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BIOTECHNIQUES 2006年第5期41卷 529-+页

作者： Walt, David R. Tufts Univ Medford MA 02155 USA

Optical fiber arrays provide a powerful substrate for creating high-density sensing systems that can address a variety of biological problems. The fiber substrate can be used, to create femtoliter wells that can be loaded with individual beads to create high-density arrays for multiplexed screening and analysis. In addition, living cells can be loaded into the arrays, and their individual responses monitored cover long time periods, enabling functional screening of biologically active compounds. Adherent cells can be attached to the fiber substrate to provide a rapid method for observing cell migration and for screening anti-migratory compounds. Finally, individual enzyme molecules can be loaded into the array wells enabling single molecule detection via enzyme-catalyzed signal amplification.

关键词： Animals Biosensing Techniques/methods Cell Movement Fiber Optic Technology Humans microarray analysis/methods Oligonucleotide Array Sequence analysis Optical Fibers

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microarrays of synthetic heparin oligosaccharides

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2006年第9期128卷 2766-2767页

作者： de Paz, JL Noti, C Seeberger, PH Swiss Fed Inst Technol ETH Zurich Organ Chem Lab CH-8093 Zurich Switzerland

We present the first preparation of microarrays containing synthetic heparin oligosaccharides in order to elucidate the heparin−protein interactions involved in a variety of biological processes. For this purpose, we have developed a novel linker strategy that is compatible with the protecting-group manipulations required for the synthesis of the highly sulfated oligosaccharides and can also be extended to an automated solid phase approach. Strategic placement of the orthogonally protected amine linker was key to the success of the array construction. These heparin chips allow for the high-throughput screening of oligosaccharides by using picomoles of protein. The potential of the new method was demonstrated by probing the carbohydrate affinity of two heparin-binding growth factors, FGF-1 and FGF-2, that are implicated in the development and differentiation of several tumors.

关键词： Carbohydrate Sequence Fibroblast Growth Factor 1/analysis Fibroblast Growth Factor 2/analysis Heparin/analogs & derivatives Heparin/chemical synthesis Heparin/chemistry microarray analysis/methods Molecular Sequence Data Oligosaccharides/chemical synthesis Oligosaccharides/chemistry

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Building addressable libraries: The use of a mass spectrometry cleavable linker for monitoring reactions on a microelectrode array

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2006年第50期128卷 16020-16021页

作者： Chen, Ceng Nagy, Gabriella Walker, Amy V. Maurer, Karl McShea, Andy Moeller, Kevin D. Washington Univ Dept Chem St Louis MO 63130 USA CombiMatrix Corp Mukilteo WA 98275 USA

Time-of-flight secondary ion mass spectrometry (TOF SIMS) has been used in conjunction with a mass spectrometry cleavable linker to determine the percent conversion of reactions that were conducted site-selectively on an addressable microelectrode array. When combined with fluorescence techniques for analysis of the reactions, the TOF SIMS experiment provides a means for optimization of both reaction confinement and reaction efficiency on the microelectrode arrays.

关键词： Calibration Cross-Linking Reagents/chemistry Databases, Factual Electrodes Mass Spectrometry/methods microarray analysis/methods Molecular Structure Oxidation-Reduction

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Spreading and segregation of lipids in air-stable lipid microarrays

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2006年第10期128卷 3158-3159页

作者： Fang, Y Corning Inc Biochem Technol Div Sci & Technol Corning NY 14831 USA

As a result of heterogeneous spreading of distinct lipids within the same microspots of air-stable lipid microarrays, ganglioside GM1 tends to segregate and thus enrich within the center area of microspots where being... 详细信息

As a result of heterogeneous spreading of distinct lipids within the same microspots of air-stable lipid microarrays, ganglioside G_M1 tends to segregate and thus enrich within the center area of microspots where being predetermined by the quill pin used for array fabrication, as indicated by the binding pattern of fluorescein−cholera toxin subunit B.

