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  • COMPLEXES  (14)
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  • 1
    Keywords: immunohistochemistry ; IN-SITU ; CARCINOMAS ; microarray ; COMPLEX ; COMPLEXES ; human ; carcinoma
    Type of Publication: Book chapter
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  • 2
    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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  • 3
    Keywords: CANCER ; Germany ; microarray ; PROTEIN ; COMPLEX ; COMPLEXES ; DNA ; TRANSPORT ; ASSAY ; microarrays ; DESIGN ; MIGRATION ; KINETICS ; sensitivity ; IMMOBILIZATION ; AFFINITY ; IMMUNOASSAYS ; PROTEOMICS ; PROTEIN MICROARRAYS ; surface chemistry ; DIFFUSION ; ANTIBODY MICROARRAYS ; SUPPORT MATERIALS ; LIMITED REACTION THEORY ; ROLLING-CIRCLE AMPLIFICATION ; SPECIMENS ; two-compartment model ; ambient analyte theory ; DNA HYBRIDIZATION ; mass transport ; protein expression profiling ; SURFACE-RECEPTORS
    Abstract: Although they are superficially similar to DNA microarrays, immunoassay microarrays represent a daunting technological challenge owing to the much wider diversity of proteins. Yet, as the leading edge of bioscience migrates from genomics to proteomics, the complexity and enormous dynamic range of proteins in a cell necessitate an analytic tool with exceptional specificity and sensitivity. In theory, microspot immunoassays could fulfill this need. However, antibody microarrays have had limited success to date, and have often required a highly sensitive detection system and/or sophisticated immobilization approach to be of any use for the profiling of complex specimens. There is a solid body of work on the theory of microspot reaction kinetics, yet much of the published experimental work on protein microarray development pays insufficient attention to the kinetic aspects of this interaction. This review explains that one of the main limitations for the sensitivity of current generation microspot immunoassays is the strong dependence of antibody microspot kinetics upon mass flux to the spot. This not only involves migration of analyte in solution, but also across the surface of the solid phase. Understanding of this effect will be discussed, along with several related effects and their significance to improving existing microarray designs. It is concluded that current efforts may be too focused on areas that cannot improve performance significantly, and that other critical areas of design should receive more attention. Finally, the review addresses the question of whether ambient analyte immunoassay is truly a separate category of microspot assay, with the conclusion that this may be a flowed concept
    Type of Publication: Journal article published
    PubMed ID: 16359272
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  • 4
    Keywords: CANCER ; EXPRESSION ; CELL ; Germany ; GENOME ; microarray ; PROTEIN ; PROTEINS ; PATIENT ; COMPLEX ; COMPLEXES ; QUALITY ; BIOLOGY ; antibodies ; antibody ; ASSAY ; microarrays ; DESIGN ; ARRAYS ; REPRODUCIBILITY ; CANCER-PATIENTS ; CANCER PATIENTS ; pancreatic cancer ; PROTEOMICS ; PROTEOMIC ANALYSIS ; SERUM ; FEATURES ; PANCREATIC-CANCER ; antibody microarray ; HEALTHY-SUBJECTS ; methods ; HUMAN PLASMA ; DEPLETION ; QUANTITATIVE PROTEOMICS ; proteomic ; ABUNDANCE PROTEINS ; BIOMARKER DISCOVERY
    Abstract: Antibody microarrays have the potential to enable comprehensive proteomic analysis of small amounts of sample material. Here, protocols are presented for the production, quality assessment, and reproducible application of antibody microarrays in a two-color mode with an array of 1,800 features, representing 810 antibodies that were directed at 741 cancer-related proteins. In addition to measures of array quality, we implemented indicators for the accuracy and significance of dual-color detection. Dual-color measurements outperform a single-color approach concerning assay reproducibility and discriminative power. In the analysis of serum samples, depletion of high-abundance proteins did not improve technical assay quality. On the contrary, depletion introduced a strong bias in protein representation. In an initial study, we demonstrated the applicability of the protocols to proteins derived from urine samples. We identified differences between urine samples from pancreatic cancer patients and healthy subjects and between sexes. This study demonstrates that biomedically relevant data can be produced. As demonstrated by the thorough quality analysis, the dual-color antibody array approach proved to be competitive with other proteomic techniques and comparable in performance to transcriptional microarray analyses.
