MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Proteome Science' source. Fri, 19 Mar 2010 17:37:29 +0100 http://www.medworm.com/index.php?rid=3377987&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F14 Conclusion: The increased expression of annexin 1 protein has been found to be associated with higher BF thickness in both crossbred steers. This result lays the foundation for future studies to develop the protein marker for assessing animals with different BF. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3377987 Thu, 18 Mar 2010 00:00:00 +0100 3377987 http://www.medworm.com/index.php?rid=3358573&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F12 Conclusions: Together, this work provided useful information to facilitate further investigation of the underlying mechanism of HIV and host cell protein interactions, and discovered novel potential biomarkers such as fragment of vinculin, filamin-A and talin-1 for anti-HIV research. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3358573 Fri, 12 Mar 2010 00:00:00 +0100 3358573 http://www.medworm.com/index.php?rid=3326589&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F11 Conclusions: The results suggest that this study provides a potential link between the alterations in RBC membrane proteome in AD subjects and AD pathology. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3326589 Wed, 03 Mar 2010 00:00:00 +0100 3326589 http://www.medworm.com/index.php?rid=3311231&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F9 Conclusion: The method is feasible and reproducible. We could obtain a fair enrichment of cells but the major benefit of the method was an effective removal of contaminants from red blood cells and plasma proteins resulting in larger proteome coverage compared to the direct lysis of frozen samples. This sample preparation method may be successfully implemented for the discovery of lung cancer biomarkers on tissue samples using mass spectrometry-based proteomics. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3311231 Fri, 26 Feb 2010 00:00:00 +0100 3311231 http://www.medworm.com/index.php?rid=3275527&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F8 Conclusions: Permutations of C- and N-terminal Y2H vectors dramatically increase the coverage of interactome studies and thus significantly reduce the number of false negatives. We suggest that future interaction screens should use such vector combinations on a routine basis, not the least because they provide a built-in quality score for Y2H interactions that can provide a measure of reproducibility without additional assays. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3275527 Mon, 15 Feb 2010 00:00:00 +0100 3275527 http://www.medworm.com/index.php?rid=3254110&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F7 The yeast-like epiphytic fungus Pseudozyma flocculosa is known to antagonize powdery mildew fungi through proliferation on colonies presumably preceded by the release of an antifungal glycolipid (flocculosin). In culture conditions, P. flocculosa can be induced to produce or not flocculosin through manipulation of the culture medium nutrients. In order to characterize and understand the metabolic changes in P. flocculosa linked to glycolipid production, we conducted a 2-DE proteomic analysis and compared the proteomic profile of P. flocculosa growing under conditions favoring the development of the fungus (control) or conducive to flocculosin synthesis (stress). A large number of protein spots (771) were detected in protein extracts of the control treatment compared to only 435 matched pro... Proteome Science journals http://www.medworm.com/rss/comments.php?id=3254110 Tue, 09 Feb 2010 00:00:00 +0100 3254110 http://www.medworm.com/index.php?rid=3250943&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F6 Conclusions: The 64 phosphorylation sites determined represent the most comprehensive list of experimentally identified sea urchin protein phosphorylation sites at present and are an important addition to the recently analyzed Strongylocentrotus purpuratus shell and tooth proteomes. The identified phosphoproteins included a major, highly phosphorylated protein, [Glean3:18919], for which we suggest the name phosphodontin. Although not sequence-related to such highly phosphorylated acidic mammalian dental phosphoproteins as phosphoryn or dentin matrix protein-1, phosphodontin may perform similar functions in the sea urchin tooth. More than half of the detected proteins were not previously identified at the protein level, thus confirming the existence of proteins only known as genomic sequenc... Proteome Science journals http://www.medworm.com/rss/comments.php?id=3250943 Mon, 08 Feb 2010 00:00:00 +0100 3250943 http://www.medworm.com/index.php?rid=3243329&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F5 Conclusions: These findings demonstrate the practicality and versatility of non-directed activity-based protein profiling (ABPP) to complement directed methods and accelerate the discovery of altered protein activities associated with pathological states such as HCV replication. Collectively, these results highlight the ability of in situ ABPP approaches to facilitate the identification of enzymes that are either predominantly or exclusively labeled in living cells. Several of these differentially active enzymes represent possible HCV-host interactions that could be targeted for diagnostic or therapeutic purposes. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3243329 Thu, 04 Feb 2010 00:00:00 +0100 3243329 http://www.medworm.com/index.php?rid=3239203&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F4 Conclusion: These results demonstrate the capacity of proteomic analysis of plasma, by confirming the presence of known biomarkers as well as revealing new biomarkers for diabetic nephropathy in plasma in type 1 diabetic patients. