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  • 1
    Keywords: GENE-EXPRESSION ; GENE ; microarray ; EXPRESSION ; gene expression ; MICROARRAY DATA
    Type of Publication: Book chapter
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  • 2
    Keywords: COMBINATION ; Germany ; INFORMATION ; GENE ; HYBRIDIZATION ; microarray ; MOLECULES ; DNA ; MARKER ; MOLECULE ; STABILITY ; ESTABLISHMENT ; FEATURES ; ARRAY ; LEVEL ; CONFORMATION ; SELECTIVITY ; MIRROR-IMAGE DNA
    Abstract: L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and selectivity as D-DNA but form a left-helical double-helix. Because of its chiral difference, L-DNA does not bind to its naturally occurring D-DNA counterpart, however. We analysed some of the properties that are typical for L-DNA. For all the differences, L-DNA is chemically compatible with the D-form of DNA, so that chimeric molecules can be synthesized. We take advantage of the characteristics of L-DNA toward the establishment of a universal microarray that permits the analysis of different kinds of molecular diagnostic information in a single experiment on a single platform, in various combinations. Typical results for the measurement of transcript level variations, genotypic differences and DNA-protein interactions are presented. However, on the basis of the characteristic features of L-DNA, also other applications of this molecule type are discussed
    Type of Publication: Journal article published
    PubMed ID: 16990248
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  • 3
    Keywords: EXPRESSION ; GENE ; GENES ; SACCHAROMYCES-CEREVISIAE ; METABOLISM ; IDENTIFICATION ; Saccharomyces cerevisiae ; MUTATION ; MUTATIONS ; MITOCHONDRIA ; KINASE CASCADE ; LEVEL ; analysis ; ROLES ; INCREASES ; D-lactate dehydrogenase ; DLD3 ; GLYOXALASE I ; GRE2 ; isoamyl alcohol-induced filamentation ; isovaleraldehyde reductase ; METHYLGLYOXAL ; PSEUDOHYPHAE
    Abstract: A transcriptome analysis was performed of Saccharomyces cerevisiae undergoing isoamyl alcohol-induced filament formation. In the crucial first 5 h of this process, only four mRNA species displayed strong and statistically significant increases in their levels of more than 10-fold. Two of these (YEL071w/DLD3 and YOL151w/GRE2) appear to play important roles in filamentation. The biochemical activities ascribed to these two genes (D-lactate dehydrogenase and methylglyoxal reductase, respectively) displayed similarly timed increases to those of their respective mRNAs. Mutants carrying dld3 mutations displayed reduced filamentation in 0.5% isoamyl alcohol and needed a higher concentration of isoamyl alcohol to effect more complete filament formation. Hence, DLD3 seems to be required for a full response to isoamyl alcohol, but is not absolutely essential for it. Mutants carrying gre2 mutations were derepressed for filament formation and formed large, invasive filaments even in the absence of isoamyl alcohol. These results indicate a previously unsuspected and novel role for the GRE2 gene product as a suppressor of filamentation by virtue of encoding isovaleraldehyde reductase activity
    Type of Publication: Journal article published
    PubMed ID: 16999827
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  • 4
    Keywords: ENERGIES ; CELLS ; EXPRESSION ; GROWTH ; CELL ; EXPOSURE ; SITE ; SITES ; GENE ; GENES ; PROTEIN ; PROTEINS ; SACCHAROMYCES-CEREVISIAE ; transcription ; METABOLISM ; RESPONSES ; DNA ; MECHANISM ; FAMILY ; INDUCTION ; mechanisms ; BINDING ; YEAST ; PROMOTER ; ARRAYS ; cold shock ; DECREASE ; ELEMENTS ; ENERGY ; ENVIRONMENTAL-CHANGES ; heat shock ; HEAT-SHOCK ; MEMBRANE ; NUMBER ; pre-adaptation ; PROMOTERS ; STRESS ; stress response ; STRESS-RESPONSE ; transcriptional profiling
