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Two-dimensional Gels (two-dimensional + gel)
Terms modified by Two-dimensional Gels Selected AbstractsHigh-efficiency protein extraction from polyacrylamide gels for molecular mass measurement by matrix-assisted laser desorption/ionization-time of flight-mass spectrometryELECTROPHORESIS, Issue 6 2005Ya Jin Abstract A simple and fast method of protein extraction from Coomassie Brilliant Blue (CBB)-stained polyacrylamide gels suited for molecular mass measurement of proteins by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) is reported. Proteins in CBB-stained gel pieces were extracted by a 10-min soaking in 0.1,M NaOH at 25°C. The recovery of this one-step extraction method was 34,73% for proteins <67,kDa. CBB adduction to proteins during mass spectrometric analysis was avoided by a destaining step before the alkaline extraction. The molecular mass values of the extracted proteins coincided with those of purified proteins within ±0.01,0.10% deviation for all the proteins <36,kDa. Because of the high extraction recovery, mass measurement was possible for the proteins extracted from CBB-stained gels with loaded protein quantities as little as 34,ng for cytochrome,c, ,-lactalbumin, myoglobin, ,-lactoglobulin, trypsinogen, and carbonic anhydrase (12.4,29.0,kDa), 340,ng for glyceraldehyde-3-phosphate dehydrogenase (35.6,kDa) and albumin (66.3,kDa). This method provides a highly efficient approach to utilize CBB-stained one- or two-dimensional gels for whole protein analysis using MALDI-TOF-MS. [source] Comparison of fluorescent stains: Relative photostability and differential staining of proteins in two-dimensional gelsELECTROPHORESIS, Issue 15 2004Gary B. Smejkal Abstract The fluorescence of proteins stained with Deep Purple and SYPRO Ruby was measured over a time course of UV transillumination to determine the relative photostability of each stain. Mean spot fluorescence (n = 200 matched spots) in gels stained with Deep Purple decreased 27% following 2 min of UV transillumination, compared to SYPRO Ruby, which decreased 17%. After 19 min, an 83% decrease in Deep Purple fluorescence was observed, compared to 44% for SYPRO Ruby. By interpolation, the half-life of Deep Purple fluorescence was estimated to be approximately 6 min. The half-life of SYPRO Ruby fluorescence was not reached during the 19 min time course. Further, differential staining of proteins was observed in gels stained with Deep Purple and SYPRO Ruby as compared to colloidal Coomassie Brilliant Blue and silver staining. [source] Multiple polypeptide forms observed in two-dimensional gels of Methylococcus capsulatus (Bath) polypeptides are generated during the separation procedureELECTROPHORESIS, Issue 4 2003Frode S. Berven Abstract We have examined two-dimensional electrophoresis (2-DE) gel maps of polypeptides from the Gram-negative bacterium Methylococcus capsulatus (Bath) and found the same widespread trains of spots as often reported in 2-DE gels of polypeptides of other Gram-negative bacteria. Some of the trains of polypeptides, both from the outer membrane and soluble protein fraction, were shown to be generated during the separation procedure of 2-DE, and not by covalent post-translational modifications. The trains were found to be regenerated when rerunning individual polypeptide spots. The polypeptides analysed giving this type of trains were all found to be classified as stable polypeptides according to the instability index of Guruprasad et al. (Protein Eng. 1990, 4, 155,161). The phenomenon most likely reflects conformational equilibria of polypeptides arising from the experimental conditions used, and is a clear drawback of the standard 2-DE procedure, making the gel picture unnecessarily complex to analyse. [source] A proteomic study of Escherichia coli O157:H7 NCTC 12900 cultivated in biofilm or in planktonic growth modeFEMS MICROBIOLOGY LETTERS, Issue 1 2002Frédéric Trémoulet Abstract Escherichia coli 0157:H7 biofilms were studied by a new method of cultivation in order to identify some of the proteins involved in the biofilm phenotype. A proteomic analysis of sessile or planktonic bacteria of the same age was carried out by two-dimensional electrophoresis, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) and database searching. Comparison of two-dimensional gels showed clear differences between protein patterns of sessile and planktonic cells. Fourteen proteins increased in biofilms, whereas three decreased. From these 17 proteins, 10 were identified by MALDI-TOF-MS and could be classified into four categories according