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  • GENES  (28)
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  • 1
    Keywords: CELLS ; EXPRESSION ; CELL ; Germany ; PATHWAY ; PATHWAYS ; ACETATE-NONUTILIZING MUTANTS ; CDNA ; CDNA CLONES ; CLONES ; CLONING ; CRASSA ; DISTINCT ; DNA-microarray analysis,transcriptional profiling,correspondence analysis,acetate metabolism,Neurosp ; ENZYMES ; FILAMENTOUS FUNGUS ; GENE ; GENE-EXPRESSION ; GENES ; GENOME ; GENOME SEQUENCE ; HYBRIDIZATION ; microarray ; NMT1 ; PROTEIN ; PROTEINS ; RNA ; SACCHAROMYCES-CEREVISIAE ; SAMPLE ; SAMPLES ; transcription
    Abstract: Nutrient-dependent variations in transcript levels of the filamentous fungus Neurospora crassa were studied on a microarray containing some 4700 cDNAs. Cells were grown in minimal and acetate medium. The isolated RNA was analyzed in comparison to the results obtained upon the hybridization of samples prepared from the RNA of cells grown in full medium. Altogether, 160 cDNA clones exhibited significant variations, falling into five distinct subgroups of very similar transcription profiles. This is indicative of the occurrence of a high degree of co-regulation of genes in N. crassa. Especially the regulation of the expression of proteins involved in metabolic pathways was found to be strongly regulated at the RNA level. (C) 2003 Elsevier Inc. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 14599890
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  • 2
    Keywords: Germany ; human ; TOOL ; GENE ; GENES ; GENOME ; microarray ; RNA ; TIME ; DNA ; BIOLOGY ; SEQUENCE ; IN-SITU ; AMPLIFICATION ; microarrays ; ESCHERICHIA-COLI ; DATABASE ; HUMAN GENOME ; oligonucleotides ; Jun ; mutagenesis ; POLYMERASE CHAIN-REACTION ; INVITRO ; MATRIX ; databases ; LIFE ; HIGH-THROUGHPUT ; SIZE ; genomic ; PRIMERS ; array-derived oligonucleotide ; CHEMICAL SYNTHESIS ; GENE SYNTHESIS ; in situ synthesised microarrays ; matrix nucleic acid synthesiser ; synthetic biology ; synthetic gene
    Abstract: The successful completion of the Human Genome Project and other sequencing projects opened the door for another quantum jump in science advancement. The most important public sequence databases are doubling in size every 18 months. By revealing the genetic program of many organisms, these efforts endow biologists with the ability to study the basic information of life in toto as an initial step toward a comprehensive understanding of the complexity of entire organisms. We review the area of synthetic biology, defined as the making and use of biosystems founded on the chemical synthesis of the coding DNA (and potentially RNA). The recent developments discussed here introduce a rich source of oligonucleotides to the field: in situ synthesised microarrays, which in fact represent nothing else but matrix nucleic acid synthesisers. With this new way of producing the oligonucleotides used in the making of synthetic genes in a very cost-effective manner, the field of synthetic biology can be expected to change dramatically in the next decade. Synthetic genes will then be the tools of choice to obtain any sequence at any time in any laboratory. (c) 2006 Elsevier B.V. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 16436303
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  • 3
    Keywords: ANGIOGENESIS ; CELLS ; ENDOTHELIAL-CELLS ; EXPRESSION ; IN-VITRO ; proliferation ; CELL ; Germany ; human ; MODEL ; VITRO ; DISEASE ; SITE ; SITES ; DISTINCT ; GENE ; GENE-EXPRESSION ; GENES ; microarray ; PROTEINS ; transcription ; SURGERY ; NF-KAPPA-B ; ACTIVATION ; RESPONSES ; DNA ; TRANSCRIPTION FACTOR ; INDUCTION ; KERATINOCYTES ; BINDING ; cell cycle ; CELL-CYCLE ; CYCLE ; treatment ; cytokines ; IDENTIFICATION ; PATTERNS ; gene expression ; microarrays ; PROMOTER ; UP-REGULATION ; NUMBER ; PROMOTERS ; STRESS ; DNA-REPAIR ; REPAIR ; EXTRACELLULAR-MATRIX ; BETA ; ADHESION ; HUMAN-PAPILLOMAVIRUS TYPE-16 ; NF-kappa B ; DNA repair ; inflammation ; CDNA MICROARRAY ; CYTOKINE ; MATRIX ; RE ; extracellular matrix ; endothelial cell ; endothelial cells ; INTERLEUKIN-1 ; GENE-TRANSCRIPTION ; INTEGRINS ; analysis ; PROFILES ; BINDING-SITE ; INTERCELLULAR-ADHESION ; ONSET ; CANDIDATE ; UNIT ; BINDING-SITES ; ENDOTHELIAL-CELL ; PROINFLAMMATORY CYTOKINES ; cDNA arrays ; CERVICAL KERATINOCYTES ; mRNA gene transcription ; nuclear factor kappa-B ; PERIODONTAL-DISEASES