    Type of Publication: Journal article published
    PubMed ID: 20164060
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  • 5
    Keywords: EXPRESSION ; evaluation ; Germany ; SUPPORT ; SYSTEM ; SYSTEMS ; DISEASE ; microarray ; PROTEIN ; STORAGE ; COMPLEX ; COMPLEXES ; MESSENGER-RNA ; IMPACT ; ANTIGEN ; ANTIGENS ; DISCOVERY ; antibodies ; antibody ; microarrays ; CANCER-CELLS ; SURFACE ; STABILITY ; FUNCTIONAL GENOMICS ; IMMOBILIZATION ; cross-linker ; glass slide ; IMMUNOASSAYS ; LINKED-IMMUNOSORBENT-ASSAY ; PROTEOMICS ; surface modification
    Abstract: Antibody microarrays could have an enormous impact on the functional analysis of cellular activity and regulation, especially at the level of protein expression and protein- protein interaction, and might become an invaluable tool in disease diagnostics. The array surface is bound to have a tremendous influence on the findings from such studies. Apart from the basic issue of how to attach antibodies optimally without affecting their function, it is also important that the cognate antigens, applied within a complex protein mixture, all bind to the arrayed antibodies irrespective of their enormous variety in structure. In this study, various factors in the production of antibody microarrays on glass support were analysed: the modification of the glass surface; kind and length of cross-linkers; composition and pH of the spotting buffer; blocking reagents; antibody concentration and storage procedures, in order to evaluate their effect on array performance. Altogether, data from more than 700 individual array experiments were taken into account. In addition to home- made slides, commercially available systems were also included in the analysis
    Type of Publication: Journal article published
    PubMed ID: 12627378
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  • 6
    Keywords: Germany ; INFORMATION ; SUPPORT ; GENE-EXPRESSION ; GENOME ; microarray ; PROTEIN ; PROTEINS ; MOLECULES ; COMPLEX ; COMPLEXES ; SEQUENCE ; MOLECULE ; ACID ; ACIDS ; antibodies ; antibody ; NUCLEIC-ACID ; NUCLEIC-ACIDS ; LTD ; EQUIVALENT ; ASSAY ; microarrays ; ARRAYS ; NUMBER ; SURFACE ; DIVERSITY ; sensitivity ; ATOMIC-FORCE MICROSCOPY ; CONSTRUCTION ; expression profiling ; glass slide ; IMMUNOASSAYS ; LINKED-IMMUNOSORBENT-ASSAY ; surface modification ; ANTIBODY IMMOBILIZATION ; ELECTROSPRAY DEPOSITION ; immunoassay ; METAL-OXIDE SURFACES ; ORIENTED IMMOBILIZATION ; POLY(ETHYLENE GLYCOL) ; POLY(L-LYSINE)-G-POLY(ETHYLENE GLYCOL) LAYERS ; protein interaction ; protein microarray ; PROTEIN MICROARRAYS ; surface chemistry
    Abstract: Stimulated by the achievements of the first phase in genomics and the resulting need of assigning functions to the acquired sequence information, novel formats of immunoassays are being developed for high-throughput multi-analyte studies. In principle, they are similar in nature to the microarray assays already established at the level of nucleic acids. However, the biochemical diversity and the sheer number of proteins are such that an equivalent analysis is much more complex and thus difficult to accomplish. The wide range of protein concentration complicates matters further. Performing microarray immunoassays already represents a challenge at the level of preparing a working chip surface. Arrays have been produced on filter supports, in microtiter plate wells and on glass slides, the last two usually coated with one-, two- or three-dimensionally structured surface modifications. The usefulness and suitability of all these support media for the construction and application of antibody microarrays are reviewed in this manuscript in terms of the different kinds of immunoassay and the various detection procedures. Additionally, the employment of microarrays containing alternative sensor molecules is discussed in this context. The sensitivity of microspot immunoassays predicted by the current analyte theory is not yet a reality, indicating the extent of both the technology's potential and the size of the task still ahead. Copyright (C) 2003 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 12898667
