Van Eyk, Dunn - Proteomic and Genomic Analysis of Cardiovascular Disease - 2003 (522919), страница 71
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K. Owens, L. Karlsson, E. S. M. Lutz,L. I. Andersson. ‘Molecular imprintingfor bio-and pharmaceutical analysis.’Trac-Trends in Analytical Chemistry 1999,18, 146–154.T. Takeuchi, D. Fukuma, J. Matsui.‘Combinatorial molecular imprinting: anapproach to synthetic polymer receptors.’Analytical Chemistry 1999, 71, 285–290.W. M.
Mullett, E. P. C. Lai. ‘Molecularlyimprinted solid phase extraction microcolumn with differential pulsed elutionfor theophylline determination.’ Microchemical Journal 1999, 61, 143–155.A. S. Blawas, W. M. Reichert. ‘Proteinpatterning.’ Biomaterials 1998, 19, 595–609.D. Stoll et al.
‘Protein microarray technology.’ Frontiers in Bioscience 2002, 7,C13–C32.C. D. Hodneland, Y. S. Lee, D. H. Min,M. Mrksich. ‘Selective immobilizationof proteins to self-assembled monolayerspresenting active site-directed capture ligands.’ Proceedings of the National Academy of Sciences of the United States ofAmerica 2002, 99, 5048–5052.C. Williams, T. A. Addona. ‘The integration of SPR biosensors with mass spectrometry: possible applications for proteome analysis.’ Trends in Biotechnology2000, 18, 45–48.A.
P. Turner. ‘Array of hope for biosensors in Europe.’ Nature Biotechnology1998, 16, 824.14.7 References166 C. Ziegler, W. Gopel. ‘Biosensor devel-167168169170171172173174175176opment.’ Curr Opin Chem Biol 1998, 2,585–91.R. Vankova et al. ‘Comparison of oriented and random antibody immobilizationin immunoaffinity chromatography of cytokinins.’ Journal of Chromatography a1998, 811, 77–84.S. Kanno, Y.
Yanagida, T. Haruyama, E.Kobatake, M. Aizawa. ‘Assembling ofengineered IgG-binding protein on goldsurface for highly oriented antibody immobilization.’ Journal of Biotechnology2000, 76, 207–214.J. F. Mooney et al. ‘Patterning of functional antibodies and other proteins byphotolithography of silane monolayers.’Proceedings of the National Academy ofSciences of the USA 1996, 93, 12287–12291.L. C. ShriverLake et al. ‘Antibody immobilization using heterobifunctional crosslinkers.’ Biosensors & Bioelectronics 1997,12, 1101–1106.K. Nakanishi, H.
Muguruma, I. Karube. ‘A novel method of immobilisingantibodies on a quartz crystal microbalance using plasma-polymerized films forimmunosensors.’ Analytical Chemistry1996, 68, 1695–1700.D. Guschin et al. ‘Manual manufacturing of oligonucleotide, DNA, and proteinmicrochips.’ Analytical Biochemistry 1997,250, 203–211.B. P. Gaber, B. D. Martin, D. C. Turner.‘Create a protein microarray using a hydrogel ‘stamper’.’ Chemtech 1999, 29, 29–24.A. Roda, M. Guardigli, C. Russo, P.Pasini, M. Baraldini. ‘Protein microdeposition using a conventional ink-jetprinter.’ Biotechniques 2000, 28, 492–496.R.
S. Kane, S. Takayama, E. Ostuni,D. E. Ingber, G. M. Whitesides. ‘Patterning proteins and cells using softlithography.’ Biomaterials 1999, 20, 2363–2376.V. N. Morozov, T. Y. Morozova. ‘Electrospray deposition as a method for massfabrication of mono- and multicomponent microarrays of biological and biologically active substances.’ AnalyticalChemistry 1999, 71, 3110–3117.177 E. Southern, K. Mir, M. Shchepinov.178179180181182183184185186187188‘Molecular interactions on microarrays.’Nature Genetics 1999, 21, 5–9.S. Granjeaud, F.
Bertucci, B. R. Jordan. ‘Expression profiling: DNA arraysin many guises.’ Bioessays 1999, 21, 781–790.A. Schulze, J. Downward. ‘Navigatinggene expression using microarrays – atechnology review.’ Nature Cell Biology2001, 3, E190–E195.V. G. Cheung et al. ‘Making and readingmicroarrays.’ Nature Genetics 1999, 21,15–19.S. SinghGasson et al. ‘Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array.’ Nature Biotechnology 1999, 17, 974–978.T. Takeuchi, J.
Matsui. ‘Miniaturizedmolecularly imprinted continuous polymer rods.’ Hrc-Journal of High ResolutionChromatography 2000, 23, 44–46.L. A. Tempelman, K. D. King, G. P. Anderson, F. S. Ligler. ‘Quantitating Staphylococcal enterotoxin B in diverse media using a portable fibre-optic biosensor.’ Analytical Biochemistry 1996, 233,50–57.H. Yu, A. W. Kusterbeck, M. J. Hale,F. S.
Ligler, J. P. Whelan. ‘Use of theUSDT flow immunosensor for quantification of benzoylecgonine in urine.’ Biosensors and Bioelectronics 1996, 11, 725–734.U. Narang, P. R. Gauger, A. W. Kusterbeck, F. S. Ligler. ‘Multianalyte detection using a capillary-based flow immunosensor.’ Analytical Biochemistry 1998,255, 13–19.E. Gizeli, C.
R. Lowe. ‘Immunosensors.’Current Opinion in Biotechnology 1996, 7,66–71.L. Laricchia-Robbio et al. ‘Mapping ofmonoclonal antibody- and receptor-binding domains on human granulocytemacrophage colony-stimulating factor(rhGM-CSF) using a surface plasmonresonance based biosensor.’ Hybridoma1996, 15, 343–350.T. P. Vikinge, A. Askendal, B.