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3239203 Wed, 03 Feb 2010 00:00:00 +0100 3239203 http://www.medworm.com/index.php?rid=3220117&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F2 Conclusions: This manuscript described a more comprehensive proteomic profile of prolactinomas compared to other previous published reports. Thanks to the application of immuno-LCM combined with online two-dimensional nano-scale liquid chromatography here permitted identification of more proteins and, to our best knowledge, generated the largest prolactinoma proteome. This enlarged proteome would contribute significantly to further understanding of prolactinoma tumorigenesis which is crucial to the management of prolactinomas. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3220117 Fri, 29 Jan 2010 00:00:00 +0100 3220117 http://www.medworm.com/index.php?rid=3220116&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F3 Conclusion: Administration of doxycycline might be a significant supportive therapeutic strategy in prevention of VILI. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3220116 Fri, 29 Jan 2010 00:00:00 +0100 3220116 http://www.medworm.com/index.php?rid=3166756&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F8%2F1%2F1 Conclusions: Many proteins identified in our study corresponded to the proteins identified in other insects. Compared to the former studies performed in insects, we presented 2-D protein maps of the hemocytes and fat bodies and showed the trends in expression of the immune-elicited proteins. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3166756 Wed, 13 Jan 2010 00:00:00 +0100 3166756 http://www.medworm.com/index.php?rid=3126456&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F48 Conclusions: Our study provides novel evidence for mitochondria as a pivotal organelle that is connected to liver regeneration, and lays the foundation for further studies on key factors and pathways involved in liver regeneration following 50% PH, a condition frequently used for partial liver transplantation and conservative liver resection. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3126456 Tue, 29 Dec 2009 00:00:00 +0100 3126456 http://www.medworm.com/index.php?rid=3110913&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F45 Conclusions: Our results indicate the physiological differences between the non-pathogenic strain, with its non-infective proliferate lifestyle, and the pathogenic strains, with its constitutive expression of adhesins, which would render the bacterium competent for adhesion and infection prior to host contact. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3110913 Mon, 21 Dec 2009 00:00:00 +0100 3110913 http://www.medworm.com/index.php?rid=3084535&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F44 Conclusions: This was the first time to study the protein expression patterns during the metamorphosis of a marine polychaete and to compare the proteomes of marine invertebrates that have different levels of morphological changes during metamorphosis. The findings provide promising initial steps towards the development of a proteome database for marine invertebrate metamorphosis, thus deciphering the possible mechanisms underlying larval metamorphosis in non-model marine organisms. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=3084535 Mon, 14 Dec 2009 00:00:00 +0100 3084535 http://www.medworm.com/index.php?rid=3018706&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F43 Background: B-cell lymphomas are thought to reflect different stages of B-cell maturation. Based on cytogenetics and molecular markers, mantle cell lymphoma (MCL) is presumed to derive predominantly from naive, pre-germinal centre (pre-GC) B lymphocytes. The aim of this study was to develop a method to investigate the similarity between MCL and different B-cell compartments on a protein expression level. Methods: Subpopulations of B cells representing the germinal centre (GC), the pre-GC mantle zone and the post-GC marginal zone were isolated from tonsils using automated magnetic cell sorting (AutoMACS) of cells based on their expression of CD27 and IgD. Protein profiling of the B cell subsets, of cell lines representing different lymphomas and of primary mantle cell lymphoma (MCL) samples... Proteome Science journals http://www.medworm.com/rss/comments.php?id=3018706 Mon, 23 Nov 2009 00:00:00 +0100 3018706 http://www.medworm.com/index.php?rid=2976992&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F42 Conclusion: In this study, we successfully identified novel salt stress-responsive protein phosphorylation sites from membrane isolates of abiotic-stressed plants by membrane shaving followed by Zr4+-IMAC enrichment. The identified phosphorylation sites can be important in the salt stress response in plants. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2976992 Tue, 10 Nov 2009 00:00:00 +0100 2976992 http://www.medworm.com/index.php?rid=2962881&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F41 Conclusion: The aqueous polymer two-phase partition is a simple, rapid and relatively inexpensive method. It is well suitable for the purification of PMs from small amount of tissues. Therefore, it is reasonable for the DRG PM to be enriched by using aqueous two-phase partition as a preferred method. Proteomic analysis showed that DRG PM was rich in proteins involved in the fundamental biological processes including material exchange, energy transformation and information transmission, etc. These data would help to our further understanding of the fundamental DRG functions. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2962881 Thu, 05 Nov 2009 00:00:00 +0100 2962881 http://www.medworm.com/index.php?rid=2950421&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F40 Conclusion: Using a proteomic approach we identified biomarkers related to the lipoprotein profile that could be used to predict growth response to GH treatment in prepubertal children who are short as a result of GH-deficiency or who have ISS.These results support our previous findings that apolipoproteins and transthyretin may have a role in GH sensitivity. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2950421 Mon, 02 Nov 2009 00:00:00 +0100 2950421 http://www.medworm.com/index.php?rid=2934406&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F39 Background: Hepatitis E, caused by the hepatitis E virus (HEV), is endemic to developing countries where it manifests as waterborne outbreaks and sporadic cases. Though generally self-limited with a low mortality rate, some cases progress to fulminant hepatic failure (FHF) with high mortality. With no identified predictive or diagnostic markers, the events leading to disease exacerbation are not known. Our aim is to use proteomic tools to identify biomarkers of acute and fulminant hepatitis E. Results: We analyzed proteins in the plasma and urine of hepatitis E patients and healthy controls by two-dimensional Differential Imaging Gel Electrophoresis (DIGE) and mass spectrometry, and identified over 30 proteins to be differentially expressed during acute hepatitis E. The levels of one plasm... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2934406 Tue, 27 Oct 2009 00:00:00 +0100 2934406 http://www.medworm.com/index.php?rid=2814281&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F36 In this study a proteomic approach was used to investigate the steady-state response of Escherichia coli to temperature up-shifts in a cascade of two continuously operated bioreactors. The first reactor served as cell source with optimal settings for microbial growth, while in the second chemostat the cells were exposed to elevated temperatures. By using this reactor configuration, which has not been reported to be used for the study of bacterial stress responses so far, it is possible to study temperature stress under well-defined, steady-state conditions. Specifically the effect on the cellular adaption to temperature stress using two-dimensional gel electrophoresis was examined and compared at the cultivation temperatures of 37degreesC and 47.5degreesC. As expected, the steady-state stu... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2814281 Sun, 20 Sep 2009 23:00:00 +0100 2814281 http://www.medworm.com/index.php?rid=2765625&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F34 Conclusions: This study shows that serum peptidome profiling using MALDI-TOF-MS coupled to pattern diagnostics may aid in prediction of treatment outcome of advanced NSCLC patients treated with chemotherapy. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2765625 Wed, 02 Sep 2009 23:00:00 +0100 2765625 http://www.medworm.com/index.php?rid=2757308&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F33 The present study examined the changes in protein expression in Spirulina platensis upon exposure to high temperature, with the changes in expression analyzed at the subcellular level. In addition, the transcriptional expression level of some differentially expressed proteins, the expression pattern clustering, and the protein-protein interaction network were analyzed. The results obtained from differential expression analysis revealed up-regulation of proteins involved in two-component response systems, DNA damage and repair systems, molecular chaperones, known stress-related proteins, and proteins involved in other biological processes, such as capsule formation and unsaturated fatty acid biosynthesis. The clustering of all differentially expressed proteins in the three cellular compartm... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2757308 Tue, 01 Sep 2009 23:00:00 +0100 2757308 http://www.medworm.com/index.php?rid=2751412&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F32 Conclusions: The present report provides new information about the protein content of human neutrophils. Importantly, our study resulted in the discovery of a series of proteins not previously reported to be associated with human neutrophils. These data are relevant to the investigation of comparative pathological states and models for novel classes of pharmaceutical drugs that could be useful in the treatment of inflammatory disorders in which neutrophils participate. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2751412 Sun, 30 Aug 2009 23:00:00 +0100 2751412 http://www.medworm.com/index.php?rid=2743797&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F31 Conclusions: This set of experiments establishes a new model system for genetic dissection of the specific HSA21 gene-overdose contributions to aberrant cell migration, adhesion, proliferation and specific proteome response to collagen VI, cellular phenotypes linked to the pathogenesis of CHD. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2743797 Thu, 27 Aug 2009 23:00:00 +0100 2743797 http://www.medworm.com/index.php?rid=2724404&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F29 Conclusions: This large-scale analysis provides a framework for understanding the cooperation between E6 and E7 oncoproteins in HPV-driven carcinogenesis. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2724404 Sat, 22 Aug 2009 23:00:00 +0100 2724404 http://www.medworm.com/index.php?rid=2688328&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F28 In this study, the acute effects of IGF-1 on the proteome of murine C2C12 cells were examined. Cells were treated with IGF-1 for up to 24 hours, lysed, and fractionated into cytosolic, nuclear, and insoluble portions. Proteins from the cytosolic fraction were further separated using a new batch ion-exchange chromatography method to reduce sample complexity, followed by twodimensional (2D) electrophoresis, and identification of selected proteins by mass spectrometry.PDQuest software was utilized to identify and catalogue temporal changes in protein expression during IGF-1 stimulation. In response to IGF-1 stimulation, expression of 23 proteins increased at least three-fold and expression of 17 proteins decreased at least three-fold compared with control un-stimulated C2C12 cells. Changes in... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2688328 Mon, 10 Aug 2009 23:00:00 +0100 2688328 http://www.medworm.com/index.php?rid=2683720&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F27 Conclusions: We present an accurate prediction method using a machine-learning approach based solely on protein sequence properties. The primary contribution of this paper is to propose new PNPRD features representing global and/or local differences in sequences, based on positively and/or negatively charged residues, to assist in predicting protein function. In addition, we identified a compact and useful feature subset for predicting the function of various proteins. Our results indicate that sequence-based classifiers can provide good results among a broad range of proteins, that the proposed features are useful in predicting several functions, and that the combination of our and traditional features may support the creation of a discriminative feature set for specific protein functions... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2683720 Sat, 08 Aug 2009 23:00:00 +0100 2683720 http://www.medworm.com/index.php?rid=2653429&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F26 Conclusion: We describe novel approaches of subcellular proteomic profiling and assessment of acute changes on a minute-based time scale. These data expand the current knowledge of acute, non-transcriptional activities of glucocorticoids, including changes in protein subcellular localization, altered translation of quiescent RNA pools, and PKC-mediated cytoskeleton remodeling. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2653429 Wed, 29 Jul 2009 23:00:00 +0100 2653429 http://www.medworm.com/index.php?rid=2610643&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F25 Conclusions: The results from this study revealed changes among both neuronal protein processing and endogenous proteolysis modulators in EAE animals. This information may provide a rationale for protease inhibitor-based therapeutic interventions for demyelinating diseases and multiple sclerosis. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2610643 Wed, 15 Jul 2009 23:00:00 +0100 2610643 http://www.medworm.com/index.php?rid=2605655&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F24 Conclusions: The identified altered proteins indicate mechanism important for altered beta-cell function in T2DM. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2605655 Wed, 15 Jul 2009 23:00:00 +0100 2605655 http://www.medworm.com/index.php?rid=2555706&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F23 Conclusions: This manuscript presents a description of a more comprehensive proteomic profile for mammalian cornea compared to past methods. The use of simple dissection procedures of the tissue and the application of long chromatographic gradients, many more proteins can be identified. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2555706 Sun, 28 Jun 2009 23:00:00 +0100 2555706 http://www.medworm.com/index.php?rid=2552696&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F22 The in vitro stationary phase proteome of the human pathogen Shigella dysenteriae serotype 1 (SD1) was quantitatively analyzed in Coomassie Blue G250 (CBB)-stained 2D gels. More than four hundred and fifty proteins, of which 271 were associated with distinct gel spots, were identified. In parallel, we employed 2D-LC-MS/MS followed by the label-free computationally modified spectral counting method APEX for absolute protein expression measurements. Of the 4502 genome-predicted SD1 proteins, 1148 proteins were identified with a false positive discovery rate of 5% and quantitated using 2D-LC-MS/MS and APEX. The dynamic range of the APEX method was approximately one order of magnitude higher than that of CBB-stained spot intensity quantitation. A squared Pearson correlation analysis revealed a... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2552696 Sun, 28 Jun 2009 23:00:00 +0100 2552696 http://www.medworm.com/index.php?rid=2506242&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F21 Conclusions: Obtained data support the notion that Ruk/CIN85 regulates vesicle-mediated transport and cancer cell invasiveness through the assembly of multimeric protein complexes governing coordinated remodelling of membranes and underlying cytoskeletal structures, and imply its important roles in formation of coated vesicles and biogenesis of invadopodia. In addition, this study points to potential involvement of Ruk/CIN85 in other cellular processes, chiefly in cell division. