The human epidermal growth factor receptor-2 (HER2) protein has been associated with breast cancer progression and the HER2 status can be used to determine the type of treatment for each breast cancer patient. The purpose of this study was to examine the HER2 protein and gene statuses in breast cancer tissue samples using two methods and analyze the concordance between them. Ten paraffin-embedded, formaldehyde-fixed breast cancer tissue samples from the Biobank at the Department of Pathology and Cytology at Sundsvall Hospital were analyzed in this study. All samples were from women born between 1931 and 1976. The methods used were immunohistochemistry (IHC) to visualise the HER2 protein and silver in situ hybridization (SISH) to detect gene amplification. The IHC staining method is an indirect detection of the HER2 protein using antibodies. The SISH method used in this study is a Dual ISH which detects both the HER2 gene and the centromere region of Chromosome 17 on the same tissue slide. A HER2 gene/Chromosome 17 ratio was calculated according to the manufacturer’s instructions. This ratio was used to determine HER2 gene status. Out of ten samples, seven were positive with IHC and three were negative. The results from the SISH staining exposed a gene amplification in three of the IHC positive samples, while seven samples did not contain any amplified HER2 genes. The conclusion was that the concordance between IHC and SISH for HER2 was 60 percent.

To enhance the scientific utility and practical application of the honey bee genome and assign the linkage groups to specific chromosomes, I identified chromosomes and characterized the karyotype of the sequenced strain DH4 of the honey bee. The primary analysis of the karyotype and ideogram construction was based on banding and Fluorescence In Situ Hybridization (FISH) for rDNA detection. FISH confirmed two locations for the NOR on telomeric regions of chromosomes 6 and 12 plus an additional less frequent signal on chromosome 1, all three of which were confirmed with silver staining (AgNO3). 4’6-diamidino-2phenylindole (DAPI), and CBanding methods were used to construct the primary ideograms that served as a basis to further identify the chromosomes and locate important structures. The primary map was compared with Giemsa banding, AgNO3-banding, Trypsin banding, and R-banding. The karyotype of the honey bee was established as two metacentric chromosomes (1 and 10), two submetacentric with ribosomal organizer (6 and 12), four submetacentric heterochromatic chromosomes (16, 15, 4 and 13), four euchromatic subtelocentric chromosomes (2, 8, 11 and 14) and four acrocentric chromosomes (3, 5, 7 and 9). In situ nick-translation banding methods were used to verify the heterochromatin distribution. The cytogenetic maps of the honey bee karyotype represented in the ideograms were subsequently used to place 35 mapped BACs (Solignac et. al. 2004) of Solignac’s BAC library. As the BACs hybridized to multiple sites, the mapping was based on strength and frequency of the signals. Location and position of the BACs was compared with those published in the different version of Map Viewer of the NCBI and BeeBase web sites. 10 BACs were confirmed with the last version of Map Viewer V4, 12 BACs were mapped based on high frequency and agreement with the earlier version of Map Viewer. 14 BACs were mapped as confirmed based on moderate frequency of the signal and agreement with the last version of MVV, most of these BACs hits as a secondary signal.

