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Results for “Protein Array Analysis”

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At least 91 records · Page 5Linked to original sources
PubMed2003

The rapid detection of low molecular mass proteins differentially expressed under biological stress for four Helicobacter spp. using ProteinChip technology.

Helicobacter pylori is one of the most prevalent human pathogens in the world and is the aetiological agent of gastritis, peptic ulcer disease and gastric malignancies. In addition H. pylori and other novel members of the genus are capable of successfully colonising the bile-rich niche of the upper intestine and are associated with a diverse range of intestinal pathologies. Surface-enhanced laser desorption/ionisation-time of flight mass spectrometry was used to analyse surface extracts from H. pylori, Helicobacter bilis, Helicobacter pullorum and "Helicobacter sp. flexispira" to characterise cell surface changes following bile stress. The system detected two distinct response patterns to bile stress on the cell surface of Helicobacter spp. in vitro. The first involved the increase under bile stress of peaks at 7.6 and 7.9 kDa for H. billis and H. pullorum, respectively. In contrast both "Helicobacter sp. flexispira" and a clinical isolate of H. pylori had similar response profiles to bile stress. Both strains had at least three low mass peaks decreased under bile stress and a single peak induced by bile stress. The present study has established the use of ProteinChip(R) technology to analyse helicobacter-related proteomics. Specifically this study has established that different patterns are generated in response to bile stress among various pathogenic Helicobacter spp. which may give insights into the ability of these strains to colonise different niches.

Bile↗
PubMed2003

Optimizing antibody immobilization strategies for the construction of protein microarrays.

Antibody microarrays have the potential to revolutionize protein expression profiling. The intensity of specific signal produced on a feature of such an array is related to the amount of analyte that is captured from the biological mixture by the immobilized antibody (the "capture agent"). This in turn is a function of the surface density and fractional activity of the capture agents. Here we investigate how these two factors are affected by the orientation of the capture agents on the surface. We compare randomly versus specifically oriented capture agents based on both full-sized antibodies and Fab' fragments. Each comparison was performed using three different antibodies and two types of streptavidin-coated monolayer surfaces. The specific orientation of capture agents consistently increases the analyte-binding capacity of the surfaces, with up to 10-fold improvements over surfaces with randomly oriented capture agents. Surface plasmon resonance revealed a dense monolayer of Fab' fragments that are on average 90% active when specifically oriented. Randomly attached Fab's could not be packed at such a high density and generally also had a lower specific activity. These results emphasize the importance of attaching proteins to surfaces such that their binding sites are oriented toward the solution phase.

Animals↗
PubMed2003

Next-generation protein-handling method: puromycin analogue technology.

Puromycin is a well-known antibiotic that inhibits protein synthesis by competitive incorporation against an aminoacyl tRNA on the ribosome A site. Novel technology using this property of puromycin has been developed for convenient handling methods in protein research. Puromycin modified with another molecule is incorporated into a protein at the C-terminus, thus linking the desired molecule to the protein. Combination of in vitro translation with puromycin analogues has resulted in novel technologies such as display technology for screening, fluorescence labeling, affinity purification, and protein chip for proteomics.

Biotechnology↗
PubMed2003

Cytokine regulation by peroxisome proliferator-activated receptor gamma in human endometrial cells.

OBJECTIVE: To determine whether peroxisome proliferator-activated receptor (PPAR)-gamma ligands can affect the expression of interleukin-6 (IL-6) and cytokines related to the pathogenesis of endometriosis. DESIGN: In vitro study to determine whether PPARs are expressed in human endometrial cells and determine the effects of various PPAR-gamma ligands on IL-6 and other cytokine expression in these cells. SETTING: Academic medical center. PATIENT(S): Women presenting for infertility workup. INTERVENTION(S): Endometrial cell cultures were treated with PPAR-gamma ligands. MAIN OUTCOME MEASURE(S): Interleukin-6, IL-8, colony stimulating factor-1 (CSF-1) and macrophage chemotactic factor (MCP-1) protein secretion, messenger RNA expression of IL-6, PPAR-alpha, -beta, and -gamma. RESULT(S): Using a human endometrial cell line (EM42), as well as primary stromal and epithelial endometrial cells, we show the presence of PPAR-alpha, -beta, and -gamma by reverse transcription-polymerase chain reaction (RT-PCR) in these cells. PPAR-gamma ligands stimulated IL-6 secretion and induced enhancement of IL-6 mRNA levels. These ligands also stimulated the secretion of IL-8 and CSF-1. CONCLUSION(S): PPAR-gamma may play a role in the pathogenesis of endometriosis related to the production of IL-6 and some other cytokines.

Benzophenones↗
PubMed2003

Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications.