Liedberg, T. Lindahl, P. Tengvall. ‘Immobilized chicken antibodies improve the25325414 Protein Chip Technologydetection of serum antigens with surfaceplasmon resonance (SPR).’ Biosensors andBioelectronics 1998, 13, 1257–1262.189 H. J. Watts, C. R. Lowe, D. V. PollardKnight.
‘Optical biosensor for monitoring microbial cells.’ Analytical Chemistry1994, 66, 2465–2470.190 J. Lahiri, L. Isaacs, J. Tien, G. M.Whitesides. ‘A strategy for the generation of surfaces presenting ligands forstudies of binding based on an active ester as a common reactive intermediate: Asurface plasmon resonance study.’ Analytical Chemistry 1999, 71, 777–790.191 T. B. Dubrovsky, Z. Hou, P.
Stroeve,N. L. Abbott. ‘Self-assembled monolayersformed on electroless gold deposited onsilica gel: a potential stationary phase forbiological assays.’ Analytical Chemistry1999, 71, 327–332.192 D. R. Baselt, G. U. Lee, K. M. Hanse,L. A. Chrisey, R. J. Colton. ‘A high-sensitivity micromachined biosensor.’ Proc.IEEE 1997, 85, 672–680.193 B.
A. Cornell et al. ‘A biosensor thatuses ion-channel switches.’ Nature 1997,387, 580–583.194 A. P. F. Turner. ‘Switching channelsmakes sense.’ Nature 1997, 387, 555–557.25515Recent Applications of Functional Proteomics:Investigations in Smooth Muscle Cell PhysiologyJustin A. MacDonald and Timothy A. J. Haystead15.1Introduction to Functional ProteomicsStudies on the proteome, the complete set of proteins that are encoded and expressed by a genome [1, 2], were initiated in the early 1970s with the goal of mapping the entire cellular protein complement. The purpose of this endevour,termed the human protein index, was to use 2-dimensional gel electrophoresis(2DE) to map and catalog all human proteins.
Unfortunately, technical limitationsprevented this project from progressing beyond an early-development stage. Itwas not until the mid to late 1990s when advances in bioinformatics, protein sequencing technologies, and the annotation of entire genomes permitted the “rebirth” of proteomic studies.
More powerful computers and software design hasdriven bioinformatics, more sensitive protein sequencing technologies were developed- first, Edman microsequencing from electroblotted proteins, and later, highlysensitive mass spectrometry methods. Finally, the enormous progress in characterizing the genomes of a wide variety of organisms has made proteomics the current buzz-word in biological studies.Although projects such as the human genome project are defining the genes involved in human disease, it is increasingly clear that this genetic information provides only a rudimentary beginning to unraveling the function of cells at the molecular level [3–5].
Proteins are not invariant products of genes, but are subject toa high degree of processing at the protein level that is a critical component of cellular function and regulation. Synthesis of mRNA is several steps removed fromthe cell phenotype. Message is subject to post-transcriptional control in the formof mRNA editing and/or alternative splicing. Regulation also occurs at the level ofprotein translation; many studies now show a poor correlation between mRNAlevels and protein expression levels. Quantification of mRNA (i.e.
with DNA micro-arrays) is not a direct reflection of the protein content or biological activity inthe cell [3, 6]. Finally, proteins are subject to numerous post-translational modifications (e.g. lipidation, proteolysis, phosphorylation, glycation, and oligomerization to name a few). Thus, although there may only be *30,000 human genes[7], there may well be 200,000 to 2 million human proteins once splice variantsand essential modifications following transcription are included [2].Proteomic and Genomic Analysis of Cardiovascular Disease.Edited by Jennifer E.
van Eyk, Michael J. DunnCopyright © 2003 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 3-527-30596-325615 Investigations in Smooth Muscle Cell PhysiologyFig. 15.1 The connectivity of biological studies. Biological information encoded in the genome is linked through the transcriptome andthe proteome to the metabolome. Multipleprotein isoforms (proteome) can be generated by RNA processing.
The mRNA population (transcriptome) can, in addition, be regu-lated by message stability and efficacy oftranslation. Post-translational processing canalter the protein’s biological activity and thereby alter the cellular concentration of metabolic substrates, products, and effectors (metabolome).Because the number of proteins can strongly exceed the number of genes, thegoal of assigning functional roles to all of these proteins is a daunting task. As aresult, the proteomics field has split into a few key approaches.15.1.1Expression Proteomics (Catalogue)A major undertaking to exhaustively map and identify all of the proteins in “thehuman proteome” in a fashion similar to genome sequencing projects continues.Post translational modifications and isoforms can potentially also be determined.This project will provide a functional annotation of the genome, integrating datawith genomic information to confirm the existence of putative gene products.15.1.2Functional Proteomics (Applied)Functional proteomics is a loosely appointed term that applies to the use of proteomic methods to monitor and analyze the spatial and temporal properties of themolecular networks and fluxes involved in living cells [8].
In practice, thisapproach allows for a select group of proteins to be studied and characterizedwith respect to a particular set of criteria (e.g. disease state, signaling pathway, orprotein/drug interaction). In contrast to the static genome, where all informationcould in principle be obtained from the DNA of a single cell, the proteome is dynamic and highly dependent not only on the type of cell, but also on the state ofthe cell. Expression proteomics will not provide adequate information to definethe molecular mechanisms of biological function. Integrated genomic and proteomic expression profiling may be able to define “the players”, but will not be ableto ascertain key elements which define their function in complex networks of pro-15.2 Proteomic Tools for Smooth Muscle Physiologiststein activities.
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