    Abstract: DNA arrays were used to measure changes in transcript levels as yeast cells responded to temperature shocks. The number of genes upregulated by temperature shifts from 30degreesC to 37degreesC or 45degreesC was correlated with the severity of the stress. Pre-adaptation of cells, by growth at 37 degreesC previous to the 45 degreesC shift, caused a decrease in the number of genes related to this response. Heat shock also caused downregulation of a set of genes related to metabolism, cell growth and division, transcription, ribosomal proteins, protein synthesis and destination. Probably all of these responses combine to slow down cell growth and division during heat shock, thus saving energy for cell rescue. The presence of putative binding sites for Xbp1p in the promoters of these genes suggests a hypothetical role for this transcriptional repressor, although other mechanisms may be considered. The response to cold shock (4degreesC) affected a small number of genes, but the vast majority of those genes induced by exposure to 4 degreesC were also induced during heat shock; these genes share in their promoters cisregulatory elements previously related to other stress responses. Copyright (C) 2003 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 18629074
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  • 5
    Keywords: EXPRESSION ; GROWTH ; COMBINATION ; SYSTEM ; SYSTEMS ; SITES ; GENE ; GENE-EXPRESSION ; GENES ; PROTEIN ; transcription ; ACTIVATION ; DNA ; FAMILY ; TRANSCRIPTION FACTOR ; ENRICHMENT ; BINDING ; MICROARRAY DATA ; ENVIRONMENTAL-CHANGES ; STRESS ; STRESS-RESPONSE ; MUTATION ; REPAIR ; SIGNALING PATHWAY ; MUTATIONS ; MAP KINASE PATHWAY ; CONSTRUCTION ; 1 ; 3-BETA-D-GLUCAN SYNTHASE ; CYCLE REGULATOR ; GLOBAL GENE-EXPRESSION
    Abstract: Perturbations of the yeast cell wall trigger a repair mechanism that reconfigures its molecular structure to preserve cell integrity. To investigate this mechanism, we compared the global gene expression in five mutant strains, each bearing a mutation (i.e. fks1, kre6, mnn9, gas1, and knr4 mutants) that affects in a different manner the cell wall construction. Altogether, 300 responsive genes were kept based on high stringency criteria during data processing. Functional classification of these differentially expressed genes showed a substantial subset of induced genes involved in cell wall construction and an enrichment of metabolic, energy generation, and cell defense categories, whereas families of genes belonging to transcription, protein synthesis, and cellular growth were underrepresented. Clustering methods isolated a single group of similar to80 up-regulated genes that could be considered as the stereotypical transcriptional response of the cell wall compensatory mechanism. The in silico analysis of the DNA upstream region of these co-regulated genes revealed pairwise combinations of DNA-binding sites for transcriptional factors implicated in stress and heat shock responses (Msn2/4p and Hsf1p) with Rlm1p and Swi4p, two PKC1-regulated transcription factors involved in the activation genes related to cell wall biogenesis and G(1)/S transition. Moreover, this computational analysis also uncovered the 6-bp 5'-AGCCTC-3' CDRE (calcineurin-dependent response element) motif in 40% of the coregulated genes. This motif was recently shown to be the DNA binding site for Crz1p, the major effector of calcineurin- regulated gene expression in yeast. Taken altogether, the data presented here lead to the conclusion that the cell wall compensatory mechanism, as triggered by cell wall mutations, integrates three major regulatory systems: namely the PKC1-SLT2 mitogen-activated protein kinase-signaling module, the "global stress" response mediated by Msn2/4p, and the Ca2+/calcineurin- dependent pathway. The relative importance of these regulatory systems in the cell wall compensatory mechanism is discussed
    Type of Publication: Journal article published
    PubMed ID: 12644457