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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: CELLS ; BLOOD ; CELL ; evaluation ; Germany ; SYSTEM ; SYSTEMS ; GENOME ; microarray ; PROTEIN ; PROTEINS ; TIME ; COMPLEX ; COMPLEXES ; T cell ; T cells ; T-CELL ; T-CELLS ; BIOLOGY ; MOLECULAR-BIOLOGY ; LINKAGE ; SIGNAL ; cytokines ; antibodies ; antibody ; PERFORMANCE ; AMPLIFICATION ; MICROARRAY DATA ; microarrays ; DESIGN ; PLASMA ; CANCER-CELLS ; PARAMETERS ; Jun ; STRATEGIES ; sensitivity ; MICROARRAY ANALYSIS ; INTERFERON-GAMMA ; IMMUNOASSAYS ; PROTEOMICS ; CYTOKINE ; molecular biology ; molecular ; CHEMISTRY ; ELISA ; monitoring ; RHEUMATOID-ARTHRITIS ; antibody microarray ; CYTOKINE PRODUCTION ; LEVEL ; analysis ; methods ; ROLLING-CIRCLE AMPLIFICATION ; EXTENT ; SPECIMENS ; MATTER ; protein profiling ; microspot kinetics ; MASS-TRANSPORT ; quantitative ; detection strategies ; INTERLEUKIN-4 PRODUCTION ; PLASMA-PROTEOME ; TRITON X-100
    Abstract: Antibody microarrays have often had limited success in detection of low abundant proteins in complex specimens. Signal amplification systems improve this situation, but still are quite laborious and expensive. However, the issue of sensitivity is more likely a matter of kinetically appropriate microarray design as demonstrated previously. Hence, we re-examined in this study the suitability of simple and inexpensive detection approaches for highly sensitive antibody microarray analysis. N-hydroxysuccinimidyl ester (NHS)- and Universal Linkage System (ULS)-based fluorescein and biotin labels used as tags for subsequent detection with anti-fluorescein and extravidin, respectively, as well as fluorescent dyes were applied for analysis of blood plasma. Parameters modifying strongly the performance of microarray detection such as labeling conditions, incubation time, concentrations of anti-fluorescein and extravidin and extent of protein labeling were analyzed and optimized in this study. Indirect detection strategies whether based on NHS- or ULS-chemistries strongly outperformed direct fluorescent labeling and enabled detection of low abundant cytokines with many dozen-fold signal-to-noise ratios. Finally, particularly sensitive detection chemistry was applied to monitoring cytokine production of stimulated peripheral T cells. Microarray data were in accord with quantitative cytokine levels measured by ELISA and Luminex, demonstrating comparable reliability and femtomolar range sensitivity of the established microarray approach
    Type of Publication: Journal article published
    PubMed ID: 17474144
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  • 9
    Keywords: Germany ; GENE-EXPRESSION ; GENOME ; microarray ; PROTEIN ; COMPLEX ; COMPLEXES ; MOLECULE ; NUMBER ; MASS-SPECTROMETRY ; SURFACE ; PROJECT ; protein microarray ; SINGLE ; review ; RE ; TASK ; LABEL-FREE DETECTION ; PROJECTS ; SUPPORT MATERIALS ; CHIP ; high throughput ; HIGH-THROUGHPUT ; multiplex ; TECHNOLOGY ; antibody chip ; DNA INTERACTIONS ; FORMAT ; RECOMBINANT ANTIBODY FRAGMENTS ; sequencing
    Abstract: The success of genome sequencing projects has provided the basis for systematic analysis of protein function and has led to a shift from the description of single molecules to the characterization of complex samples. Such a task would not be possible without the provision of appropriate high-throughput technologies, such as protein microarray technology. In addition, the increasing number of samples necessitates the adaptation of such technologies to a multiplex format. This review will discuss protein microarray technology in the context of multiplex analysis and highlight its current prospects and limitations
    Type of Publication: Journal article published
    PubMed ID: 16097884
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  • 10
    Keywords: Germany ; GENE-EXPRESSION ; microarray ; COMPLEX ; COMPLEXES ; DNA ; MECHANISM ; mechanisms ; COMPARATIVE GENOMIC HYBRIDIZATION ; ASSAY ; DNA microarray ; microarrays ; ARRAYS ; TUMOR-SUPPRESSOR GENE ; PROTEIN MICROARRAYS ; POINT MUTATIONS ; GENE-EXPRESSION PATTERNS ; ASSAYS ; TECHNOLOGY ; PRIMER EXTENSION ; OLIGONUCLEOTIDE MICROARRAYS ; COSMID CLONES
    Abstract: Understanding complex functional mechanisms requires the global and parallel analysis of different cellular processes. DNA microarrays have become synonymous with this kind of study and, in many cases, are the obvious platform to achieve this aim. They have already made important contributions, most notably to gene-expression studies, although the true potential of this technology is far greater. Whereas some assays, such as transcript profiling and genotyping, are becoming routine, others are still in the early phases of development, and new areas of application, such as genome-wide epigenetic analysis and on-chip synthesis, continue to emerge
    Type of Publication: Journal article published
    PubMed ID: 16485019
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