to their function: (1) general metabolism proteins (malate dehydrogenase, thiamine-phosphate pyrophosphorylase), (2) sugar and amino acid transporters (d -ribose-binding periplasmic protein, d -galactose-binding protein, YBEJ), (3) regulator proteins (DNA starvation protein and H-NS) and (4) three proteins with unknown function. The results of this study showed that E. coli O157:H7 modified the expression of several proteins involved in biofilm growth mode. [source] EVIDENCE FOR A SPECIALIZED LOCALIZATION OF THE CHLOROPLAST ATP-SYNTHASE SUBUNITS ,, ,, AND , IN THE EYESPOT APPARATUS OF CHLAMYDOMONAS REINHARDTII (CHLOROPHYCEAE),JOURNAL OF PHYCOLOGY, Issue 2 2007Melanie Schmidt The eyespot apparatus (EA) of Chlamydomonas reinhardtii P. A. Dang. consists of two layers of carotenoid-rich lipid globules subtended by thylakoids. The outermost globule layer is additionally associated with the chloroplast envelope membranes and the plasma membrane. In a recent proteomic approach, we identified 202 proteins from isolated EAs of C. reinhardtii via at least two peptides, including, for example, structural components, signalling-related proteins, and photosynthetic-related membrane proteins. Here, we have analyzed the proteins of the EA with regard to their topological distribution using thermolysin to find out whether the arrangement of globules and membranes provides protection mechanisms for some of them. From about 230 protein spots separated on two-dimensional gels, the majority were degraded by thermolysin. Five major protein spots were protected against the action of this protease. These proteins and some that were degradable were identified by mass spectrometry. Surprisingly, the thermolysin-resistant proteins represented the , and , subunits of the soluble CF1 complex of the chloroplast ATP synthase. Degradable proteins included typical membrane proteins like LHCs, demonstrating that thermolysin is not in general sterically prevented by the EA structure from reaching membrane-associated proteins. A control experiment showed that the CF1 complex of thylakoids is efficiently degraded by thermolysin. Blue native PAGE of thermolysin-treated EAs followed by SDS-PAGE revealed that the , and , subunits are present in conjunction with the , subunit in a thermolysin-resistant complex. These results provide strong evidence that a significant proportion of these ATP-synthase subunits have a specialized localization and function within the EA of C. reinhardtii. [source] Glycoproteomics of N -glycosylation by in-gel deglycosylation and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry mapping: Application to congenital disorders of glycosylationPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 10 2005Dijana Abstract A general strategy for the structural evaluation of N -glycosylation, a common post-translational protein modification, is presented. The methods for the release of N -linked glycans from the gel-separated proteins, their isolation, purification and matrix-assisted laser desorption/ionisation-mass spectrometry (MALDI-MS) analysis of their mixtures were optimised. Since many glycoproteins are available only at low quantities from sodium dodecyl sulphate-polyacrylamide gel electrophoresis or two-dimensional gels, high attention was paid to obtain N -glycan mixtures representing their actual composition in human plasma by in-gel deglycosylation. The relative sensitivity of solid MALDI matrices for MS analysis of acidic N -glycans was compared. The most favourable results for native acidic N -glycans were obtained with 2,4,6-trihydroxyacetophenone monohydrate/diammoniumcitrate as a matrix. This matrix provided good results for both neutral and acidic mixtures as well as for methylated N -glycans. In the second part of this paper the potential of such an optimised MS strategy alone or in combination with high pH anion-exchange chromatography profiling for the clinical diagnosis of congenital disorders of glycosylation is presented. [source] The role of bioinformatics in two-dimensional gel electrophoresisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2003Andrew W. Dowsey Abstract Over the last two decades, two-dimensional electrophoresis (2-DE) gel has established itself as the de facto approach to separating proteins from cell and tissue samples. Due to the sheer volume of data and its experimental geometric and expression uncertainties, quantitative analysis of these data with image processing and modelling has become an actively pursued research topic. The results of these analyses include accurate protein quantification, isoelectric point and