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  • 6
    Keywords: CELLS ; GROWTH ; KINASE ; PATHWAYS ; GENE ; GENES ; PROTEIN ; SACCHAROMYCES-CEREVISIAE ; ACCUMULATION ; RESPONSES ; mechanisms ; MICROARRAY DATA ; Saccharomyces cerevisiae ; YEAST ; DISPLAY ; GLUCOSE ; REPRESSION ; GENE- EXPRESSION ; GLUCONEOGENIC MESSENGER-RNAS ; HEXOSE TRANSPORTERS ; RAS PROTEINS ; SENSING MECHANISMS
    Abstract: Glucose exerts profound effects upon yeast physiology. In general, the effects of high glucose concentrations (〉1%) upon Saccharomyces cerevisiae have been studied. In this paper, we have characterized the global responses of yeast cells to very low (0.01%), low (0.1%) and high glucose signals (1.0%) by transcript profiling. We show that yeast is more sensitive to very low glucose signals than was previously thought, and that yeast displays different responses to these different glucose signals. Genes involved in central metabolic pathways respond rapidly to very low glucose signals, whereas genes involved in the biogenesis of cytoplasmic ribosomes generally respond only to glucose concentrations of〉 0.1%. We also show that cytoplasmic ribosomal protein mRNAs are transiently stabilized by glucose, indicating that both transcriptional and post- transcriptional mechanisms combine to accelerate the accumulation of ribosomal protein mRNAs. Presumably, this facilitates rapid ribosome biogenesis after exposure to glucose. However, our data indicate that yeast activates ribosome biogenesis only when sufficient glucose is available to make this metabolic investment worthwhile. In contrast, the regulation of metabolic functions in response to very low glucose signals presumably ensures that yeast can exploit even minute amounts of this preferred nutrient
    Type of Publication: Journal article published
    PubMed ID: 12694616
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  • 7
    Keywords: CELLS ; CELL ; Germany ; GENE ; GENES ; PROTEIN ; PROTEINS ; SACCHAROMYCES-CEREVISIAE ; transcription ; TIME ; ACID ; ACIDS ; FORM ; DELETION ; MUTANT ; YEAST ; MEMBRANE ; SIGNALING PATHWAY ; WILD-TYPE ; INSTABILITY ; STABILITY ; PLASMA-MEMBRANE ; Jun ; WALL ; AMINO-ACIDS ; MASSES ; ABSENCE ; GENOME-WIDE ANALYSIS ; A-AGGLUTININ ; ALPHA-AGGLUTININ ; BGL2 GENE ; chitin ; DEFECTS ; GROWTH SITES ; KINASE PATHWAY
    Abstract: The c ovalently linked cell wall protein Ccw12p of Saccharomyces cerevisiae is a GPI-anchored protein (V. Mrsa et al., 1999, J Bacteriol 181: 3076-3086). Although only 121 amino acids long, the haemagglutinin-tagged protein released by laminarinase from the cell wall possesses an apparent molecular mass of 〉 300 kDa. A membrane-bound form with an apparent molecular mass of 58 kDa is highly O- and N-glycosylated and contains the GPI anchor. With a half-life of 2 min, the membrane form is transformed to the 〉 300 kDa form. The deletion mutant ccw12Delta grows slower than the wild type, is highly sensitive to Calcofluor white and contains 2.5 times more chitin. Further, compared with wild-type yeast, significantly more proteins are released from intact cells when treated with dithiothreitol. Interestingly, these defects become less pronounced when further GPI-anchored cell wall proteins are deleted. Mutant DeltaGPI (simultaneous deletion of CCW12, CCW13/DAN1, CCW14, TIP1 and CWP1) is similar in many respects to wild-type yeast. To find out how the cell wall is stabilized in mutant DeltaGPI, a genome-wide transcription analysis was performed. Of 159 significantly regulated genes, 14 encode either known or suspected cell wall-associated proteins. Analysis of genes affected in transcription revealed that SED1 and SRL1 in particular are required to reconstruct cell wall stability in the absence of multiple GPI-anchored mannoproteins
    Type of Publication: Journal article published
    PubMed ID: 15165243
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