The performance of protein and antibody microarrays is dependent on various factors, one of which is the use of an appropriate microarray surface for the immobilisation of either protein or antibody samples. We have investigated the properties of seven new surfaces in the context of both protein and antibody microarray technology. We have demonstrated the functionality of all new slide coatings and investigated the mean signal to spotted concentration ratio, determined detection limits and calculated coefficients of variation. Moreover, new concepts for slide coatings such as dendrimer and poly(ethylene glycol)-epoxy slides were evaluated and improved qualities of novel slide surfaces were observed. Optimal slide coatings for antibody and protein chips were proposed and the requirements for both technologies were discussed.

Antibodies↗
PubMed2003

Expression of soluble recombinant proteins in a cell-free system using a 96-well format.

For structural and functional genomics programs, new high-throughput methods to obtain well-expressing and highly soluble proteins are essential. Here, we describe a rapid procedure to express recombinant proteins in an Escherichia coli cell-free system using a 96-well format. The identification of soluble proteins is performed by the Dot Blot procedure using an anti-His tag antibody. The applications and the automation of this method are described.

Cell-Free System↗
PubMed2003

Isolating ligands specific for human vasculature using in vivo phage selection.

The endothelium lining blood vessels expresses molecules that are restricted in their expression to a particular tissue or organ. These molecules are attractive targets for therapy and diagnosis because they allow agents to be delivered specifically to the blood vessels supplying the desired tissue. However, it is difficult to identify these tissue-specific molecules because endothelium loses much of its tissue-specific nature when it is removed from the organ. This can be overcome by using in vivo phage selection - injecting libraries of phage bearing antibodies or peptides into an animal and isolating phage that bind to the relevant tissue. A variation on this approach, in which in vivo phage selection is performed in animals bearing human tissue xenografts, allows the isolation of peptides (and presumably other molecules) specific for human vasculature.

Animals↗
PubMed2003

Antibodies in proteomics II: screening, high-throughput characterization and downstream applications.

There are many ways in which the use of antibodies and antibody selection can be improved and developed for high-throughput characterization. Standard protocols, such as immunoprecipitation, western blotting and immunofluorescence, can be used with antibody fragments generated by display technologies. Together with novel approaches, such as antibody chips and intracellular immunization, these methods will yield useful proteomic data following adaptation of the protocols for increased reliability and robustness. To date, most work has focused on the use of standard, well-characterized commercial antibodies. Such protocols need to be adapted for broader use, for example, with antibody fragments or other binders generated by display technologies, because it is unlikely that traditional approaches will provide the required throughput.

Antibodies↗
PubMed2002

Dimensionality is the issue: use of photoaptamers in protein microarrays.

The development of high-density arrays for proteomics has become a goal of SomaLogic, many other companies, and a wide variety of academic entities. Unfortunately, the word proteomics has come to mean virtually everything. We define proteomics as being derived from arrays of analyte-specific reagents (ASRs) used to measure (something about) proteins. As the density of the ASRs on a chip increases toward the number of proteins in an organism, the concept of proteomics moves toward comprehensive proteomics. At issue then, is what constitutes an ASR, and what differences between them lead toward more or less biological information from a high-density panel of ASRs.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2002

Peptide arrays: from macro to micro.

Over the past decade of proteome research peptide arrays have become a widespread and powerful tool to study molecular recognition events and to identify biologically active peptides. A variety of applications such as epitope mapping, characterisation of protein-protein interactions, enzyme-substrate or inhibitor interactions, and many more, have been published. Today's technologies for array production, inspired by DNA chips, have recently turned to the miniaturisation of peptide arrays. These advances open up an expanding spectrum of applications and the information obtained will be well-suited to developing substrates and inhibitors for diagnostic and therapeutic purposes.

Anti-Bacterial Agents↗
PubMed2002

Developing site-specific immobilization strategies of peptides in a microarray.

In peptide-based microarrays, most existing methods do not allow for site-specific immobilization of peptides on the glass surface. We have developed two new approaches for site-specific immobilization of kinase substrates onto glass slides: (1) slides were functionalized with avidin for attachment of biotinylated peptides; and (2) slides were functionalized with thioester for attachment of N-terminally cysteine-containing peptides via a native chemical ligation reaction.

Amino Acid Sequence↗
PubMed2002

Directed evolution of high-affinity antibody mimics using mRNA display.

