The strand-Cartesian grid approach is a unique method of generating and computing fluid dynamic simulations. The strand-Cartesian approach provides highly desirable qual- ities of fully-automatic grid generation and high-order accuracy. This thesis focuses on the implementation of the Spalart-Allmaras turbulence model to the strand-Cartesian grid framework. Verification and validation is required to ensure correct implementation of the turbulence model.Mathematical code verification is used to ensure correct implementation of new algo- rithms within the code framework. The Spalart-Allmaras model is verified with the Method of Manufactured Solutions (MMS). MMS shows second-order convergence, which implies that the new algorithms are correctly implemented.Validation of the strand-Cartesian solver is completed by simulating certain cases for comparison against the results of two independent compressible codes; CFL3D and FUN3D. The NASA-Langley turbulence resource provided the inputs and conditions required to run the cases, as well as the case results for these two codes. The strand solver showed excellent agreement with both NASA resource codes for a zero-pressure gradient flat plate and bump- in-channel. The treatment of the sharp corner on a NACA 0012 airfoil is investigated, resulting in an optimal external sharp corner configuration of strand vector smoothing with a base Cartesian grid and telescoping Cartesian refinement around the trailing edge. Results from the case agree well with those from CFL3D and FUN3D. Additionally, a NACA 4412 airfoil case is examined, and shows good agreement with CFL3D and FUN3D, resulting in validation for this case.

<p>Totally 84 differentially expressed mRNA clones from infective L3 larvae of the parasite <em>Haemonchus contortus</em>, a blood sucking nematode,<em> </em>were analyzed with single strand hybridization assay (SSH). Altogether 79 clones were sequenced, edited, and compared with proteins found via BLAST in GeneBank. The aim was to investigate gene expression and potential protein expression following storage at 5 °C for 32 weeks. mRNA was extracted from fresh and stored L3. The SSH derived products were cloned into <em>E. coli,</em> purified and sequenced with Big Dye Terminator v3.1, and then compared with uploaded sequences in GeneBank. BLAST showed 59 (70 %) reliable protein results, where 39 (66 %) were of nematode origin.. Three sequences (4 %) were recognized as <em>H. contortus</em>-related metabolic proteins. Further research is necessary to elucidate the role of these proteins in relation to storage<em>. </em>Many of the sequences (36 %) are also present in other nematodes, such as <em>Caenorhabditis briggsae </em>and <em>C. elegans,</em> where whole-genome projects have been conducted. Bigger and more accurate databases need to be developed. Maybe the most significant future project is to sequence the whole genome of <em>H. contortus</em>.</p>

Totally 84 differentially expressed mRNA clones from infective L3 larvae of the parasite Haemonchus contortus, a blood sucking nematode, were analyzed with single strand hybridization assay (SSH). Altogether 79 clones were sequenced, edited, and compared with proteins found via BLAST in GeneBank. The aim was to investigate gene expression and potential protein expression following storage at 5 °C for 32 weeks. mRNA was extracted from fresh and stored L3. The SSH derived products were cloned into E. coli, purified and sequenced with Big Dye Terminator v3.1, and then compared with uploaded sequences in GeneBank. BLAST showed 59 (70 %) reliable protein results, where 39 (66 %) were of nematode origin.. Three sequences (4 %) were recognized as H. contortus-related metabolic proteins. Further research is necessary to elucidate the role of these proteins in relation to storage. Many of the sequences (36 %) are also present in other nematodes, such as Caenorhabditis briggsae and C. elegans, where whole-genome projects have been conducted. Bigger and more accurate databases need to be developed. Maybe the most significant future project is to sequence the whole genome of H. contortus.