relative molecular mass estimation, and the detection of differential expression between samples run on different gels. Systematic errors such as current leakage and regional expression inhomogeneities are corrected for, followed by each protein spot in the gel being segmented and modelled for quantification. To assess differential expression of protein spots in different samples run on a series of two-dimensional gels, a number of image registration techniques for correcting geometric distortion have been proposed. This paper provides a comprehensive review of the computation techniques used in the analysis of 2-DE gels, together with a discussion of current and future trends in large scale analysis. We examine the pitfalls of existing techniques and highlight some of the key areas that need to be developed in the coming years, especially those related to statistical approaches based on multiple gel runs and image mining techniques through the use of parallel processing based on cluster computing and the grid technology. [source] An improved mechanically durable electrophoresis gel matrix that is fully compatible with fluorescence-based protein detection technologiesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2003Birte Schulenberg Abstract Unfortunately, conventional large-format polyacrylamide gels are mechanically fragile, often tearing during the subsequent manipulations required for visualization of the proteins. This problem is compounded when large-format two-dimensional gels are subjected to multiple staining procedures in order to detect different classes of proteins, such as total protein, phosphoproteins, and glycoproteins. A mechanically durable liquid polyacrylamide-based matrix has been developed that, upon polymerization, facilitates the handling of one-dimensional and two-dimensional gels. The matrix, referred to as Rhinohide liquid acrylamide, is stable as a refrigerated solution for up to one year, and forms a polymer-reinforced polyacrylamide gel suitable for electrophoresis, upon addition of catalysts. The matrix is superior to previously reported durable gel matrices in that it does not cause distortion of high-molecular-weight bands and does not suffer from other spot morphology artifacts, such as doubling of protein spots in the molecular weight dimension. The matrix is particularly valuable for the analysis of proteins applying multiple applications of fluorescent dyes, as required with serial staining of proteins for phosphorylation, glycosylation, and total protein expression, using Pro-Q Diamond phosphoprotein stain, Pro-Q Emerald glycoprotein stain and SYPRO® Ruby protein gel stain, respectively. [source] An efficient solubilization buffer for plant proteins focused in immobilized pH gradientsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2003Valérie Méchin Abstract The solubilization of a large array of proteins before electrophoresis itself is a very critical point for proteomic analyses. We compared the efficiency of several different solubilization buffers. From this work, we defined a very efficient solubilization buffer, including two chaotropes, two reducing agents (R2), two detergents (D2), and two kinds of carrier ampholytes in combination. This so-called R2D2 buffer (5 M urea, 2 M thiourea, 2% 3-[(3-cholamidopropyl) dimethyl-ammonio]-1-propane-sulfonate, 2% N -decyl- N,N -dimethyl-3-ammonio-1-propane-sulfonate, 20 mM dithiothreitol, 5 mM Tris(2-carboxyethyl) phosphine, 0.5% carrier ampholytes 4,6.5, 0.25% carrier ampholytes 3-10) proved to be very efficient for a large range of different samples and allowed us to obtain two-dimensional gels of high resolution and quality. [source] Using statistical image models for objective evaluation of spot detection in two-dimensional gelsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2003Mike Rogers Abstract Protein spot detection is central to the analysis of two-dimensional electrophoresis gel images. There are many commercially available packages, each implementing a protein spot detection algorithm. Despite this, there have been relatively few studies comparing the performance characteristics of the different packages. This is in part due to the fact that different packages employ different sets of user-adjustable parameters. It is also partly due to the fact that the images are complex. To carry out an evaluation, "ground truth" data specifying spot position, shape and intensities needs to be defined subjectively on selected test images. We address this problem by proposing a method of evaluation using synthetic images with unambiguous interpretation. The