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Proteomic Methodologies (proteomic + methodology)
Selected AbstractsComparison of the specificity and sensitivity of traditional methods for assessment of nephrotoxicity in the rat with metabonomic and proteomic methodologiesJOURNAL OF APPLIED TOXICOLOGY, Issue 4 2005Andy Gibbs Abstract There is currently a great deal of scientific interest and debate concerning the possible advantages that proteomic and metabonomic technologies might have over traditional biomarkers of toxicity (blood and urine chemistry, histopathology). Numerous papers have been published that make impressive claims concerning potential applications for these novel technologies, however there appears to be little hard evidence in the literature of their advantages over the traditional techniques for assessing toxicity. The aim of this review was to evaluate the relative sensitivity and specificity of proteomic and metabonomic techniques, compared with traditional techniques, for assessing xenobiotic-induced nephrotoxicity. A review of studies was performed where both one of the novel methods as well as traditional techniques were used for assessment of xenobiotic-induced nephrotoxicity. There was no consistent evidence from the literature that the novel methodologies were any more sensitive than the traditional methods for assessing nephrotoxicity. This could be due to the relatively small number of studies available for review (n = 13), the fact that generally these studies were not aimed at determining relative sensitivity or specificity and may not be the case with other target organs, such as the liver. However, it was clear that the novel methodologies were able to discriminate between the effects caused by different toxicants. There was evidence both that this discrimination was on the basis of different mechanisms of toxicity and on the basis of different locations of nephrotoxic lesion. A great deal of validation work is necessary before these techniques could gain full acceptance by regulatory authorities, and it is unclear whether their use in anything other than non-regulatory, mechanistic studies is likely to become widespread. Copyright © 2005 John Wiley & Sons, Ltd. [source] Analysis of outer membrane proteome of Escherichia coli related to resistance to ampicillin and tetracyclinePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 2 2006Changxin Xu Abstract The elucidation of the molecular details of antibiotic resistance will lead to improvements in extending the efficacy of current antimicrobials. In the current study, proteomic methodologies were applied to characterize functional outer membrane proteins (Omps) of E.,coli,K-12 responded to tetracycline and ampicillin resistance for understanding of universal pathways that form barriers for antimicrobial agents. For this purpose, E.,coli,K-12 expressional outer membrane proteome was characterized and identified with the use of 2-DE and MALDI-TOF/MS methods. Then, differential Omps due to tetracycline or ampcilin resistance were determined by comparison between tetracycline minimum inhibitory concentration (MIC)10, ampicillin,MIC10, control0 and control10, showing 9,proteins with 11,spots for tetracycline and 8,protein with 9,spots for ampicillin, showing a difference in only 1,protein (decreased LamB in tetracyclin) between the two antibiotics. Among the proteins, 3,were known as antibiotic-resistant proteins, including TolC, OmpC and YhiU, while FimD precursor, LamB, Tsx, YfiO, OmpW, NlpB were first reported here to be antibiotic-resistance-related proteins. Our findings will be helpful for further understanding of antibiotic-resistant mechanism(s). This study also shows that the combination of Omp purification methods certainly contributes the sensitivity of Omp detection. [source] Proteomics and the lung: Analysis of bronchoalveolar lavage fluidPROTEOMICS - CLINICAL APPLICATIONS, Issue 9 2009Praveen Govender Abstract Our knowledge of the complex bronchoalveolar lavage fluid (BALF) proteome has increased significantly over the last decade; but still, there remain many aspects of the BALF proteome that need characterization. Current proteomic methodologies resolve proteins within limited dynamic ranges: thereby, being limited in their ability to examine important areas of the BALF proteome, such as low molecular weight, low abundance proteins. To ensure proper coverage of these proteins in the BALF proteome, a refined 2-DE standard operation protocol is presented, highlighting important issues in sample collection, sample preparation, and 2-D DIGE analysis. It is hoped that