Breast cancer is the most common cancer in women worldwide. However, the genetic alterations that lead to breast cancer are not fully understood. This thesis aims to identify novel genes of potential mechanistic, diagnostic or therapeutic interest in breast cancers by mutational analysis and whole-genome sequencing. In paper I, sequencing of 36 previously identified candidate genes in 96 breast tumors with patient-matched normal DNA determined the somatic mutation prevalence of these candidate genes and identified additional mutations in Notch, NF-κB, PI3K, and Hedgehog pathways as well as in processes mediating DNA methylation, RNA processing and calcium signaling. In paper II, comparison of massively parallel mate-pair sequencing results of a human genome before and after phi29-mediated multiple displacement amplification (MDA) revealed that MDA introduces structural alteration artifacts, with an emphasis on false positive inversions, and impairs the sensitivity to detect true inversions. Therefore, MDA has limited value in sample preparation for whole-genome sequencing for structural alteration detection. In paper III, massively parallel paired-end sequencing identified gene rearrangements in 15 hormone receptor negative breast cancers. Forty validated rearrangements were predicted to directly affect 30 genes, involved in epigenetic regulation, cell mitosis, signalling transduction and glycolytic flux. RNA interference-based assays revealed the potential roles in cell growth of some affected genes, among which DDX10 was implicated to be involved in apoptosis. In paper IV, a method for statistical evaluation of putative translocations detected by massively parallel paired-end sequencing was proposed. In an application of this method to analyse translocations detected by cancer genome deep paired-end sequencing, 76 putative translocations were classified into four categories, with the majority likely to be caused by mismapping due to repetitive regions. Taken together, this thesis provides insights into genes and pathways mutated in sporadic breast cancer genomes, which broaden our understanding of the genetic basis of breast cancer and may ultimately facilitate the diagnosis and treatment of this disease.

Research Doctorate - Doctor of Philosophy (PhD) / Sound field distribution is becoming increasingly known as a method to overcome problems associated with noise, distance, and reverberation in classrooms. No robust research on this intervention has been conducted in the New Zealand context. Changing pedagogies in the education of New Zealand children and young people have been observed particularly since the 1970’s, resulting in noisier classrooms (Wilson, 2000). Acoustic standards for New Zealand classrooms that were adopted in 2003 apply only to new or renovated classrooms, and not to the majority of existing classrooms (Ministry of Education, 2003a). This study investigated: (a) the efficacy of sound field distribution in 30 New Zealand classrooms from five schools and compared outcome measures with a representative control group; (b) the variations of benefit for groups from specific populations, in particular children from five different socio-economic backgrounds and those with histories of middle ear dysfunction; and (c) the effects on teachers who use this equipment. Data were collected from standardized objective measurement tools and from the teachers and students who were participating in the study. Results revealed that sound field distribution, with the equipment configuration of boom microphones and four speakers, can enhance the listening and learning environment resulting in significant positive benefits in raising the achievement levels of children and young people. These results were observed in listening comprehension, which has a flow-on effect on the overall scholastic achievement of all students. Evidence of improved outcomes in areas with a strong link to mastery of literacy were significant, in particular in the areas of phonologic skills, reading comprehension, and reading vocabulary. Results of the study strongly support the use of sound field distribution in all mainstream school settings irrespective of whether the children and young people belong to a particular ethnic group, have had a history of middle ear dysfunction, or attend schools of a particular socio-economic status. Classroom sound field distribution seemingly benefits all children and young people. As a result of the positive results of this study and given the stated goals for education by the New Zealand Ministry of Education (Ministry of Education, 2003b), sound field distribution needs to be considered at a policy level as an intervention to assist in reducing disparity and to improve learning outcomes for all young New Zealanders in mainstream school settings.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 7 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2002. / Härtill 5 uppsatser.

Thesis (M.Med.Sc.)--University of Hong Kong, 2000. / Includes bibliographical references (leaves 35-42). Also available in print.

