Frankfurt (Main), Univ., Diss., 2004.

<p>In this thesis project housekeeping genes in differentiating human embryonic stem cells were investigated. Housekeeping genes are involved in basic functions in the cells and are assumed to be expressed at relatively constant levels across different cell types and experimental conditions. Based on these features, housekeeping genes are frequently used as controls in calibration of gene expression data. Commonly used housekeeping genes in somatic tissues have shown to vary notably in human embryonic stem cells and are therefore inappropriate as reference genes in this unique cell type. In the present work a novel set of gene expression data obtained by profiling of undifferentiated and early differentiating cardiac cells, was analyzed. Stably expressed genes were identified in this data set and were subsequently intersected with a previously proposed set of 292 stable genes in human embryonic stem cells. A resulting set of 73 genes show stability across all investigated cell lines and experimental conditions. These genes are suggested as a more reliable set of reference genes in differentiating human embryonic stem cells than frequently used housekeeping genes in somatic tissue. In addition, a novel set of 20 genes was identified as very stably expressed during the differentiation towards the cardiac lineage. After further validation of stability with RT-PCR, these genes could be useful as controls in studies of human embryonic stem cells that differentiate towards the cardiac lineage.</p>

Techn. University, Diss., 2004--Berlin.

Universiẗat, Diss., 2004--Bremen.

Techn. Hochsch., Diss., 2005--Aachen.

JPEG and Excel data files for six siRNAs designed to silence Renilla luciferase transfected in Hela cells. For experimental details please see associated manuscript to be published in Cell Biology Education, 2006. A smaller data set and practice exercise are also included here.

Doctor of Philosophy / Department of Plant Pathology / Bikram S. Gill / Wheat is the most widely grown and consumed grain crop in the world. In order to meet future agricultural production requirements of a growing population, it is essential that we achieve an increased understanding of the basic components and mechanisms shaping growth and productivity of the polyploid wheat plant. Fusarium head blight (FHB) (syn. "scab") poses a serious threat to the quantity and safety of the world's food supply. The resistance locus Fhb1 has provided partial resistance to FHB of wheat for nearly four decades. Map-based cloning of Fhb1 is justified by its significant and consistent effects on reducing disease levels, the importance of FHB in global wheat production and food safety, and because this gene confers partial resistance to this disease and does not appear to behave in a gene-for-gene manner. A bacterial artificial chromosome (BAC) contig spanning the Fhb1 region was developed from the cultivar 'Chinese Spring', sequenced and seven candidate genes were identified in an ~250 kb region. Cosmid clones for each of the seven candidate genes were isolated from a line containing Fhb1 and used for genetic transformation by biolistic bombardment. Transgenic lines were recovered for five candidate genes and evaluated for FHB resistance. All failed to complement the Fhb1 phenotype. Fhb1 is possibly one of the two remaining candidate genes, an unknown regulatory element in this region, or is not present in Chinese Spring. Traditional views on the effects of polyploidy in allohexaploid wheat have primarily emphasized aspects of coding sequence variation and the enhanced potential to acquire new gene functions through mutation of redundant loci. At the same time, the extent and significance of regulatory variation has been relatively unexplored. Recent investigations have suggested that differential expression of homoeologous transcripts, or subfunctionalization, is common in natural bread wheat. In order to establish a timeline for such regulatory changes and estimate the frequency of non-additive expression of homoeologous transcripts in newly formed T. aestivum, gene expression was characterized in a synthetic T. aestivum line and its T. turgidum and Aegilops tauschii parents by cDNA-SSCP and microarray expression experiments. The cDNA-SSCP analysis of 30 arbitrarily selected homoeologous transcripts revealed that four (~13%) showed differential expression of homoeoalleles in seedling leaf tissue of synthetic T. aestivum. In microarray expression experiments, synthetic T. aestivum gene expression was compared to mid-parent expression level estimates calculated from parental expression levels. Approximately 16% of genes were inferred to display non-additive expression in synthetic T. aestivum. Six homoeologous transcripts classified as non-additively expressed in microarray experiments were characterized by cDNA-SSCP. Expression patterns of these six transcripts suggest that cis-acting regulatory variation is often responsible for non-additive gene expression levels. These results demonstrate that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and non-additive gene expression in synthetic T. aestivum.

