authors claim that mouse and human alternative splicing is comparable. Our conclusion that the mouse exon-skipping frequency may be lower than the human estimate remains to be tested with a larger mouse multi-exon gene set. However, the mouse exon-skipping frequency may represent the highest estimate that can be obtained given that the current number (87) of mouse genes orthologous to chromosome 22 in Ensembl (v1 30th Jan. 2002) does not deviate significantly from our total number (72) of mouse multi-exon genes. The quality of the current mouse genomic data is higher than the one utilized in this study. The capture of mouse exon-skipping events may increase as the quality and quantity of mouse genomic and transcript sequences improves. / South Africa

A cytological examination of the life-history of Nereocystis luetkeana has shown that an alternating chromosome number corresponds to the morphological alternation of generations. The first division sequence of the zoosporangial nucleus is meiotic and is followed by three mitotic divisions. The result is a mature sporangium containing 32 nuclei. Thirty-two zoospores are liberated from each sporangium and their germination gives rise to male and female gametophytes. Genotypic determination of the sexes is believed to take place in Nereocystis. Mitosis in the gametophytes is regular and cytokinesis follows each nuclear division, producing few cells in the female and many cells in the male gametophytes. Thirty-one chromosomes can be counted at the mitotic prophase. Oogamy exists in Nereocystis and fertilization takes place after the egg is extruded from the oogonium. The sporophyte develops initially into a uniseriate filament of 5 - 8 cells before divisions in a second plane give rise to a flat, monostromatic thallus. Nuclear division in the sporophyte appears to be preceded by division of the nucleolus. Colorless and non-septate rhizoids develop as elongations of the basal cells of the sporophyte. Some of the unfertilized eggs develop parthenogenetically and give rise to stunted, deformed plants with multinucleate cells. Temperature is an important factor in the development of various stages of the life cycle of Nereocystis grown in culture. This is particularly evident in the gametophytic stage where sexual structures are produced only at temperatures less than- 10° C, and vegetative growth is most prolific at 14 - 18° C. / Science, Faculty of / Botany, Department of / Graduate

It has been suggested (Suzuki, 1965a) that the extrinsic and intrinsic factors which increase crossing over in the centromere regions of Drosophila do so by inactivating these regions at the time of crossing over; the inactivation resulting in altered chromosome structure which permits the intimate synapsis necessary for crossing over. This hypothesis predicts that the 3L heterochromatic marker w⁺ carried in Dp(wm)264.58a, which exhibits position effect variegation, would tend to be inactivated by chromosome aberrations, known to increase crossing over. The reversed acrocentric (RA) compound X chromosome, the X chromosome inversions sc⁴sc⁸ and sc⁸, the autosomal inversions Cy, Sb, and Ubx, and the Minute mutants M(2) and M(3) were tested for their effects on the expression of w⁺ in various coisogenic stocks. The amount of pigment in each eye was visually scored into twelve classes. Crossover analyses of the centromere regions of chromosomes 2 and 3 were performed to confirm the effects of sc⁴sc⁸, Cy, Ubx, and Sb on crossing over. The RA, sc⁴sc⁸, Cy, and Ubx all increase crossing over and significantly depress the activity of w⁺. The degree of pigment reduction is correlated with the amount of increase in crossing over. Combination of these aberrations produces an effect on pigmentation and crossing over greater than that produced by either considered singly. Sb has a slight effect in increasing crossing over and decreasing pigmentation. M(3), known to increase crossing over, significantly decreases pigmentation whereas M(2) does not. The effect of the X chromosome inversion sc⁸ is doubtful. Expression of w⁺ is affected similarly in males and females, an observation suggesting that the chromosome physiology of both sexes is similar although the actual factor(s) mediating crossing over are absent in the males. These results lend support to the proposed hypothesis but, with fluctuating parental source effects and variations found within a stock testifying to the general lability of the system, further tests under stringently controlled conditions are necessary before such experiments can be considered critical. / Science, Faculty of / Zoology, Department of / Graduate

Two populations derived by crossing LDN x LDN Dic-3A (Population I) and LDN x LDN Dic-3B (Population II) were genetically characterized for the seed dormancy present on chromosome 3A and 3B of durum wheat. The genes for seed dormancy in these two populations were contributed by the wild parent T. dicoccoides. Although the populations showed transgressive segregants for both dormant as well as nondormant parent, the populations were similar to the dormant parent at Langdon and Prosper 2006 field locations for Population I and at Langdon 2007 and Autumn greenhouse season for Population II. Genotypic and phenotypic analysis over the combined populations showed an environmental effect on expression of the trait. Different QTL were identified for both field and greenhouse season for the population derived from the cross between LDN x LDN Dic-3A. Five QTL for seed dormancy were identified on chromosome 3A for the QTL analysis performed over combined field locations. One QTL ranging between marker interval Xcfa2193 and Xcfd2a was consistently present for the 30 day period of seed germination and was also found to be linked to red grain color trait. The QTL analysis performed on the population derived from the cross between LDN x LDN Dic-3B identified only one major QTL on the long arm of chromosome 3B between the marker interval Xbarc84 and Xwmc291. This QTL was consistently present for all the field and spring greenhouse season for the seed germination period of 30 days. The QTL x E effect was also observed for this QTL, however it was very small.

"This thesis is a report on the feasibility of isolating a certain group of mutants. I call these mutants the "p.i.-related" mutants; an explanation of what they are and of my rule for grouping them together is given here. Bacterial chromosome replication consists of at least three steps: initiation, polymerization and termination/segregation (which may or may not comprise a single step). Inhibition of the polymerization step ("polymerization inhibition" or "p.i.") in a rapidly-growing bacterial population causes morphological distortion of the cells, a high death rate among them, and a number of other consequences. Recently, two great regulatory systems for bacterial cell behavior (described in Chapters IX and X) have been elucidated, and it appears that many of the consequences of p.i. might be explainable as the malfunctioning of these two systems. I define a "p.i.-related mutation" as a mutation that satisfies two criteria: First, it either causes p.i., mimics p.i., prevents p.i. or blocks the effects of p.i. Second, it exerts its effects by disrupting one of the two above-mentioned regulatory systems. The main question asked and answered in this report is: How good is each of three different methods of selection for p.i.-related mutants?"-- / Typescript. / "August, 1979." / "Submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science." / Advisor: Johan H. Stuy, Professor Directing Thesis. / Includes bibliographical references (leaves 383-434).