Thesis (M.Med.Sc.)--University of Hong Kong, 2004. / Also available in print.

Made available in DSpace on 2014-10-09T12:46:36Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T13:56:41Z (GMT). No. of bitstreams: 1 08350.pdf: 7511291 bytes, checksum: 18b3142f54961c0556b2d92490449a3a (MD5) / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN/CNEN-SP

Reliable detection of low template DNA (LTDNA) is dependent on reproducible allelic peaks and use of appropriately set thresholds. Analyzing LTDNA at different thresholds than high template DNA samples is discouraged by some scientists [1]. Thus, enhancing LTDNA samples is preferred if thresholds set for high template DNA are maintained for LTDNA samples. Post-amplification purification with the use of silica columns increases peak heights of single source LTDNA, while maintaining heterozygote balances of the sample before purification. LTDNA samples are difficult to interpret due to stochastic effects: allelic dropout and heterozygote imbalance. Interpretation of LTDNA mixtures is even more complex due to allelic sharing between contributors and allelic masking by artifacts. To determine if post-amplification purification of DNA from two-person LTDNA mixtures can improve profile interpretation, variable concentrations and mixture ratios of saliva extracts were applied to Macherey-Nagel NucleoSpin® and Qiagen MinElute® columns. The peak heights and heterozygote balance of two-person LTDNA mixtures were compared before and after purification with each silica column. Contributor proportion and heterozygote balance were not significantly affected by purification, and the peak heights of samples improved with use of either silica column. However, peak heights were higher in samples purified with Qiagen MinElute® columns. Given the higher peak heights, fewer dropouts occurred in samples purified with Qiagen MinElute® columns, but the occurrence of locus dropout reduced after purification with either column. The performance of each silica column was characterized by comparing fold increase and their individual effect on the primer front. The fold increase of samples purified with Qiagen MinElute® columns was higher than samples purified with Macherey-Nagel NucleoSpin® columns, but replicate purifications of Macherey-Nagel NucleoSpin® columns were more precise than replicate purifications of Qiagen MinElute® columns. Samples purified with Macherey-Nagel NucleoSpin® columns removed more primers than samples purified with Qiagen MinElute® columns. Post-amplification purification with silica columns is a useful investigative tool for LTDNA, especially for LTDNA mixtures. Both silica columns increased peak height, maintained contributor proportion, maintained heterozygote balance, and reduced primer front, but the degree of fold increase and reduction in primer front must be considered to facilitate the decision of which silica column to use for post-amplification purification of LTDNA. Due to its precision, Macherey-Nagel NucleoSpin® columns are ideal for LTDNA mixture samples while Qiagen MinElute® columns are ideal for single source LTDNA due to its ability to elevate peak heights.

The main objective of this research was to study the buckling and post-buckling response of axially restrained beam-columns under thermal loading. Also the effects of slenderness ratios on pre-buckling and post-buckling behavior which is neglected in AISC specification was examined. The results of this study indicate that: a) Both the deflection and end moment amplification factors are significantly smaller for the restrained beam-columns subjected to temperature increase than the corresponding unrestrained beam-columns subjected to (mechanical) axial loads. b) The deflection amplification factors tend to decrease with decreasing ratio of end moments. However, reverse seems to occur for the moment amplification factors and as the moment amplification factors tend to increase with decreasing moment ratio particularly in the pre-buckling and the initial post-buckling range (0.1 < T/Tcr < 1.5). c) The thermal amplification factors tend to be smaller than the AISC values even in the pre-buckling range with those for the slender beam-columns significantly smaller than those for the shorter beam-columns.

