Transcription profiling of yeast mutant strains vs WT: YIA29 (mdl1::HIS3); YIA30 (yme1::KAN); YIA31 (mdl1::HIS3 yme1::KAN);
ABSTRACT: All yeast strains were in the genetic background W303-1A (MATa leu2-3,112 trp1-1 ura3-1 can1-100 ade2-1 his3-11,15). Gene expression profiles of the following mutant strains were compared with WT: YIA29 (mdl1::HIS3); YIA30 (yme1::KAN); YIA31 (mdl1::HIS3 yme1::KAN); 2 independent RNA preparations per strain were used (A and B); 2 independent array hybridisations per RNA preparation were performed (color switch experiments).
Project description:Stomatal guard-cells modulate gas exchange between the plant and the atmosphere.<br><br>Regulation of transcription is emerging as an important mechanism in<br><br>controlling guard cells activity. The Arabidopsis transcription factor<br><br>AtMYB60, is specifically expressed in guard cells and controls stomatal<br><br>movements. Opening of stomatal pores is constitutively reduced in the<br><br>atmyb60-1 null allele, and water loss during drought is diminished in<br><br>the mutant compared to wild type. To address the effect of the AtMYB60<br><br>disruption on global gene expression, total mRNAs, derived from<br><br>atmyb60-1 and WT rosette leaves, grown in standard conditions, were hybridized to a cDNA microarray.
Project description:Ovarian cancer is the leading cause of death in gynaecological malignancies in women. However, currently there are no clinical or pathologic parameters available that can reliably predict clinical outcome. In a previously published pilot study we explored the performance of microarrays in predicting clinical behaviour of ovarian tumours. For this purpose we performed microarray analysis on 20 patients and estimated that we could predict disease stage with 100% accuracy and the response to platin-based chemotherapy with 76.92% accuracy using leave-one-out cross validation techniques in combination with Least Squares Support Vector Machines (LS-SVMs). In the current study we prospectively evaluate models, built on the pilot data set, on a set of 49 new patients. Principal component analysis showed that the gene expression data from stage I, platin-sensitive advanced stage and platin-resistant advanced stage tumours in the prospective study did not correspond to their respective classes in the pilot study. Additionally, LS-SVM models built using the data from the pilot study, only misclassified one of four stage I tumours and correctly classified all 45 advanced stage tumours but this model was not able to predict resistance to platin-based chemotherapy. We discuss possible reasons for prospective failure of these models and conclude that existing results based on gene expression patterns of ovarian tumours need to be thoroughly scrutinized before this technology could be considered ready for clinical use.
Project description:We investigated whether prognostic information is reflected in the expression patterns of ovarian carcinoma samples. RNA obtained from seven FIGO stage I without recurrence, seven platin-sensitive advanced-stage (III or IV), and six platin-resistant advanced-stage ovarian tumors was hybridized on a complementary DNA microarray with 21,372 spotted clones. The results revealed that a considerable number of genes exhibit nonaccidental differential expression between the different tumor classes. Principal component analysis reflected the differences between the three tumor classes and their order of transition. Using a leave-one-out approach together with least squares support vector machines, we obtained an estimated classification test accuracy of 100% for the distinction between stage I and advanced-stage disease and 76.92% for the distinction between platin-resistant versus platin-sensitive disease in FIGO stage III/IV. These results indicate that gene expression patterns could be useful in clinical management of ovarian cancer.<br> KEYWORDS: clinical, FIGO stage, microarrays, ovarian cancer, platin resistance.
Project description:One of the major primary features of the neurocutaneous genetic disorder Neurofibromatosis type 1 are the hyperpigmentary café-au-lait macules where dysregulation of melanocyte development, proliferation and differentiation is considered to play a key etiopathogenic role. To gain better insight in the possible role of the tumor suppressor gene NF1, a transcriptomic microarray analysis was performed on human NF1 heterozygous (NF1+/-) melanocytes of a Neurofibromatosis type 1 patient and NF1 wild type (NF1+/+) melanocytes of a healthy control patient, both cultured from normally pigmented and hyperpigmented lesional café-au-lait skin. Out of 13,850 unique genes, a total of 137 had a significant twofold or more up- (72) or down-regulated (65) expression in NF1+/- melanocytes compared to NF1+/+ melanocytes (genotype effect). Considering possible intrinsic genetic variation in lesional skin, melanocytes showed a total of 51 genes having a significant twofold or more up- (37) or down-regulated (14) expression when they were cultured from hyperpigmentary café-au-lait skin compared to normally pigmented skin (lesional skin type effect). NF1+/- café-au-lait skin melanocytes showed 468 genes with a significant two-fold or more up- (183) or down-regulated (285) expression going beyond the sum of the separate main effects (interaction). Detailed analysis enabled the identification of several modulated genes in NF1+/- (café-au-lait skin) melanocytes, mainly involved in controlling cell proliferation and cell maintenance, in cell adhesion and, surprisingly, in the immune response. An interesting finding was that a high number of transcription factor genes were differentially modulated, among which a specific subset - important in melanocyte-lineage development - showed downregulation in a transcriptional cis-regulatory network governing the activation of the melanocyte-specific dopachrome tautomerase (DCT) gene.
Project description:Differences in radiosensitivity existing among cells which constitute the lymphocyte population have been known for a long time, although the molecular basis of this differential radiation sensitivity remains unclear. In an attempt to get more insight into the molecular mechanisms leading to radiation effects, we used microarray analysis to study transcriptional changes in CD4+ T lymphocytes to an irradiation dose of 1 Gy. The contribution of the cell type to the radiation response of CD4+ lymphocytes was deduced by comparing our results with a gene expression profile observed in Peripheral Blood Lymphocytes published by other groups (Amundson, 2000; Kang, 2003, Jen, 2003).
Project description:A time-course experiment, in which the gene expression in the primary hippocampal neurons isolated from E17 embryos and undergoing differentiation in the culture for 7h, 18h, 33h, 72h, 8 days, 12 days (at which time points the RNA was extracted) was compared by competitive hybridization with a common reference sample which was RNA isolated from a newborn brain.
Project description:Arabidopsis leaf blades were sampled throughout development from meristematic through expanding to mature state at 10 different timepoints. The transcript data can be compared to a kinematic and flowcytometric characterisation of the system.