    Abstract: Proinflammatory cytokines such as interleukin-1 beta are known to be synthesized in oral gingivitis and periodontitis and lead to the activation of the transcription factor nuclear factor-kappa B (NF-kappa B). Although numerous effects of interleukin-1 beta on mesenchymal cells are known, e.g. up-regulation of intercellular adhesion moelcule-1 in endothelial cells, little is known of the effects of interleukin-1 beta on oral keratinocytes. The purpose of the present study was to seek interleukin-1 beta-mediated alterations in mRNA gene transcription and a putative activation of NF-kappa B in oral gingival keratinocytes. As an in vitro model for gingivitis and periodontitis, immortalized human gingival keratinocytes (IHGK) were stimulated with the proinflammatory cytokine interleukin-1 beta. An epithelia-specific cDNA microarray was used to analyze mRNA expression profiles from IHGK cells treated with 200 units interleukin-1 beta/ml for 3, 6, 9, 12, and 24 h. Indirect immunofluorescence was carried out to detect NF-kappa B in IHGK following interleukin-1 beta treatment. Detailed analysis revealed distinct patterns of time-dependent changes, including genes induced or repressed early (3-6 h) or late (12-24 h) after interleukin-1 beta treatment. Differentially expressed genes were involved in (i) cell stress, (ii) DNA repair, (iii) cell cycle and proliferation, (iv) anti-pathogen response, (v) extracellular matrix turnover, and (vi) angiogenesis. A large number of genes were responsive to NF-kappa B and induction was concomitant with nuclear translocation of the p65 RelA subunit of NF-kappa B. Interestingly, many of these genes contain multiple NF-kappa B binding sites in their promoters. Analysis of altered gene expression allows identification of gene networks associated with inflammatory responses. In addition to a number of well-known genes involved in gingivitis and periodontitis, we identified novel candidates that might be associated with the onset and maintenance of an inflammatory disease
    Type of Publication: Journal article published
    PubMed ID: 16953820
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  • 4
    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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  • 5
    Keywords: CANCER ; CELLS ; EXPRESSION ; tumor ; TUMOR-CELLS ; carcinoma ; CELL ; Germany ; MODEL ; INFORMATION ; SYSTEM ; SYSTEMS ; EXPOSURE ; SITE ; SITES ; GENE ; GENES ; GENOME ; transcription ; DRUG ; TUMORS ; LINES ; DNA ; BIOLOGY ; CELL-LINES ; BREAST ; PROGRESSION ; resistance ; CARCINOMA CELLS ; TUMOR PROGRESSION ; CELL-LINE ; chemotherapy ; LINE ; DNA methylation ; CANCER-CELLS ; BREAST-CARCINOMA ; FREQUENT ; drug resistance ; DRUG-RESISTANCE ; METHYLATION ; SCIENCE ; development ; PROGNOSTIC MARKER ; PROFILES ; breast carcinoma ; DRUGS ; TOPOISOMERASE-II-ALPHA ; CANCERS ; epigenetic regulation ; Type ; CONTRIBUTE ; ANTHRACYCLINES ; MCJ GENE ; MDR1 PROMOTER
    Abstract: Acquired drug resistance represents a frequent obstacle which hampers efficient chemotherapy of cancers. The contribution of aberrant DNA methylation to the development of drug resistant tumor cells has gained increasing attention over the past decades. Hence, the objective of the presented study was to characterize DNA methylation changes which arise from treatment of tumor cells with the chemotherapeutic drug doxorubicin. DNA methylation levels from CpG islands (CGIs) linked to twenty-eight genes, whose expression levels had previously been shown to contribute to resistance against DNA double strand break inducing drugs or tumor progression in different cancer types were analyzed. High-definition DNA methylation profiles which consisted of methylation levels from 800 CpG sites mapping to CGIs around the transcription start sites of the selected genes were determined. In order to investigate the influence of CGI methylation on the expression of associated genes, their mRNA levels were investigated via qRT-PCR. It was shown that the employed method is suitable for providing highly accurate methylation profiles, comparable to those obtained via clone sequencing, the gold standard for high-definition DNA methylation studies. In breast carcinoma cells with acquired resistance