Made available in DSpace on 2014-06-11T19:35:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-05-15Bitstream added on 2014-06-13T20:45:44Z : No. of bitstreams: 1 rocha_kcg_dr_botfca.pdf: 895303 bytes, checksum: cd87505fac20f9742a811226a9c1fc11 (MD5) / Considerando o aumento de begomovírus e mosca-branca no campo o presente trabalho teve como objetivos a detecção, a caracterização molecular e a análise da diversidade genética de begomovírus em pimentão e tomateiro em diferentes municípios do Estado de São Paulo: Piraju, Tejupá, Santa Cruz do Rio Pardo, São Pedro do Turvo, São Miguel Arcanjo, Itapetininga, Lins, Sabino, Timburí, Iacanga, Pirajuí, Avaí, Reginópolis e Salto; a identificação de biótipos de B. tabaci por meio da amplificação do gene mitocondrial (citocromo oxidase I - mtCOI) seguido de seqüenciamento ou RFLP utilizando a enzima Taq I e a avaliação para resistência de acessos de Capsicum spp. a dois isolados de ToSRV. A análise da variabilidade foi realizada por meio de seqüenciamento da região da capa protéica (DNA-A) com oligonucleotídeos universais e, paralelamente, as mesmas amostras foram testadas por amplificação por círculo rolante (RCA) sendo, posteriormente, clivadas com a enzima de restrição HpaII. Um total de 812 amostras foi analisado, sendo 709 de pimentão e 103 de tomate. Por PCR tradicional, foram detectadas positivas para presença de begomovírus 98 amostras provenientes de pimentão e 39 de tomateiro, e por RCA-PCR, foram 332 e 82 respectivamente, evidenciando maior sensibilidade desta técnica. Dessas amostras, foram seqüenciadas 39 de pimentão e 25 de tomateiro, verificando-se ocorrência prevalente da espécie ToSRV no estado de São Paulo. Infecção mista com ToSRV e ToYVSV foi observada tomateiro. Por RCA-RFLP, foram observados quatro padrões de clivagem com a enzima HpaII e todos foram confirmados como sendo da espécie ToSRV indicando variabilidade molecular intraespecífica. Para tomateiro, foram observados 18 padrões de restrição, dois idênticos aos verificados em plantas de pimentão indicando, possivelmente, infecção pelos mesmos isolados de ToSRV, porém... / Considering the high incidence of begomoviruses and the whitefly on the field, the objetives of this work were to analyze the genetic diversity of begomoviruses infecting pepper and tomato plants in different counties of São Paulo State: Piraju, Tejupá, Santa Cruz do Rio Pardo, São Pedro do Turvo, São Miguel Arcanjo, Itapetininga, Lins, Sabino, Timburí, Iacanga, Pirajuí, Avaí, Reginópolis and Salto; the identification of biotypes of B. tabaci through the amplification of the mitochondrial gene (cytochrome oxidase I) 4 followed by sequencing the gene or analysis by RFLP using the enzyme TaqI and the evaluation of Capsicum spp. for the resistance source for two isolates of ToSRV. The coat protein from the DNA A of the begomovirus was amplified and sequenced, and the same samples were amplified by rolling circle amplification (RCA) followed by analysis by RCA-RFLP using the HpaII enzyme. A total of 812 samples were analyzed, 709 from pepper and 103 from tomato. By PCR, 98 samples from pepper and 39 from tomato were positives for the presence of begomoviruses, while by RCA-PCR 332 and 82 respectively. Thirty-nine samples from pepper and 25 from tomato were sequenced indicating the prevalence of the ToSRV species in São Paulo State. Mixed infections with ToSRV and ToYVSV were found in tomato plants. By RCA-RFLP four restriction profiles were found for ToSRV in pepper plants. In tomato 18 profiles were observed: two identical as observed for ToSRV in pepper, indicating possible infection with the same ToSRV isolates, a profile for ToSRV and ToYVSV mixed infections and also different profiles for ToSRV isolates didn’t found in pepper plants. The sequencing of 17 samples of B. tabaci mitochondrial citochrome oxidase I gene and analysis by Taq I digestion of whiteflies collected in growers areas of pepper and tomato indicated only the presence of the B biotype... (Complete abstract click electronic access below)