We constructed a library of >10(12) unique, covalently coupled mRNA-protein molecules by randomizing three exposed loops of an immunoglobulin-like protein, the tenth fibronectin type III domain (10Fn3). The antibody mimics that bound TNF-alpha were isolated from the library using mRNA display. Ten rounds of selection produced 10Fn3 variants that bound TNF-alpha with dissociation constants (K(d)) between 1 and 24 nM. After affinity maturation, the lowest K(d) measured was 20 pM. Selected antibody mimics were shown to capture TNF-alpha when immobilized in a protein microarray. 10Fn3-based scaffold libraries and mRNA-display allow the isolation of high-affinity, specific antigen binding proteins; potential applications of such binding proteins include diagnostic protein microarrays and protein therapeutics.

Amino Acid Sequence↗
PubMed2003

Immobilized peptides as high-affinity capture agents for self-associating proteins.

There is currently great interest in the fabrication of protein-detecting arrays comprised of large numbers of immobilized protein capture agents. While most efforts in this arena have focused on the use of biomolecules such as antibodies and nucleic acid aptamers as capture agents, synthetic species have many potential advantages. However, synthetic molecules isolated from combinatorial libraries generally do not bind target proteins with the high affinity necessary for array applications. Here, we demonstrate that simple linear peptides bind dimeric proteins tenaciously when immobilized, although they exhibit only modest affinity in solution. These data show that high-affinity bidentate capture agents for dimeric proteins can be created by simply immobilizing modest-affinity ligands on a surface at high density, bypassing the requirement for careful optimization of linker length and geometry that is normally required to create a high-affinity solution bidentate ligand.

Combinatorial Chemistry Techniques↗
PubMed2003

Protein chip technology.

Microarray technology has become a crucial tool for large-scale and high-throughput biology. It allows fast, easy and parallel detection of thousands of addressable elements in a single experiment. In the past few years, protein microarray technology has shown its great potential in basic research, diagnostics and drug discovery. It has been applied to analyse antibody-antigen, protein-protein, protein-nucleic-acid, protein-lipid and protein-small-molecule interactions, as well as enzyme-substrate interactions. Recent progress in the field of protein chips includes surface chemistry, capture molecule attachment, protein labeling and detection methods, high-throughput protein/antibody production, and applications to analyse entire proteomes.

Protein Array Analysis↗
PubMed2002

Affinity-capture reagents for protein arrays.

The simultaneous identification and quantitative measurement of the production levels of thousands of different proteins in a biological specimen remains an unachieved goal of modern proteomic research. Advances in the development of microarray-based platforms for highly parallel detection of proteins have therefore received a considerable impulse during the last few years. Here, we review the existing reagents for affinity capture of protein targets, as well as the techniques used for their immobilization on solid supports and methods for the detection of binding events, underlining the problems and the opportunities in this continuously evolving research field.

Biotechnology↗
PubMed2002

A microarray immunoassay for simultaneous detection of proteins and bacteria.

We report the development and characterization of an antibody microarray biosensor for the rapid detection of both protein and bacterial analytes under flow conditions. Using a noncontact microarray printer, biotinylated capture antibodies were immobilized at discrete locations on the surface of an avidin-coated glass microscope slide. Preservation of capture antibody function during the deposition process was accomplished with the use of a low-salt buffer containing sucrose and bovine serum albumin. The slide was fitted with a six-channel flow module that conducted analyte-containing solutions over the array of capture antibody microspots. Detection of bound analyte was subsequently achieved using fluorescent tracer antibodies. The pattern of fluorescent complexes was interrogated using a scanning confocal microscope equipped with a 635-nm laser. This microarray system was employed to detect protein and bacterial analytes both individually and in samples containing mixtures of analytes. Assays were completed in 15 min, and detection of cholera toxin, staphylococcal enterotoxin B, ricin, and Bacillus globigii was demonstrated at levels as low as 8 ng/mL, 4 ng/mL, 10 ng/mL, and 6.2 x 10(4) cfu/mL, respectively. The assays presented here are very fast, as compared to previously published methods for measuring antibody-antigen interactions using microarrays (minutes versus hours).

Animals↗
PubMedDate not supplied

Antibody detection in human serum using a versatile protein chip platform constructed by applying nanoscale self-assembled architectures on gold.

We report a novel high-throughput (HTP) protein chip platform, constructed on gold using self-assembly techniques, for conducting high quality antigen-antibody interactions. Biotinylated monolayers were used to immobilize a streptavidin surface with high packing density. This biocompatible platform was then used for detection of serum IgM antibodies. Serum samples of patients suspected to suffer from Lyme borreliosis were used to validate the protein chip platform using biotinylated peptide AAOspC8 molecules as the test probes. Various experimental parameters such as the effect of concentration of probes, targets, temperature of incubation, and their effect on the resulting signal-to-noise ratio are described in detail. Highly specific protein interaction data with a high signal-to-noise ratio were obtained with serum sample solutions as low as 1 microL/spot (1/10 diluted).

Antibodies, Bacterial↗