characteristics of the spots in the synthetic images are determined from statistical models of the shape, intensity, size, spread and location of real spot data. The distribution of parameters is described using a Gaussian mixture model obtained from training images. The synthetic images allow us to investigate the effects of individual image properties, such as signal-to-noise ratios and degree of spot overlap, by measuring quantifiable outcomes, e.g. accuracy of spot position, false positive and false negative detection. We illustrate the approach by carrying out quantitative evaluations of spot detection on a number of widely used analysis packages. [source] Determination of wheat quality by mass spectrometry and multivariate data analysisRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 21 2002David Mark Gottlieb Multivariate analysis has been applied as support to proteome analysis in order to implement an easier and faster way of data handling based on separation by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The characterisation phase in proteome analysis by means of simple visual inspection is a demanding process and also insecure because subjectivity is the controlling element. Multivariate analysis offers, to a considerable extent, objectivity and must therefore be regarded as a neutral way to evaluate results obtained by proteome analysis. Proteome analysis of storage proteins from the wheat gluten complex based on two-dimensional electrophoresis and analysis of the N-terminal sequence has revealed a protein homologous to ,-gliadins, tentatively associated with quality and within the molecular weight range 27,35,kDa. Further examinations of gliadin data based on mass spectrometry revealed that quality among wheat varieties could be determined by means of principal component analysis. Further examinations by interval partial least squares made it possible to encircle an overall optimal molecular weight interval from 31.5 to 33.7,kDa. The use of multivariate analysis on data from mass spectrometry has thus shown to be a promising technique to minimize the number of two-dimensional gels within the field of proteome analysis. Copyright © 2002 John Wiley & Sons, Ltd. [source] Functional and proteomic analysis of serum and cerebrospinal fluid derived from patients with traumatic brain injury: a pilot studyANZ JOURNAL OF SURGERY, Issue 7-8 2010Dieter Cadosch Abstract Background:, An enhanced fracture healing response has been reported in patients with traumatic brain injury (TBI). This has been attributed to circulating humoral factors that are thought to be proteins produced and released by the injured brain. However, these factors remain unknown. The aim of this study was to identify osteogenic factors in serum and cerebrospinal fluid (CSF) from TBI patients. This was carried out using in vitro proliferation assays with the human foetal osteoblastic 1.19 cell line (hFOB) combined with a novel proteomic approach. Methods:, Serum was collected from brain-injured (n = 12) and non-brain-injured (n = 9) patients with a comorbid femur shaft fracture. Similarly, CSF was obtained from TBI (n = 7) and non-TBI (n = 9) patients. The osteoinductive potential of these samples was determined by measuring the in vitro proliferation rate of hFOB cells. Highly osteogenic serum and CSF samples of TBI patients were chosen for protein analysis and were compared to those of non-brain-injured patients. A new hFOB cell-based method was used to enrich the proteins in these samples, which had a functional affinity for these osteoprogenitor cells. These enriched protein fractions were mapped using two-dimensional gel electrophoresis and protein imaging methods displaying serum and CSF proteins of brain-injured and control subjects that had an affinity for human osteoprogenitor cells. Results:, Serum and CSF derived from brain-injured patients demonstrated a greater osteoinductive potential (P < 0.05) than their non-brain-injured counterparts. Clear-cut differences in the pattern of proteins in two-dimensional gels were detected between TBI and control patients. Fourteen proteins were exclusively present in the serum of TBI patients, while other proteins were either up- or downregulated in samples collected from TBI patients (P < 0.05). Conclusion:, Osteoinductive factors are present in the serum and CSF of brain-injured patients. These may include one or more of those proteins identified as having an affinity for osteoprogenitor cells that are either exclusively present or up- or downregulated in the serum and CSF of brain-injured patients. [source] | |||||||||||||