Made available in DSpace on 2018-08-27T13:37:21Z (GMT). No. of bitstreams: 1 tese_12502_Tese - Lidiane Pignaton Agostini.pdf: 2963143 bytes, checksum: 76cc790c5543c25d309bc0feced39101 (MD5) Previous issue date: 2018-06-27 / O Glifosato [N-(fosfonometil)glicina] é um herbicida pós-emergente, não seletivo e sistêmico. No processo de criação das formulações comerciais de herbicidas a base de glifosato (GBHs, do inglês glyphosate-based herbicides), como o Roundup®, são adicionados surfactantes com o intuito de aumentar a eficiência do composto base. A rota prioritária de degradação do glifosato por micro-organismos no solo resulta na formação do ácido aminometilfosfônico (AMPA). As respostas moleculares ao glifosato têm sido extensivamente estudadas em espécies de plantas e em alguns vertebrados. Em humanos, apesar dos estudos até agora realizados, não se conhece exatamente quais os riscos e mecanismos de atuação que explicariam a toxicidade ao glifosato relatada em alguns experimentos. Sendo assim, a hipótese dessa tese é de que a exposição rápida ao Roundup® e ao AMPA leva à alterações de expressão gênica em importantes processos celulares. Dessa forma, o objetivo desse trabalho é identificar genes diferencialmente expressos (DEGs, do inglês differentially expressed genes) em células mononucleares do sangue periférico (PBMCs, do inglês, peripheral blood mononuclear cells) humano submetidas à exposição rápida com herbicida à base de glifosato (Roundup®) e AMPA. O teste de MTT [3(4,5-dimetiltiazol-2-il)-2,5-difeniltetrazólio brometo], realizado em triplicatas, foi utilizado para avaliar a viabilidade celular e para a escolha das condições de tratamento utilizadas na técnica de microarray (GeneChip® Human Transcriptome Array 2.0, Affymetrix). As condições analisadas foram controle (3 chips), AMPA (10 mM; 3 chips) e Roundup® (0,05%; 2 chips), expostos durante 3 horas. Utilizando um valor de p<0,05 e fold-change de 1,5 foram identificados 5 DEGs no tratamento com o AMPA e 26 no tratamento com Roundup®. As análises de enriquecimento mostraram que os genes com expressão alterada após exposição ao Roundup® estavam associados a 33 processos celulares, principalmente relacionados à regulação destes processos. A plataforma digital Pathview foi utilizada para identificar a atuação dos DEGs após exposição ao Roundup® em diferentes vias. Os genes TNF, LTA, TAB2 e ATM foram relacionados à via de sinalização NF-kappa &#946;; BCL2L11 e ATM à via de sinalização FoxO; SESN3 e ATM à via de sinalização p53; e TNF, BCL2L11 e ATM à apoptose. Dessa forma, os resultados sugerem que o Roundup® altera o padrão de expressão gênica de diversos genes associados com o controle do ciclo celular, regulação de processos celulares e apoptose.

Early detection is one of the most important factors for successful treatment of cancer. Currently, scientists are searching for molecular markers that can help identify and predict outcome and chance of recurrence in patients. In this study, we demonstratet he potential impact of Y-Box binding protein-1 (YB-1) as a marker of aggressiveness and cancer recurrence in breast malignancies by screening one of the largest tissue microarrays in North America. YB-1 is an oncogenic transcription/translation factor, which is over-expressed in the majority of malignancies, including breast cancer. In the cohort of 4049 primary breast tumours, we show that YB-1 is a strong marker of aggressiveness, poor survival and cancer recurrence in all subtypes of human breast cancer with a particularly high frequency of expression in the ER negative basal-like and HER-2 breast cancer subtypes. This suggests that targeting YB-1 may provide a new avenue for therapeutic intervention in these breast cancers that are currently challenging to treat. Cox regression multivariate analysis indicates that YB-1 is second only to nodal status as a strong independent prognostic marker for poor outcome and relapse compared to established clinico-pathological biomarkers, including tumour size, age, grade, ER and HER-2 status. This finding suggests that YB-1 has great potential to be in a priority list of biomarkers for identifying the patients with a higher risk of relapse and poor outcome. Subsequently, we find an association between YB-1 and urokinase Plasminogen Activator (uPA) expression in the basal-like subtype. We then show that YB-1 is involved in the regulation of uPA expression. More importantly, silencing YB-1 or uPA results in a significant reduction in cancer cell invasion. As there are no commercially available YB-linibitors we examine the efficacy of BMS-536924, a small molecule inhibitor for activated IGF-1R/IR on SUM149 cells. We demonstrate that activated IGF-1R is associated with poor survival in primary breast tumours and, that BMS-536924 reduces uPA expression through inhibition YB-1 in SUM149 cells. We therefore conclude that YB-1 is a bio-marker for poor survival and relapse. We also indicate that YB-1 has potential use as a molecular marker in a clinical setting. Inhibiting YB-1 may provide an ideal opportunity for targeted therapy in breast cancer. / Medicine, Faculty of / Graduate

Submitted to the Faculty of the School of Informatics in parial fulfillment of the requirements for the degree of Master of Schience in Bioinformatics Indiana University August 2006 / Decoding the human genome resulted in generating large amount of data that need to be analyzed and given a biological meaning. The field of Life Schiences is highly information driven. The genomic data are mainly the gene expression data that are obtained from measurement of mRNA levels in an organism. Efficiently processing large amount of gene expression data has been possible with the help of high throughput technology. Research studies working on microarray data has led to the possibility of finding disease biomarkers. Carrying out biomarker discovery experiments has been greatly facilitated with the emergence of various analytical and visualization tools as well as annotation databases. These tools and databases are often termed as 'bioinformatics services'. The main purpose of this research was to develop SIBIOS (Bystem for Integration of Bioinformatics Services) as a platform to carry out microarray experiments for the purpose of biomarker discovery. Such experiments require the understanding of the current procedures adopted by researchers to extract biologically significant genes. In the course of this study, sample protocols were built for the purpose of biomarker discovery. A case study on the BCR-ABL subtype of ALL was selected to validate the results. Different approaches for biomarker discovery were explored and both statistical and mining techniques were considered. Biological annotation of the results was also carried out. The final task was to incorporate the new proposed sample protocols into SIBIOS by providing the workflow capabilities and therefore enhancing the system's characteristics to be able to support biomarker discovery workflows.