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  • GENES  (28)
  • BIOLOGY  (15)
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  • 1
    Keywords: microarray ; SAMPLE ; microarrays ; MOLECULAR-BIOLOGY ; BIOLOGY ; molecular biology
    Type of Publication: Book chapter
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  • 2
    Keywords: gene expression ; BIOLOGY ; EXPRESSION ; CELL ; GENE ; GENE-EXPRESSION ; representational difference analysis ; analysis
    Type of Publication: Book chapter
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  • 3
    Keywords: molecular biology ; MOLECULAR-BIOLOGY ; BIOLOGY ; SAMPLE
    Type of Publication: Book chapter
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  • 4
    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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  • 5
    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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  • 6
    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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  • 7
    Keywords: CELL ; Germany ; VOLUME ; HYBRIDIZATION ; DNA ; BIOLOGY ; SEQUENCE ; SEQUENCES ; polymorphism ; POLYMORPHISMS ; single nucleotide polymorphism ; SPECTROSCOPY ; TARGET ; IDENTIFICATION ; ASSAY ; SNP ; MUTATIONS ; specificity ; FLUORESCENCE ; PERIPHERAL-BLOOD ; real-time PCR ; IMMUNODEFICIENCY-VIRUS TYPE-1 ; SINGLE ; RESIDUES ; INCREASE ; LEADS ; SINGLE NUCLEOTIDE POLYMORPHISMS ; SNPs ; MYCOBACTERIUM-TUBERCULOSIS ; single-nucleotide ; fluorescence spectroscopy ; technique ; BREAST-CANCER PATIENTS ; ELECTRON-TRANSFER ; single-molecule spectroscopy ; RESISTANT ; CONTACT ; INCREASES ; DNA hairpin probes ; MONONUCLEOTIDE MOLECULES
    Abstract: This article presents a new, highly sensitive method for the identification of single nucleotide polymorphisms (SNPs) in homogeneous solutions using fluorescently labeled hairpin-structured oligonucleotides (smart probes) and fluorescence single-molecule spectroscopy. While the hairpin probe is closed, fluorescence intensity is quenched due to close contact between the chromophore and several guanosine residues. Upon hybridization to the respective target SNP sequence, contact is lost and the fluorescence intensity increases significantly. High specificity is achieved by blocking sequences containing mismatch with unlabeled oligonucleotides. Time-resolved single-molecule fluorescence spectroscopy enables the detection of individual smart probes passing a small detection volume. This method leads to a subnanomolar sensitivity for this single nucleotide specific DNA assay technique. (c) 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 17399707
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  • 8
    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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  • 9
    Keywords: CELLS ; EXPRESSION ; CELL ; GENE ; GENE-EXPRESSION ; SACCHAROMYCES-CEREVISIAE ; METABOLISM ; MECHANISM ; REDUCTION ; mechanisms ; BIOLOGY ; PHOSPHORYLATION ; SIGNAL ; ALPHA ; gene expression ; heat shock ; NUMBER ; STRESS ; MAMMALIAN-CELLS ; INCREASE ; mRNA ; LEVEL ; ENGLAND ; PROCESSING BODIES ; TRANSLATION INITIATION ; STRESS GRANULES ; P-BODIES ; TURNOVER ; AFRICAN TRYPANOSOME ; UNTRANSLATED REGION ; CYTOPLASMIC FOCI ; CELL BIOLOGY ; POSITION ; trypanosome ; Trypanosoma brucei ; BLOOD-STREAM ; eIF2 alpha ; LEISHMANIA-MAJOR ; MESSENGER-RNA DEGRADATION ; SPLICED-LEADER RNA ; stress granule
    Abstract: In trypanosomes there is an almost total reliance on post-transcriptional mechanisms to alter gene expression; here, heat shock was used to investigate the response to an environmental signal. Heat shock rapidly and reversibly induced a decrease in polysome abundance, and the consequent changes in mRNA metabolism were studied. Both heat shock and polysome dissociation were necessary for (1) a reduction in mRNA levels that was more rapid than normal turnover, (2) an increased number of P-body-like granules that contained DHH1, SCD6 and XRNA, (3) the formation of stress granules that remained largely separate from the P-body-like granules and localise to the periphery of the cell and, (4) an increase in the size of a novel focus located at the posterior pole of the cell that contain XRNA, but neither DHH1 nor SCD6. The response differed from mammalian cells in that neither the decrease in polysomes nor stress-granule formation required phosphorylation of eIF2 alpha at the position homologous to that of serine 51 in mammalian eIF2 alpha and in the occurrence of a novel XRNA-focus
    Type of Publication: Journal article published
    PubMed ID: 18713834
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  • 10
    Keywords: CANCER ; tumor ; CELL ; Germany ; human ; SYSTEM ; SYSTEMS ; DISEASE ; liver ; PROTEIN ; PROTEINS ; SAMPLE ; SAMPLES ; MOLECULES ; TISSUE ; TISSUES ; BIOLOGY ; MOLECULE ; IDENTIFICATION ; MEMBRANE ; INSTABILITY ; ELECTROPHORESIS ; pancreatic cancer ; SECTIONS ; molecular biology ; pancreas ; PANCREATIC-CANCER ; EXTRACTION ; SEPARATION ; USA ; protein fractionation ; CELL-CELL ; EFFECTOR MOLECULE ; ISLETS ; protein extraction
    Abstract: Proteins are the major class of effector molecules in cellular systems. For the identification of functional differences between normal and diseased tissues, a reliable analysis of their protein content is essential. Reproducible isolation and fractionation of intact proteins are important in this respect, but their complexity in structure and concentration, their close interaction, and their instability represent major challenges. For protein isolation in tissues, the breakdown of cell-cell and cell-matrix connections within a tissue without affecting protein quality is a critical factor. We compared different processes for a compartmental protein preparation from pancreatic tissue, one of the most challenging tissues for protein isolation because of its high protease content. Success of the different procedures varied greatly. Based on a scheme of tissue-slicing and subsequent cell isolation, we established a reliable workflow for the fractional extraction of cytosolic proteins, membrane and organelle proteins, nuclear proteins, and cytoskeletal filaments. The tissue slices also allow for a representative confirmation of individual samples' cellular status by histochemical processes, and a proper separation or mixing of cellular material from across a tumor if required
    Type of Publication: Journal article published
    PubMed ID: 19450236
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