关键词： Air Biotin/chemistry Cholera Toxin/chemistry Gangliosides/chemistry Lipids/chemistry microarray analysis/methods Phosphatidylethanolamines/chemistry Streptavidin/chemistry Surface Properties

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MAMMOT - a set of tools for the design, management and visualization of genomic tiling arrays

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BIOINFORMATICS 2006年第7期22卷 883-884页

作者： Ryder, E Jackson, R Ferguson-Smith, A Russell, S Univ Cambridge Dept Genet Cambridge CB2 3EH England Univ Cambridge Dept Anat Cambridge CB2 3DY England

Summ.: The MAMMOT software suite is a collection of Perl and PHP scripts for designing, annotating and visualizing genome tiling arrays to, for example, facilitate studies into the epigenetics of gene regulation. The web design allows rapid experimental data entry from multiple users, and results can easily be shared between groups and individuals.

关键词： Animals Chromosome Mapping/methods Computational Biology Database Management Systems Drosophila Information Dissemination/methods Internet Mice microarray analysis/methods Software User-Computer Interface

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The daunting process of MIAME

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NATURE 2006年第7115期444卷 31-31页

作者： Galbraith, David W. Univ Arizona Bio5 Inst Tucson AZ 85721 USA Univ Arizona Dept Plant Sci Tucson AZ 85721 USA

A letter to the editor on 'Quality control' published in the Vol. 442, of the issue 2006 is presented.

关键词： Arabidopsis/genetics Arabidopsis/genetics microarray analysis/methods microarray analysis/standards Quality Control Reproducibility of Results

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Disposable microfluidic devices: fabrication, function, and application

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BIOTECHNIQUES 2005年第3期38卷 429-446页

作者： Fiorini, GS Chiu, DT Univ Washington Dept Chem Seattle WA 98195 USA

This review article describes recent developments in microfluidics, with special emphasis on disposable plastic devices. Included is an overview of the common methods used in the fabrication of polymer microfluidic systems, including replica and injection molding, embossing, and laser ablation. Also described are the different methods by which on-chip operations-such as the pumping and valving of fluid flow, the mixing of different reagents, and the separation and detection of different chemical species-have been implemented in a microfluidic format. Finally, a few select biotechnological applications of microfluidics are presented to illustrate both the utility of this technology and its potential for development in the future.

关键词： Biosensing Techniques/instrumentation Biosensing Techniques/methods Biosensing Techniques/trends Chemistry, Analytical/instrumentation Chemistry, Analytical/methods Chemistry, Analytical/trends Disposable Equipment Equipment Design Equipment Failure analysis microarray analysis/instrumentation microarray analysis/methods microarray analysis/trends Microfluidic Analytical Techniques/instrumentation Microfluidic Analytical Techniques/methods Microfluidic Analytical Techniques/trends Technology Assessment, Biomedical

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Fluorous-based carbohydrate microarrays

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2005年第38期127卷 13162-13163页

作者： Ko, KS Jaipuri, FA Pohl, NL Iowa State Univ Dept Chem Ames IA 50011 USA Iowa State Univ Inst Plant Sci Ames IA 50011 USA

The success of microarrays,such as DNA chips,for biosample screening withminimal sample usage has led to a variety of technologies for assays on ***,for small molecules,such as sugars,these methods usually rely on covalent bondformation,which requires unique functional handles and multiple chemical ***,we present anew simpler concept in microarray formation that is based on noncovalent fluorous-based interactionsand demonstrate the strength of these interactions in the direct formation of carbohydratemicroarrays for biological screening.