against the double strand break inducing drug doxorubicin, changes in methylation of specific cytosines from CGIs linked to thirteen genes were detected. Moreover, similarities between methylation profiles obtained from breast and ovarian carcinoma cell lines with acquired doxorubicin resistance were found. The expression levels of a subset of analyzed genes were shown to be linked to the methylation levels of the analyzed CGIs. Our results provide detailed DNA methylation information from two separate model systems for acquired doxorubicin resistance and suggest the occurrence of similar methylation changes in both systems upon exposure to the drug
    Type of Publication: Journal article published
    PubMed ID: 20544021
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  • 6
    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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  • 7
    Keywords: Germany ; TOOL ; GENE ; GENES ; microarray ; SACCHAROMYCES-CEREVISIAE ; transcription ; COMPLEX ; COMPLEXES ; IDENTIFICATION ; MICROARRAY DATA ; NUMBER ; COLORECTAL-CANCER ; adenocarcinoma ; CLUSTER ; SINGLE ; GENE ONTOLOGY
    Abstract: Motivation: The functional interpretation of microarray datasets still represents a time-consuming and challenging task. Up to now functional categories that are relevant for one or more experimental context(s) have been commonly extracted from a set of regulated genes and presented in long lists. Results: To facilitate interpretation, we integrated Gene Ontology (GO) annotations into Correspondence Analysis to display genes, experimental conditions and gene-annotations in a single plot. The position of the annotations in these plots can be directly used for the functional interpretation of clusters of genes or experimental conditions without the need for comparing long lists of annotations. Correspondence Analysis is not limited in the number of experimental conditions that can be compared simultaneously, allowing an easy identification of characterizing annotations even in complex experimental settings. Due to the rapidly increasing amount of annotation data available, we apply an annotation filter. Hereby the number of displayed annotations can be significantly reduced to a set of descriptive ones, further enhancing the interpretability of the plot. We validated the method on transcription data from Saccharomyces cerevisiae and human pancreatic adenocarcinomas
    Type of Publication: Journal article published
    PubMed ID: 15746280
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  • 8
    Keywords: CANCER ; CELLS ; carcinoma ; Germany ; TOOL ; GENE ; GENES ; microarray ; RESOLUTION ; LINES ; DNA ; tumour ; CELL-LINES ; PATTERNS ; ASSAY ; PROMOTER ; NUMBER ; colorectal cancer ; COLORECTAL-CANCER ; LINE ; DNA methylation ; REGION ; PROBES ; LENGTH ; cell lines ; METHYLATION ; HYPERMETHYLATION ; HYPOMETHYLATION ; HIGH-RESOLUTION ; OLIGONUCLEOTIDE ; CPG ISLANDS ; SUPPRESSOR ; EVENTS ; INDIVIDUAL CELLS ; PROMOTER REGION ; HUMAN CANCERS ; EPIGENETICS
    Abstract: Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limited number of cytosines. Here, we present an oligonucleotide microarray that permits the parallel analysis of the methylation status of individual cytosines, thus combining high throughput and high resolution. The approach was used to study the CpG island in the promoter region of the tumour suppressor gene p16(INK4A). In total, 876 oligonucleotide probes of 21 nt in length were used to inspect the methylation status of 53 CpG dinucleotides, producing correct signals in colorectal cancer cell lines as well as control samples with a defined methylation status. The information was validated by established alternative methods. The overall methylation pattern was consistent for each cell line, while different between them. At the level of individual cytosines, however, significant variations between individual cells of the same type were found, but also consistencies across the panel of cancer cell lines were observed
    Type of Publication: Journal article published
    PubMed ID: 15860770
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  • 9
