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  • 1
    Keywords: COMBINATION ; Germany ; GENOME ; microarray ; COMPLEX ; COMPLEXES ; DNA ; SEQUENCE ; SEQUENCES ; antibodies ; antibody ; ARRANGEMENT ; ASSAY ; DNA microarray ; DNA microarray technology ; microarrays
    Abstract: While the deciphering of basic sequence information on a genomic scale is yielding complete genomic sequences in ever-shorter intervals, experimental procedures for elucidating the cellular effects and consequences of the DNA-encoded information become critical for further analyses. In recent years, DNA microarray technology has emerged as a prime candidate for the performance of many such functional assays. Technically, array technology has come a long way since its conception some 15 years ago, initially designed as a means for large-scale mapping and sequencing. The basic arrangement, however, could be adapted readily to serve eventually as an analytical tool in a large variety of applications. On their own or in combination with other methods, microarrays open up many new avenues of functional analysis. Copyright (C) 2003 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 18629015
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  • 2
    Abstract: RNA-binding proteins (RBPs) exert a broad range of biological functions. To explore the scope of RBPs across eukaryotic evolution, we determined the in vivo RBP repertoire of the yeast Saccharomyces cerevisiae and identified 678 RBPs from yeast and additionally 729 RBPs from human hepatocytic HuH-7 cells. Combined analyses of these and recently published data sets define the core RBP repertoire conserved from yeast to man. Conserved RBPs harbour defined repetitive motifs within disordered regions, which display striking evolutionary expansion. Only 60% of yeast and 73% of the human RBPs have functions assigned to RNA biology or structural motifs known to convey RNA binding, and many intensively studied proteins surprisingly emerge as RBPs (termed 'enigmRBPs'), including almost all glycolytic enzymes, pointing to emerging connections between gene regulation and metabolism. Analyses of the mitochondrial hydroxysteroid dehydrogenase (HSD17B10) uncover the RNA-binding specificity of an enigmRBP.
    Type of Publication: Journal article published
    PubMed ID: 26632259
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  • 3
    Keywords: CELLS ; EXPRESSION ; Germany ; SYSTEM ; GENE ; GENES ; GENOME ; HYBRIDIZATION ; microarray ; transcription ; DIFFERENTIATION ; validation ; TIME ; MACROPHAGES ; TRANSCRIPTION FACTOR ; INDUCTION ; NERVOUS-SYSTEM ; TRANSCRIPTION FACTORS ; IN-SITU ; ENCODES ; microarrays ; DESIGN ; Drosophila ; NUMBER ; genetics ; CENTRAL-NERVOUS-SYSTEM ; specificity ; expression profiling ; CELL-DIFFERENTIATION ; in situ hybridization ; SUBSET ; DEPENDENCE ; TARGET GENES ; function ; glial cells ; BARRIER FORMATION ; Drosophila embryogenesis ; EMBRYONIC NERVOUS-SYSTEM ; FATE ; gcm ; glial development ; glial genes ; IDENTIFIED NEUROBLASTS ; macrophage ; MOLECULAR MARKERS ; PROMOTING FACTOR ; SEPTATE JUNCTION
    Abstract: In the central nervous system of Drosophila, the induction of the glial cell fate is dependent on the transcription factor glial cells missing (gcm). Though a considerable number of other genes have been shown to be expressed in all or in subsets of glial cells, the course of glial cell differentiation and subtype specification is only poorly understood. This prompted us to design a whole genome microarray approach comparing gem gain-of-function and, for the first time, gem loss-of-function genetics to wildtype in time course experiments along embryogenesis. The microarray data were analyzed with special emphasis on the temporal profile of differential regulation. A comparison of both experiments enabled us to identify more than 300 potential gcm target genes. Validation by in situ hybridization revealed expression in glial cells, macrophages, and tendon cells (all three cell types depend on gem) for 70 genes, of which more than 50 had been unknown to be under gem control. Eighteen genes are exclusively expressed in glial cells, and their dependence on gem was confirmed in situ. Initial considerations regarding the role of the newly discovered glial genes are discussed based on gene ontology and the temporal profile and subtype specificity of their expression. This collection of glial genes provides an important basis for the clarification of the genetic network controlling various aspects of glial development and function. (c) 2006 Elsevier Inc. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 16762338
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  • 4
    Abstract: BACKGROUND: Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. RESULTS: We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel) and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. CONCLUSION: Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.