ABSTRACT In the record of the theory, we found out that the competitive advantage always be focused on the thinking of strength, the strength aiming at ¡ugood¡v¡B¡ustrong¡vresources or conditions, whatever in the resource-based theory or the strategy-based theory. The reason is all research was deeply influenced by SWOT. Japanese Industry successfully growing up, ¡§with small to win huge¡¨, to beat global deader, had highlighted the important issue, ¡§ Shall small always be small? Shall big always be big? ¡§ Gray hamel and C.K. Prahalad in ¡uCompeting in the future¡vdeclared¡G ¡¨ Mastering industrial spaces is not by company¡¦s small or big, not by less or much resource, not by less or much market-share.¡¨ In case, it shall convince of us to study the factor of competitive advantage shall be in a vision more than ¡ustrength¡v, good , strong, or much resources and conditions. Meanwhile, in the record of theory, we also found out that the efficient method of resource & strategy must carefully consider the differentiation of product, industry and industrial structure. On fact, the differentiation of product, industry and industrial structure formed at each industry¡¦s differentiation and each industry¡¦s specificity. Concluding all of above, the writer is interested in the research of the topic; the key of factor of competitive advantage shall be emphasized and aimed at the specificity of the industry. In order to studying the relevance between the competitive advantage and the industry¡¦s specificity, the writer design the researching range as followings as: 1. The original of the competitive advantage. 2. The relevance between the competitive advantage and resource, strategy. 3. The relevance between the competitive advantage and the industry¡¦s specificity. Keywords: Competitive advantage ¡BIndustrial specificity¡B Chains-strand competitive advantage

Retrovirus gene therapy vectors can deliver therapeutic genes to mammalian cells in a permanent manner by integrating their genome into host chromosomes and therefore provide the potential for long term therapeutic gene expression. Retrovirus integration, however, can be oncogenic. Apart from insertional mutagenesis (IM) genotoxicity may be caused by other factors including DNA damage following infection and integration and epigenetic effects related to incoming viral particles. Thus, using retrovirus and lentivirus infected murine tumour tissue and infected cell lines in vitro this thesis was directed at investigating whether virus infection and integration could cause genotoxicity by alternative route(s) other than IM. Using clonally derived liver tumours that developed in mice, and normal liver and kidney tissues, following EIAV and HIV delivery in utero, comparative genome hybridisation methodology was used to examine for copy number variation. This showed amplification and deletions only in EIAV derived tumours. Real time Q-PCR analysis was then used to measure gene expression changes relating to genes contained within or near to amplifications observed in two tumours of individual mice. The STRING database was then used to find networks linking genes with differential expression profiles and genes in one of these tumours identified with provirus insertions that were also differentially expressed. These data provided preliminary data implicating a role for LV in Hepatocellular carcinoma (HCC). DNA damage is known to cause chromosomal instability that can lead to tumour development. The relationship between double strand breaks (DSB) and virus infection was also investigated in-vitro to find alternative routes to genotoxicity other than IM. Cell viability analysis demonstrated cells with a defective DNA damage response (DDR) have decreased cell viability compared with cells with intact DDR when infected with RV or LV vectors. DSB assays showed RV and LV infection to generate foci over a 6 hour period followed by DDR. Where no viral integrase is present, no DDR appears, however, where the vector is used with or without a genome to infect cells, DDR occurs as shown by the presence of 53BP1 foci indicative of DNA damage. The relationship between DNA damage and methylation was also investigated. Global methylation was found elevated in the genomic DNA of LV and RV infected cells and not in control uninfected cells. In contrast, methylation changes were not found in infected cells lacking the NHEJ repair pathway. These data suggest the DNA damage response is linked to genome methylation. The E2F transcription factor plays a key role in regulating expression of genes known to control oncogenesis and cancer, and E2F is regulated by methylation of its related target gene promoters. Taking into account all genes in the human genome the number of genes that bind E2F is 32.77%. However, using microarray to represent genes differentially expressed after infection, 59% of these were E2F targets. Overall, taking the data obtained in this thesis into account it may be suggested that RV and LV infection causes a number of potentially related changes to cells that include DNA damage and repair and methylation changes that could influence E2F that is an important factor involved in oncogenesis. Combining this with IM, attenuated RV and LV currently in use for gene therapy may cause genotoxicity to infected cells and increase the risk of oncogenesis especially where DNA damage is not correctly repaired. Further work is required to show in greater detail the extent of this genotoxicity, possible by whole genome sequencing of treated host genomes or cell transformation assays linked to the genotoxicity assays presented here. Collectively these data show that alternative factors to IM might exist that could act independently or synergistically to IM.