    Keywords: EXPRESSION ; GROWTH ; Germany ; KINASE ; screening ; EXPOSURE ; GENE ; GENES ; PROTEIN ; PROTEINS ; METABOLISM ; RESPONSES ; MECHANISM ; mechanisms ; STRESS ; STRESS-RESPONSE ; REGION ; REGIONS ; ADHESION ; STABILITY ; HELICOBACTER-PYLORI ; TRANSPORTER ; PROFILES ; uptake ; genomic ; transcriptome ; ALKANE DEGRADATION PATHWAY ; AROMATIC CATABOLIC PATHWAYS ; BACILLUS-SUBTILIS ; BETA-KETOADIPATE ; ESCHERICHIA-COLI O157-H7 ; FERRIC ENTEROBACTIN RECEPTOR ; SOLVENT TOLERANCE ; SULFUR METABOLISM ; UBIQUINOL OXIDASE
    Abstract: The metabolically versatile soil bacterium Pseudomonas putida has to cope with numerous abiotic stresses in its habitats. The stress responses of P. putida KT2440 to 4 degrees C, pH 4.5, 0.8 M urea, and 45 mM sodium benzoate were analyzed by determining the global mRNA expression profiles and screening for stress-intolerant non-auxotrophic Tn5 transposon mutants. In 392 regulated genes or operons, 36 gene regions were differentially expressed by more than 2.5-fold, and 32 genes in 23 operons were found to be indispensable for growth during exposure to one of the abiotic stresses. The transcriptomes of the responses to urea, benzoate, and 4 degrees C correlated positively with each other but negatively with the transcriptome of the mineral acid response. The CbrAB sensor kinase, the cysteine synthase CysM, PcnB and VacB, which control mRNA stability, and BipA, which exerts transcript-specific translational control, were essential to cope with cold stress. The cyo operon was required to cope with acid stress. A functional PhoP, PtsP, RelA/SpoT modulon, and adhesion protein LapA were necessary for growth in the presence of urea, and the outer membrane proteins OmIA and FepA and the phosphate transporter PstBACS were indispensable for growth in the presence of benzoate. A lipid A acyltransferase (PP0063) was a mandatory component of the stress responses to cold, mineral acid, and benzoate. Adaptation of the membrane barrier, uptake of phosphate, maintenance of the intracellular pH and redox status, and translational control of metabolism are key mechanisms of the response of P. putida to abiotic stresses
    Type of Publication: Journal article published
    PubMed ID: 16707699
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  • 10
    Keywords: CELLS ; EXPRESSION ; IN-VITRO ; tumor ; carcinoma ; CELL ; Germany ; MODEL ; VITRO ; GENE ; GENES ; HYBRIDIZATION ; PROTEIN ; PROTEINS ; SAMPLES ; TUMORS ; MARKER ; prognosis ; CARCINOGENESIS ; SEQUENCE ; SUPPRESSION ; ALPHA ; MOUSE ; COMPARATIVE GENOMIC HYBRIDIZATION ; CANCER-CELLS ; TRANSFORMATION ; adenocarcinoma ; ki-ras ; K-RAS ; HUMAN BREAST-TUMORS ; MOLECULAR-CLONING ; PROTEOMICS ; Ras ; PROTEOMIC ANALYSIS ; 2-DIMENSIONAL GEL-ELECTROPHORESIS ; DRUG-INDUCED APOPTOSIS ; RE ; TRANSFECTION ; development ; pancreatic ; BOVINE ; UNIT ; BINDING PROTEINS ; pancreatic carcinogenesis ; ANNEXIN-I ; SV40 large T ; transcriptomics
    Abstract: Pancreatic carcinoma has an extremely bad prognosis due to lack of early diagnostic markers and lack of effective therapeutic strategies. Recently, we have established an in vitro model recapitulating the first steps in the carcinogenesis of the pancreas. SV40 large T antigen-immortalized bovine pancreatic duct cells formed intrapancreatic adenocarcinoma tumors on k-ras(mut) transfection after orthotopic injection in the nude mouse pancreas. Here we identified genes and proteins differentially expressed in the course of malignant transformation using reciprocal suppression subtractive hybridization and 2D gel electrophoresis and mass spectrometry, respectively. We identified 34 differentially expressed genes, expressed sequence tags, and 15 unique proteins. Differential expression was verified for some of the genes or proteins in samples from pancreatic carcinoma. Among these genes and proteins, the majority had already been described either to be influenced by a mutated ras or to be differentially expressed in pancreatic adenocarcinoma, thus proving the feasibility of our model. Other genes and proteins (e.g., BBC1, GLTSCR2, and rhoGDI alpha), up to now, have not been implicated in pancreatic tumor development. Thus, we were able to establish an in vitro model of pancreatic carcinogenesis, which enabled us to identify genes and proteins differentially expressed during the early steps of malignant transformation
    Type of Publication: Journal article published
    PubMed ID: 17356710
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