    Type of Publication: Journal article published
    PubMed ID: 17181856
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  • 5
    Keywords: APOPTOSIS ; CELLS ; GROWTH ; SURVIVAL ; CELL ; GENE ; GENES ; GENOME ; GENOME SEQUENCE ; PROTEIN ; RNA ; CULTURED-CELLS ; SEQUENCE ; SEQUENCES ; CELL-SURVIVAL ; MUTANT ; IDENTIFICATION ; ASSAY ; Drosophila ; NUMBER ; leukemia ; DATABASE ; PHENOTYPE ; acute myeloid leukemia ; CELL-GROWTH ; ALLELE ; CELL-VIABILITY ; ELEGANS ; INTERFERENCE ; SCALE
    Abstract: A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale
    Type of Publication: Journal article published
    PubMed ID: 14764878
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  • 6
    Keywords: AB-INITIO ; EXPRESSION ; COMBINATION ; evaluation ; Germany ; human ; GENE ; GENES ; GENOME ; GENOME SEQUENCE ; HYBRIDIZATION ; microarray ; PROTEIN ; transcription ; validation ; DNA ; FAMILY ; PROTEIN FAMILIES ; PROTEIN FAMILY ; BIOLOGY ; SEQUENCE ; SEQUENCES ; DISCOVERY ; IDENTIFICATION ; IN-SITU ; DESIGN ; Drosophila ; DROSOPHILA-MELANOGASTER ; MELANOGASTER ; NUMBER ; DATABASE ; HUMAN GENOME ; RT-PCR ; PREDICTION ; MICROARRAY ANALYSIS ; PROJECT ; max ; RESOURCE ; ANOPHELES-GAMBIAE ; SYSTERS
    Abstract: Background: While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software.Results: Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly.Conclusions: The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species
    Type of Publication: Journal article published
    PubMed ID: 14709175
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  • 7
    Keywords: Germany ; COMMON ; GENOME ; microarray ; chromosome ; AMPLIFICATION ; Drosophila ; DROSOPHILA-MELANOGASTER ; MELANOGASTER ; PCR ; LENGTH ; PROJECT ; RESOURCE ; LIBRARIES
    Abstract: On the basis of shotgun subclone libraries used in the sequencing of the Drosophila melanogaster genome, a minimal tiling path of subclones across much of the genome was determined. About 320,000 shotgun clones for chromosomes X(12-20), 2R, 2L, 3R, and 4 were available from the Berkeley Drosophila Genome Project. The clone inserts have an average length of 3.4 kb and are amenable to standard PCR amplification. The resulting tiling path covers 86.2% of chromosome X(12-20), 86.2% of chromosomal arm 2R, 79.0% of 2L, 89.6% of 3R, and 80.5% of chromosome 4. In total, the 25,135 clones represent 76.7 Mb-equivalent to about 67% of the genome-and would be suitable for producing a microarray on a single slide
    Type of Publication: Journal article published
    PubMed ID: 15335221
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  • 8
    ISSN: 1432-1041
    Keywords: stereoisomers ; α-blockade ; β-blockade ; carvedilol
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary The racemic compound carvedilol possesses two complementary pharmacological effects, vasodilation and β-blockade. TheR- andS-enantiomers of carvedilol and the racemate were investigated with respect to the β-blocking, vasodilating, and hypotensive actions. In agreement with results obtained with other β-blockers, only theS-enantiomer of carvedilol exerts β-blocking effects. In contrast, no substantial difference between the enantiomers could be seen with respect to α-blockade. The greater hypotensive activity ofS-carvedilol may be attributed to β-blockade, which inhibits counter-regulatory mechanisms provoked by vasodilation. From these results it is concluded that there is a rationale for using carvedilol as the racemate. Using theS-enantiomer would lead to relatively strong β-blockade with only a weak vasodilating effect. TheR-enantiomer alone would act only as a hypotensive agent without β-blockade.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-1041
    Keywords: carvedilol ; nitrendipine ; antihypertensive treatment ; elderly patients ; essential hypertension
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary Carvedilol and nitrendipine were given for 12 weeks in a double-blind study to 81 elderly patients (≥ 60 years) with essential hypertension. The effects on blood pressure were measured (Riva Rocci) before medication and after 2 h with the patient in a lying and standing position after 4 weeks of placebo therapy as well as after 4, 8 and 12 weeks of treatment. Carvedilol (25 mg/o. d.) reduced blood pressure measured in the supine and erect position very successfully, similar to the reduction achieved with nitrendipine (20 mg/o. d.), without influencing the pulse rate. Both substances were well tolerated. Carvedilol is an alternative substance for lowering high blood pressure in elderly hypertensive patients.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-0827
    Keywords: Key words: Bisphosphonates — Estrogens — Conjugates — Osteoporosis therapy.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract. In order to target 17β-estradiol directly at bone we synthesized three 17β-estradiol-bisphosphonate conjugates (E2-BPs) with different esterase-sensitive linkers between both molecular moieties. The systemic administration of these compounds should result primarily in local estrogenic effects on bone with no or negligible systemic hormonal effects. Only if a considerable margin exists between the doses required for inhibition of bone loss and those for systemic hormonal effects can such a pro-drug be considered acceptable for patients refusing systemic estrogen replacement therapy for several reasons. The conjugates were tested in vitro for their 17β-estradiol release in rat serum and in vivo for their local and systemic effects in rats: in vitro, the conjugates expressed cleavage resistance, low cleavage (4.8%), or high cleavage (33.1%) within 48 hours of incubation. The conjugate with the low-cleavage doubled 17β-estradiol serum half-life (3.78 hours) whereas the high-cleavage conjugate resulted in approximately four times higher serum half-life (8.36 hours) when compared with free 17β-estradiol. In ovariectomized rats, bone loss was optimally prevented by 50 nmol/kg/day of 17β-estradiol when administered S.C. over a period of 5 weeks, and protection against uterine atrophy was achieved at doses as low as 5 nmol/kg/day. The cleavage-resistant conjugate was ineffective in preserving bone and uterus in doses ranging from 5 to 150 nmol/kg/day. The other two E2-BPs revealed a dose-dependent inhibition of bone loss which was paralleled by the respective uterus weight with a dose range of 1.5–150 nmol/kg/day being fully effective in a range similar to 17β-estradiol alone. The higher sensitivity of the uterus versus bone to protective estrogenic effects (1:10) was abolished by the conjugates. We conclude that E2-BPs containing esterase-sensitive linkers failed to act as bone-seeking pro-drugs expressing primarily local effects on bone without systemic effects.
    Type of Medium: Electronic Resource
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