Benzene is an ubiquitous pollutant and industrial solvent that has been identified as a human leukemogen. Early exposure to environmental carcinogens such as benzene has been postulated to play a role in the etiology of childhood leukemia, however the association remains controversial. Genotoxic agents such as benzene can cause an increase in the frequency of DNA double-strand breaks, which may remain unrepaired or result in the initiation of DNA recombinational repair mechanisms. The first objective was to investigate the induction of DNA double-strand breaks following in utero treatment to 200 mg/kg and 400 mg/kg benzene i.p. using the phosphorylated histone γ-H2A.X as a marker. Using immunoblotting, treatment with benzene did not increase the formation of γ-H2A.X in bone marrow cells of adult C57Bl/6N male mice and in maternal bone marrow, fetal liver, and post-natal bone marrow cells following in utero exposure to 200 mg/kg or 400 mg/kg benzene throughout gestational days 7 to 15. Secondly, the study investigated the induction of micronuclei following in utero exposure to benzene. Acute exposure to 400 mg/kg benzene resulted in a statistically significant increase in the percentage of micronucleated cells in adult male bone marrow cells. In utero exposure to 400 mg/kg benzene throughout gestational days 7 to 15 also caused a statistically significant increase in the percentage of micronucleated cells in maternal bone marrow and post-natal bone marrow cells. Fetal liver cells also demonstrated a statistically significant increase in the percentage of micronucleated cells following 200 mg/kg and 400 mg/kg benzene. The third objective was to investigate the initiation of DNA recombination following in utero exposure to benzene using the pKZ1 mutagenesis mouse model as a surrogate marker for non-homologous end joining activity. Adult pKZ1 mouse tissue yielded no recombination events; however, post-natal bone marrow cells did contain detectable recombination frequencies. iii In utero benzene exposure did cause an increasing trend in recombination events, and upon analysis of only the samples containing detectable levels of recombination, in utero exposure to 400 mg/kg of benzene caused a statistically significant increase in recombination frequency within this group. These results demonstrate that benzene does not increase the formation of γ-H2A.X after acute and in utero exposure, however, the induction of micronuclei following acute and in utero benzene exposure confirmed that benzene is a genotoxic agent causing chromosomal breaks. In utero benzene exposure increased the frequency of DNA recombination in bone marrow from post-natal day 9 pups exhibiting detectable levels of recombination. Further investigations into different types of DNA damage and repair pathways are warranted to fully elucidate the role of genotoxic mechanisms in the etiology of benzene-induced childhood leukemias. / Thesis (Master, Pharmacology & Toxicology) -- Queen's University, 2008-08-22 11:07:49.162

No description available.

Radiation therapy targets cancer cell death by overwhelming cells with harmful DNA damage. Understanding how cells repair radiation damage and in particular how they become resistant to radiation therapy is important for effective cancer treatment. Our lab made the novel discovery that Bcl10, a cytoplasmic protein important for NF-B activation, localizes to endogenous H2AX foci in the nucleus of breast cancer cells. We determined that following radiation treatment Bcl10 is recruited to ionizing radiation-induced foci in a dose-dependent matter and that it is important for the repair of radiation-induced DNA damage. We also observed that breast cancer cells are extremely sensitive to Bcl10 knockdown, causing cellular senescence, while normal breast epithelial cells are insensitive. Our findings identify Bcl10 as potent anti-cancer target. / Experimental Oncology

Abstract As the defects in DNA repair and cell cycle control are known to promote tumorigenesis, a proportion of inherited breast cancers might be attributable to mutations in the genes involved in these functions. In the present study, three such genes, TP53, CHK2 and ATM, which are also associated with known cancer syndromes, were screened for germline mutations in Finnish breast cancer patients. In combination with our previous results, three TP53 germline mutations, Tyr220Cys, Asn235Ser and Arg248Gln, were detected in 2.6% (3/108) of the breast cancer families. The only observed CHK2 alteration with a putative effect on cancer susceptibility, Ile157Thr, segregated ambiguously with the disease, and was also present in cancer-free controls. The available functional data, however, suggests that the altered CHK2 in some way promote tumorigenesis. Furthermore, compared to the other studied populations, Ile157Thr seems to be markedly enriched in Finland. Thus, the clinical significance of Ile157Thr requires further investigation among Finnish cancer patients. ATM germline mutations appear to contribute to a small proportion of the hereditary breast cancer risk, as two distinct ATM mutations, Ala2524Pro and 6903insA, were found among three families (1.9%, 3/162) displaying breast cancer. They all originated from the same geographical region as the AT families with the corresponding mutations, possibly referring to a founder effect concerning the distribution of these mutations in the Finnish population. The genes important for tumorigenesis in sporadic disease might also contribute to familial breast cancer. Therefore, four putative LOH targets genes in chromosome 11q21-q24 were screened for intragenic mutations, and five were analyzed for epigenetic inactivation in sporadic breast tumors. The lack of somatic intragenic mutations in MRE11A, PPP2R1B, CHK1 and TSLC1 led us next to investigate promoter region hypermethylation as a mechanism capable of silencing these genes, as well as the ATM gene. Only TSLC1 demonstrated involvement of CpG island methylation, which was especially prominent in three tumors. This suggests that together with LOH, methylation could result in biallelic inactivation of the TSLC1 gene in breast cancer.