The genus Salvia L. is significantly important with regard to both its worldwide distribution and usage areas including food, medical and perfumary industries. In this current study, it is targeted to address the chromosome numbers and karyomorphology of the ten species and one variety of the genus Salvia. All of the eleven taxa examined in this study are economically significant and nine of these are endemic to Turkey. To define the chromosome numbers and karyomorphology of these eleven taxa somatic chromosomes of the each were examined. Mitotic metaphase chromosomes were obtained from root meristems of germinating seeds, which were pre-treated in &amp / #945 / -bromonaphtalene at 4&ordm / C for 16 h, then fixed in Carnoy solution (3 parts of ethanol: 1 parts of glacial acetic acid) at 4&ordm / C for 24h and stored in 70 % ethanol. Fixed root tips were stained in 2 % aceto-orcein and squashed in a drop of 45 % acetic acid. Long arm, short arm, total length of the each chromosomes were measured / relative length, arm ratio, centromeric index of the each chromosome were calculated. Karyogram and haploid idiograms were drawn by computer-aided analysis programme (Bs200pro). A cluster analysis of the karyotype data was carried out to examine karyotype similarity among taxa. Somatic chromosome numbers have been counted as 2n=2x=14 for the endemic taxa S. divaricata Montbret &amp / Aucher, S. euphratica Montbret &amp / Aucher ex Bentham (var. leiocalycina (Rech. fil.) Hedge) and S. recognita Fisch. &amp / Mey. / 2n=2x=14-1B for Salvia rosifolia Sm. / 2n=20 for S. longipedicellata Hedge, S. vermifolia Hedge &amp / Hub.-Mor. and S. yosgadensis Freyn &amp / Bornm. / 2n=2x=22 for S. aethiopis L., S. cilicica Boiss. &amp / Kotschy, S. hypargeia Fisch. &amp / Mey. and 2n=2x=32 for S. napifolia Jacq. respectively. In general, the chromosomes are short with median and submedian centromeres. The current study is essential for being the first report about chromosome numbers and karyomorphology of the six endemic taxa, namely S. divaricata, S. euphratica var. leiocalycina, S. longipedicellata, S. rosifolia, S. vermifolia and S. yosgadensis. Moreover, in spite of the chromosome numbers of S. aethiopis, S. cilicica, S. hypargeia and S. recognita are known, this research is the first study for their karyomorphologies.

The reliability of genome analysis and proficiency of genetic manipulation in vivo and in vitro are increased by assignment of linkage groups to specific chromosomes, placement of centromeres, orientation with respect to telomeres, and linear alignment with respect to chromosomal features and dimensions. I undertook five studies aimed at integrating sorghum genomics and cytogenetics at several levels. The results help establish an entirely new "cyto-genomics" resource, impacts of which are likely to be broad. In the first study, I developed a FISH-based karyotyping system for Sorghum bicolor Moench. I used integrated structural genomic resources, including linkage maps and large-insert clonal libraries of sorghum genomic DNA to develop a 17-locus probe cocktail for simultaneous fluorescent in situ hybridization (FISH). This probe enabled facile identification of all chromosome pairs in mitotic chromosome spreads. Perhaps just as important, I established time-efficient means to select sorghum BAC clones for multi-probe FISH. Thus, an integrated cyto-genomics system for sorghum can be constructed without need of chromosome flow sorting or microdissection, both of which are difficult and costly. In the second study, hybridization of DNA clones from 37 different genomic regions enabled the assignment of linkage groups and orientation of linkage maps to chromosomes. Comparisons between genetic and physical distances throughout the genome enabled a new nomenclature for linkage group designation in sorghum. The results provide an integrated nomenclature system of Sorghum bicolor chromosomes and linkage groups. In the third study, I created high-resolution maps by FISH to pachytene bivalents for two linkage groups (B and H), and defined relationships between pericentromeric heterochromatin, centromeres, mapped markers and recombination rates. These relationships will help guide the development and use of sorghum genomics. In the fifth study, I used FISH in two ongoing gene-targeted efforts. For the maturity gene ma5 and fertility restoration gene rfl, I estimated physical lengths between currently available flanking molecular markers. This enables estimation of recombination densities in these regions and assessment of the applicability of map-based and -assisted cloning.

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references (leaves 168-176). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2001. / Typescript. Vita. Includes bibliographical references (leaves 117-121). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2001. / Typescript. Vita. Includes bibliographical references (leaves 117-121). Also available on the Internet.

Thesis (Ph. D.)--University of Hong Kong, 2009. / Includes bibliographical references (leaves 146-173). Also available in print.

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references (leaves 168-176). Also available on the Internet.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 59-68).