this will help advance the field of BALF proteomics, BALFomics, which has lagged behind similar biofluids such as plasma and serum. [source] Modern strategies to identify new molecular targets for the treatment of liver diseases: The promising role of Proteomics and Redox Proteomics investigationsPROTEOMICS - CLINICAL APPLICATIONS, Issue 2 2009Andrea Scaloni Dr. Abstract Oxidative stress, due to an imbalance between the generation of ROS and the antioxidant defense capacity of the cell, is a major pathogenetic event occurring in several liver diseases, ranging from metabolic to proliferative. Main sources of ROS are represented by mitochondria and cytochrome P450 enzymes in the hepatocytes, Küppfer cells, and neutrophils. Oxidative stress affects major cellular components including lipids, DNA, and proteins. Through modulation of protein structure/function, ROS can influence gene expression profile by affecting intracellular signal transduction pathways. While several enzymatic and nonenzymatic markers of chronic oxidative stress are well known in liver, early protein targets of oxidative injury are yet poorly defined. Identification of these biomarkers will enable early detection of liver diseases and will allow monitoring the degree of liver damage, the response to pharmacological therapies, and the development of new therapeutic approaches. In the era of molecular medicine, new proteomic methodologies promise to establish a relationship between pathological hallmarks of the disease and protein structural/functional modifications, thus allowing a better understanding and a more rational therapy on liver disorders. Purpose of this review is to critically analyze the application of proteomic and redox proteomic approaches to the study of oxidative stress-linked liver diseases. [source] Cover Picture: Electrophoresis 10'2010ELECTROPHORESIS, Issue 10 2010Article first published online: 18 MAY 2010 Issue no. 10 is a regular issue comprising 19 manuscripts distributed over four distinct parts. Part I is on microfluidics and miniaturized systems and has 5 articles; Part II is on nucleic acids with 4 articles on restriction endonuclease fingerprinting, mutation detection and DNA separation and detection; Part III has 7 articles on monolithic stationary phases for CEC, single walled carbon nanohorns as pseudo-stationary phases for CEC and EKC, MEEKC, cyclodextrin-modified gold nanoparticles for enantioseparations by CEC, use of divalent dipeptides as counter ions in CE and capillary coating for CE of proteins; and Part IV has 3 articles on proteomics methodologies. Featured articles include: Microfluidic preparative free-flow isoelectric focusing in a triangular channel: System development and characterization ((10.1002/elps.200900577)) Separation and recovery of nucleic acids with improved biological activity by acid-degradable polyacrylamide gel electrophoresis ((10.1002/elps.200900783)) Evaluation of the performance of single-walled carbon nanohorns in capillary electrophoresis ((10.1002/elps.200900628)) The inter- and intra-operator variability in manual spot segmentation and its effect on spot quantitation in two dimensional electrophoresis analysis. ((10.1002/elps.200900674)) [source] Bioaffinity magnetic reactor for peptide digestion followed by analysis using bottom-up shotgun proteomics strategyJOURNAL OF SEPARATION SCIENCE, JSS, Issue 3 2008Lucie Korecká Abstract We report an efficient and streamlined way to improve the analysis and identification of peptides and proteins in complex mixtures of soluble proteins, cell lysates, etc. By using the shotgun proteomics methodology combined with bioaffinity purification we can remove or minimize the interference contamination of a complex tryptic digest and so avoid the time-consuming separation steps before the final MS analysis. We have proved that by means of enzymatic fragmentation (endoproteinases with Arg-C or/and Lys-C specificity) connected with the isolation of specific peptides we can obtain a simplified peptide mixture for easier identification of the entire protein. A new bioaffinity sorbent was developed for this purpose. Anhydrotrypsin (AHT), an inactive form of trypsin with an affinity for peptides with arginine (Arg) or lysine (Lys) at the C-terminus, was immobilized onto micro/nanoparticles with superparamagnetic properties (silica magnetite particles (SiMAG),Carboxyl, Chemicell, Germany). This AHT carrier with a determined binding capacity (26.8 nmol/mg of carrier) was tested with a model peptide, human neurotensin, and the resulting MS spectra confirmed the validity of this approach. [source] | |||||||||||||