关键词： Carbohydrate Conformation Carbohydrates/analysis Carbohydrates/chemistry Humans Hydrocarbons, Fluorinated/chemistry Male microarray analysis/methods Surface Properties

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Genome-wide transcriptional changes associated with enhanced activity in the Drosophila nervous system

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NEURON 2005年第1期48卷 91-107页

作者： Guan, Z Saraswati, S Adolfsen, B Littleton, JT MIT Picower Inst Learning & Memory Dept Biol Cambridge MA 02139 USA MIT Picower Inst Learning & Memory Dept Brain & Cognit Sci Cambridge MA 02139 USA

Neuronal plasticity is an important feature of the developing brain and requires neuronal circuits to reconfigure their functional connectivity depending upon activity patterns. To explore changes in neuronal function that occur downstream of altered activity, we performed an expression analysis in Drosophila mutants with acute or chronic alterations in neuronal activity. We find that seizure induction leads to an over-proliferation of synaptic connections, indicating that activity-dependent neuronal rewiring occurs in Drosophila. To analyze transcriptional recoding during altered neuronal activity, we performed genome-wide DNA microarray analysis following multiple seizure induction and recovery paradigms. Approximately 250 genes implicated in cell adhesion, membrane excitability, and cellular signaling are differentially regulated, including the Kek 2 neuronal cell adhesion protein, which, as we demonstrate, functions as a regulator of synaptic growth. These data identify a collection of activity-regulated transcripts that may link changes in neuronal firing patterns to transcription-dependent modulation of brain function, including activity-dependent synaptic rewiring.

关键词： Action Potentials/genetics Action Potentials/physiology Animals Animals, Genetically Modified Animals, Genetically Modified Base Sequence Blotting, Western/methods Blotting, Western/methods Drosophila/metabolism Drosophila/physiology Drosophila Proteins/metabolism Drosophila Proteins/metabolism Drosophila Proteins/physiology Drosophila Proteins/physiology Gene Expression Regulation/physiology Genome Immunohistochemistry/methods Immunohistochemistry/methods Membrane Proteins/metabolism microarray analysis/methods Models, Neurological Muscles/physiology Nerve Tissue Proteins/metabolism Nervous System/metabolism Neuromuscular Junction/physiology Reverse Transcriptase Polymerase Chain Reaction/methods RNA, Messenger/metabolism Transcription, Genetic

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Oncogene regulation of tumor suppressor genes in tumorigenesis

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CARCINOGENESIS 2005年第2期26卷 487-494页

作者： Sung, J Turner, J McCarthy, S Enkemann, S Li, CG Yan, P Huang, T Yeatman, TJ Univ S Florida H Lee Moffitt Canc Ctr & Res Inst Dept Surg & Interdisciplinary Oncol Tampa FL 33612 USA Ohio State Univ Ctr Comprehens Canc Dept Mol Virol Columbus OH 43210 USA

We attempted to demonstrate whether there is an epigenetic link between oncogenes and tumor suppression genes in tumorigenesis. We designed a high throughput model to identify a candidate group of tumor suppressor genes potentially regulated by oncogenes. Gene expression profiling of mock-transfected versus v-src-transfected 3Y1 rat fibroblasts identified significant overexpression of DNA methyltransferase 1, the enzyme responsible for aberrant genome methylation, in v-src-transfected fibroblasts. Secondary microarray analyses identified a number of candidate tumor suppressor genes that were down-regulated by v-src but were also re-expressed following treatment with 5-aza-2'-deoxycytidine, a potent demethylating agent. This candidate group included both tumor suppressor genes that are known to be silenced by DNA hypermethylation and those that have not been previously identified with promoter hypermethylation. To further validate our model, we identified tsg, a tumor suppressor gene that was shown to be down-regulated by v-src and found to harbor dense promoter hypermethylation. Our model demonstrates a cooperative relationship between oncogenes and tumor suppressor genes mediated through promoter hypermethylation.

关键词： Animals Azacitidine/analogs & derivatives Azacitidine/pharmacology Cells, Cultured DNA Methylation/drug effects DNA Modification Methylases/metabolism Fibroblasts/metabolism Gene Expression Regulation, Neoplastic/drug effects Gene Expression Regulation, Neoplastic/physiology Genes, src/genetics Genes, Tumor Suppressor microarray analysis/methods Oncogenes Promoter Regions, Genetic/genetics Rats

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