Meiosis is necessary for sexual reproduction in eukaryotes. Genetic recombination between non-sister homologous chromosomes is needed in most organisms for successful completion of the first meiotic division. Proteins that function during meiotic recombination have been studied extensively in model organisms. However, less is known about the evolution of these proteins, especially among protists. We searched the genomes of diverse eukaryotes, representing all currently recognized supergroups, for 26 genes encoding proteins important for different stages of interhomolog recombination. We also performed phylogenetic analyses to determine the evolutionary relationships of gene homologs. At least 23 of the genes tested (nine that are known to function only during meiosis in model organisms) are likely to have been present in the Last Eukaryotic Common Ancestor (LECA). These genes encode products that function during: i) synaptonemal complex formation; ii) interhomolog DNA strand exchange; iii) Holliday junction resolution; and iv) sister-chromatid cohesion. These data strongly suggest that the LECA was capable of these distinct and important functions during meiosis. We also determined that several genes whose products function during both mitosis and meiosis are paralogs of genes whose products are known to function only during meiosis. Therefore, these meiotic genes likely arose by duplication events that occurred prior to the LECA. The Rad51 protein catalyzes DNA strand exchange during both mitosis and meiosis, while Dmc1 catalyzes interhomolog DNA strand exchange only during meiosis. To study the evolution of these important proteins, we performed degenerate PCR and extensive nucleotide and protein sequence database searches to obtain data from representatives of all available eukaryotic supergroups. We also performed phylogenetic analyses on the Rad51 and Dmc1 protein sequence data obtained to evaluate their utility as phylogenetic markers. We determined that evolutionary relationships of five of the six currently recognized eukaryotic supergroups are supported with Bayesian phylogenetic analyses. Using this dataset, we also identified ten amino acid residues that are highly conserved among Rad51 and Dmc1 protein sequences and, therefore, are likely to confer protein-specific functions. Due to the distributions of these residues, they are likely to have been present in the Rad51 and Dmc1 proteins of the LECA. To address an important issue with the gene inventory method of scientific inquiry, we developed a heuristic metric for determining whether apparent gene absences are due to limitations of the sequence search regimen or represent true losses of genes from genomes. We collected RNA polymerase I (Pol I), Replication Protein A (RPA), and DNA strand exchange (SE) sequence data from 47 diverse eukaryotes. We then compared the numbers of apparent absences to a single measure of protein sequence length and sequence conservation (Smith-Waterman pairwise alignment (S-W) scores) obtained by comparing yeast and human protein sequence data. Using Poisson correlation regression to analyze the Pol I and RPA subunit datasets, we confirmed that S-W scores and apparent gene absences are correlated. We also determined that genes encoding products that are critical for interhomolog SE in model organisms (Rad52, Rad51, Dmc1, Rad54, and Rdh54) have been lost frequently during eukaryotic evolution. Saccharomyces cerevisiae null rad52, dmc1, rad54, and rdh54 mutant phenotypes are suppressed by rad51 overexpression or mutation. If rad51 overexpression or mutation affects other eukaryotes in a similar fashion, this phenomenon may account for frequent losses of genes whose products are critical for the completion of meiosis in model organisms. Finally, we place this work into greater context with a review of hypotheses for the selective forces and mechanisms that resulted in the origin of meiosis. The review and the data presented in this thesis provide the basis for a model of the origin of meiotic genes in which meiosis arose from mitosis by large-scale gene duplication, following a preadaptation that served to reduce increased numbers of chromosomes (from diploid to haploid) caused by erroneous eukaryotic cell-cell fusions.