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2506242 Mon, 15 Jun 2009 23:00:00 +0100 2506242 http://www.medworm.com/index.php?rid=2440197&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F20 Conclusions: The robust analytical platform in combination with a well-defined compendium of mitochondrial proteins allowed quantification of single proteins as well as mapping of entire pathways. This enabled characterization of the interplay between metabolism and stress response in human cells exposed to mild stress. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2440197 Thu, 28 May 2009 04:00:00 +0100 2440197 http://www.medworm.com/index.php?rid=2414176&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F19 Conclusions: We use classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Both pre-processing methods lead to similar classification results on an ovarian cancer and a Gaucher disease dataset. However, the settings for pre-processing parameters lead to large differences in classification accuracy and are therefore of crucial importance. We advocate the evaluation over a range of parameter settings when comparing pre-processing methods. Our analysis also demonstrates that reliable classification results can be obtained with a combination of strict sample handling and a well-defined classification protocol on clinical samples. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2414176 Thu, 14 May 2009 04:00:00 +0100 2414176 http://www.medworm.com/index.php?rid=2397475&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F18 Conclusions: Functional assessment of proteins with significantly altered expression levels revealed several mechanisms thought to be involved in bacterial heavy metal detoxification, including general stress adaptation, anti-oxidative stress and heavy metal efflux proteins. This information may contribute to the development of plant growth-promoting bacteria mediated phytoremediation processes. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2397475 Thu, 07 May 2009 04:00:00 +0100 2397475 http://www.medworm.com/index.php?rid=2397476&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F17 Conclusion: We demonstrated here that CVF colposcopy samples can be used in proteomics experiments and hence are applicable for biomarker discovery experiments. The delineation of an overlapping set of proteins that is identified in most proteomics studies on CVF may help in the description of a reference proteome when performing proteomics studies on human CVF. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2397476 Fri, 17 Apr 2009 04:00:00 +0100 2397476 http://www.medworm.com/index.php?rid=2341263&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F16 Conclusions: Our results provide insights into the gender differences associated to the decline of kidney function in aging. Thus, we show that proteomics can provide valuable information on age-related changes in expression levels of proteins and related modifications. This pilot study is still far from providing candidates for aging-biomarkers. However, we suggest that the analysis of these proteins could suggest mechanisms of cellular aging in kidney, and improve the kidney selection for transplantation. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2341263 Thu, 09 Apr 2009 04:00:00 +0100 2341263 http://www.medworm.com/index.php?rid=2341264&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F15 Conclusions: Serum and plasma spotted in the reverse phase array format allow for reliable and reproducible high-throughput validation of a mid-abundant blood biomarker such as clusterin. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2341264 Mon, 06 Apr 2009 04:00:00 +0100 2341264 http://www.medworm.com/index.php?rid=2341265&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F14 Conclusion: We identified a group of ZSTK474-sensitive phosphoproteins as the multi-phosphorylated form of 4E-BP1 by combining IMAC, SELDI-TOF MS and antibodies. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2341265 Tue, 31 Mar 2009 04:00:00 +0100 2341265 http://www.medworm.com/index.php?rid=2297437&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F13 Conclusions: The data presented constitute the first reference map for S. zooepidemicus and provide new information on the identity and characteristics of the more abundantly expressed proteins. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2297437 Sat, 28 Mar 2009 04:00:00 +0100 2297437 http://www.medworm.com/index.php?rid=2297441&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F12 Conclusions: We postulate that SP-A plays a role in reactive oxidant scavenging in WT mice and that its absence in the KO mice in the presence or absence of ozone exposure results in more pronounced, and presumably chronic, oxidative stress. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2297441 Thu, 26 Mar 2009 04:00:00 +0100 2297441 http://www.medworm.com/index.php?rid=2297444&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F11 Conclusions: The proteins identified in this study combined with other published proteomic data provide the most comprehensive Synechocystis proteome catalog, which will serve as a useful reference for further detailed studies to address protein functions through both traditional gene-by-gene and systems biology approaches. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2297444 Wed, 25 Mar 2009 04:00:00 +0100 2297444 http://www.medworm.com/index.php?rid=2284271&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F10 Conclusions: This study represents to date the first detailed and reproducible 2D protein map of human duodenum. Spots identifications, reported in a database, will be helpful to identify the variability in protein expression levels, in isoforms expression, or in post-translational modifications associated to pathology or to a therapy. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2284271 Thu, 19 Mar 2009 04:00:00 +0100 2284271 http://www.medworm.com/index.php?rid=2274274&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F9 Conclusions: The proposed denoising algorithm can be integrated into current popular peptide identification algorithms such as Mascot to improve the reliability of assigning peptides to spectra. Availability of the software: The software created from this work is available upon request. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2274274 Tue, 17 Mar 2009 04:00:00 +0100 2274274 http://www.medworm.com/index.php?rid=2267760&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F7 Conclusion: Platelet factor (PF4), connective tissue activating peptide III (CTAP-III) and two fragments of C3a may be potential protein biomarkers of pediatric ALL and used to distinguish pediatric ALL patients from healthy controls and pediatric AML patients. Further studies with additional populations or using pre-diagnostic sera are needed to confirm the importance of these findings as diagnostic markers of pediatric ALL. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2267760 Mon, 16 Mar 2009 04:00:00 +0100 2267760 http://www.medworm.com/index.php?rid=2239807&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F6 Conclusion: GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics. GOEx is available at http://pcarvalho.com/patternlab. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2239807 Tue, 24 Feb 2009 05:00:00 +0100 2239807 http://www.medworm.com/index.php?rid=2209472&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F6 Conclusions: GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a useful, friendly, and simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics. GOEx is available at http://pcarvalho.com/patternlab. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2209472 Tue, 24 Feb 2009 05:00:00 +0100 2209472 http://www.medworm.com/index.php?rid=2199814&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F4 Conclusions: This relatively simple method allows deep investigation into macrophages proteomics producing discrete and accurate protein fractions, especially membrane-associated and integral proteins. The adapted protocol seems highly suitable for further studies of clinical proteomics, especially for the elucidation of the molecular mechanisms controlling iron homeostasis in normal and disease conditions. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2199814 Thu, 19 Feb 2009 05:00:00 +0100 2199814 http://www.medworm.com/index.php?rid=2199813&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F7%2F1%2F5 Yersinia pestis proteins were sequentially extracted from crude membranes with a high salt buffer (2.5 M NaBr), an alkaline solution (180 mM Na2CO3, pH 11.3) and membrane denaturants (8 M urea, 2 M thiourea and 1% amidosulfobetaine-14). Separation of proteins by 2D gel electrophoresis was followed by identification of more than 600 gene products by MS. Data from differential 2D gel display experiments, comparing protein abundances in cytoplasmic, periplasmic and all three membrane fractions, were used to assign proteins found in the membrane fractions to three protein categories: (i) integral membrane proteins and peripheral membrane proteins with low solubility in aqueous solutions (220 entries); (ii) peripheral membrane proteins with moderate to high solubility in aqueous solutions (127 ... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2199813 Thu, 19 Feb 2009 05:00:00 +0100 2199813 http://www.medworm.com/index.php?rid=2097716&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F35 Conclusion: Our results suggest that transthyretin and apolipoprotein A-II may have a role in GH sensitivity and could be used as markers to predict which short prepubertal children with ISS will show a good or poor response to GH treatment. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2097716 Thu, 11 Dec 2008 05:00:00 +0100 2097716 http://www.medworm.com/index.php?rid=2026271&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F35 Conclusion: Our results suggest that transthyretin and apolipoprotein A-II may have a role in GH sensitivity and could be used as markers to predict which short prepubertal children with ISS will show a good or poor response to GH treatment. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=2026271 Thu, 11 Dec 2008 05:00:00 +0100 2026271 http://www.medworm.com/index.php?rid=2021254&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F33 Conclusion: This report presents the most comprehensive list of sea urchin tooth matrix proteins available at present. The complex mixture of proteins identified may reflect many different aspects of the mineralization process. A comparison between intact tooth matrix, presumably containing odontoblast remnants, and crushed tooth matrix served to differentiate between matrix components and possible contributions of cellular remnants. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Knowledge of the components of this model system may stimulate further experiments aiming at the elucidation of structure, function, and interaction of biomineral matrix components. (Source: Proteome Scien... Proteome Science journals http://www.medworm.com/rss/comments.php?id=2021254 Tue, 09 Dec 2008 05:00:00 +0100 2021254 http://www.medworm.com/index.php?rid=1933773&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F31 Conclusions: Nano-porous silicon, when combined with white light interferometry, is a powerful technique for the measurement of protein-protein interactions. In addition to studying the binary interactions of biomolecules in clean buffer systems, the newly developed surfaces are also suited for studying interactions in complex samples, such as plasma. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1933773 Tue, 04 Nov 2008 05:00:00 +0100 1933773 http://www.medworm.com/index.php?rid=1900868&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F29 Conclusions: Proteomics and Gene Ontology reveal, for the first time, differential enzyme activities between HepG2 cells and normal human liver tissues, which may be a promising new prognostic marker of Hepatocellular carcinoma. Two independent sets of bioinformatics calculations that employ two BLAST program versions, and searched different databases, arrived at essentially the same conclusion: oxidoreductases are down-regulated in HepG2 cells by approximately 57%, when compared to normal human liver tissues. Down-regulation of oxidoreductases in hepatoma is additionally supported by Gene Ontology analysis of isomerises. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1900868 Fri, 24 Oct 2008 04:00:00 +0100 1900868 http://www.medworm.com/index.php?rid=1900867&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F30 Conclusions: For proteomics of solid tumors, a two-step extraction process is recommended. First, proteins in the tumor specimen should be extracted with RIPA buffer. Second, the RIPA-insoluble material should be extracted with the urea-based buffer employed in this work. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1900867 Fri, 24 Oct 2008 04:00:00 +0100 1900867 http://www.medworm.com/index.php?rid=1872819&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F27 Conclusion: The combined use of iTRAQ labelling and OFFGEL fractionation allows a considerable increase in proteome coverage of very complex samples prepared from total cell extracts and supports the low-concentrated protein identification. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1872819 Mon, 13 Oct 2008 04:00:00 +0100 1872819 http://www.medworm.com/index.php?rid=1859127&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F25 Conclusion: We report a simple and reliable protocol for serum proteome analysis that combines an optimized resolution of 2-D gels spots and improved sample-matrix preparations for MALDI-MS analysis. The protocol allowed automated data acquisition for both CHCA and DHB and simplified the MS data acquisition therefore avoiding time-consuming procedures. The simplicity and reliability of the developed protocol may be applied universally. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1859127 Fri, 12 Sep 2008 04:00:00 +0100 1859127 http://www.medworm.com/index.php?rid=1805992&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F26 Conclusion: We offer some insight into the strengths and limitations of this emerging proteomic platform. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1805992 Fri, 12 Sep 2008 04:00:00 +0100 1805992 http://www.medworm.com/index.php?rid=1708178&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F21 In recent years proteomic techniques have started to become very useful tools in a variety of model systems of developmental biology. Applications cover many different aspects of development, including the characterization of changes in the proteome during early embryonic stages. During early animal development the embryo becomes patterned through the temporally and spatially controlled activation of distinct sets of genes. Patterning information is then translated, from gastrulation onwards, into regional specific morphogenetic cell and tissue movements that give the embryo its characteristic shape. On the molecular level, patterning is the outcome of intercellular communication via signaling molecules and the local activation or repression of transcription factors. Genetic approaches hav... Proteome Science journals http://www.medworm.com/rss/comments.php?id=1708178 Thu, 24 Jul 2008 04:00:00 +0100 1708178 http://www.medworm.com/index.php?rid=1652107&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F21 In recent years proteomic techniques have started to become very useful tools in a variety of model systems of developmental biology. Applications cover many different aspects of development, including the characterization of changes in the proteome during early embryonic stages. During early animal development the embryo becomes patterned through the temporally and spatially controlled activation of distinct sets of genes. Patterning information is then translated, from gastrulation onwards, into regional specific morphogenetic cell and tissue movements that give the embryo its characteristic shape. On the molecular level, patterning is the outcome of intercellular communication via signaling molecules and the local activation or repression of transcription factors. Genetic approaches hav... Proteome Science journals http://www.medworm.com/rss/comments.php?id=1652107 Thu, 24 Jul 2008 04:00:00 +0100 1652107 http://www.medworm.com/index.php?rid=1521857&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F19 Background: Colorectal cancer is the second most common cause of cancer related death in the developed world. To date, no blood or stool biomarkers with both high sensitivity and specificity for potentially curable early stage disease have been validated for clinical use. SELDI and MALDI profiling are increasingly being used to search for biomarkers in both blood and urine. Both techniques provide information predominantly on the low molecular weight proteome ( (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1521857 Mon, 16 Jun 2008 04:00:00 +0100 1521857 http://www.medworm.com/index.php?rid=1507510&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F18 Conclusions: Some of the commonly differentially expressed proteins are also differentially expressed in other tumours and may be putative diagnostic and/or prognostic markers for lymphomas. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1507510 Tue, 10 Jun 2008 04:00:00 +0100 1507510 http://www.medworm.com/index.php?rid=1494139&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F17 Conclusions: This study clearly demonstrates the utility of proteomic approaches to studying dimorphism in P. marneffei. Moreover, this strategy complements and extends current genetic methodologies directed towards understanding the molecular mechanisms of phase transition. Finally, the documented increased levels of RanA expression suggest that cellular development in this fungus involves additional signaling mechanisms than have been previously described in P. marneffei. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1494139 Wed, 04 Jun 2008 04:00:00 +0100 1494139 http://www.medworm.com/index.php?rid=1481685&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F16 Conclusions Pooling sera results in significant potential biomarker loss when using SELDI-ToF MS. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1481685 Sun, 01 Jun 2008 04:00:00 +0100 1481685 http://www.medworm.com/index.php?rid=1465382&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F15 Conclusion: A whole tissue extract of the mouse kidney cortex was analyzed by an unbiased proteomic approach, yielding a dataset of ~2,000 unique proteins identified with strict criteria to ensure a high level of confidence in protein identification. As a result of extracting all proteins from the renal cortex, we identified an exceptionally wide range of renal proteins in terms of pI, MW, hydrophobicity, abundance, and subcellular location. Many of these proteins, such as low-abundance proteins, membrane proteins and proteins with extreme values in pI or MW are traditionally under-represented in 2-DE-based proteomic analysis. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1465382 Fri, 23 May 2008 04:00:00 +0100 1465382 http://www.medworm.com/index.php?rid=1463481&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F14 Conclusions: At a proteomic level, short term sleep deprivation is characterized by a higher expression of some proteins in the hippocampus and a lower abundance of other proteins in the adrenals (compared to normal sleep control). Altogether, this could indicate a general activation of a number of cellular mechanisms involved in the maintenance of wakefulness and in increased energy expenditure during sleep deprivation. These findings are relevant to suggested functions of sleep like energy repletion and the restoration of molecular stocks or a more global homeostasis of synaptic processes. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1463481 Thu, 22 May 2008 04:00:00 +0100 1463481 http://www.medworm.com/index.php?rid=1458104&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F13 Conclusions: We found 19 separate proteins that changed in response to LPS or AEBSF, including ATP synthase, coagulation factor XIII, ferritin, coronin, HN ribonuclear proteins, integrin alpha IIb, pyruvate kinase, ras suppressor protein, superoxide dismutase, transketolase, tropomyosin, vimentin, and others. Interestingly, in response to LPS, precursor proteins for interleukin-1 beta appeared; and in response to AEBSF, there was an increase in elastase inhibitor. The increase in elastase inhibitor provides support for our hypothesis that priming requires an endogenous serine protease. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1458104 Tue, 20 May 2008 04:00:00 +0100 1458104 http://www.medworm.com/index.php?rid=1379251&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F12 Conclusions: We show that the methodology reduces the complexity of the proteome analysis and highlights proteins implicated in other processes than telomere elongation. hTERT induced proteome changes suggest that telomerase expression enhances natural cell repair mechanisms and stress resistance probably required for long term resistance of immortalized cells. Thus, hTERT transfected cells can not be only consider as an immortal equivalent to parental cells but also as cells which are over-resistant to stresses. These findings are the prerequisite for any larger proteomics aiming to evaluate anti-telomerase drugs proteome alteration and thus therapeutics induced cell reactions. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1379251 Thu, 17 Apr 2008 04:00:00 +0100 1379251 http://www.medworm.com/index.php?rid=1290909&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F10 Conclusion: The NAP-2 may be a specific proteomic biomarker of hepatitis B-related HCC. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1290909 Mon, 10 Mar 2008 04:00:00 +0100 1290909 http://www.medworm.com/index.php?rid=1257827&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F9 Conclusion: The reported data showed that OFFGEL system provides a highly valuable tool to fractionate peptides from complex eukaryotic proteomes (plasma and secretome) and is compatible with iTRAQ labeling quantitative studies. We therefore consider peptides OFFGEL fractionation as an effective addition to our strategy and an important system for quantitative proteomics studies. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1257827 Tue, 26 Feb 2008 05:00:00 +0100 1257827 http://www.medworm.com/index.php?rid=1224961&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F7 Conclusions: The proteins identified represent potential target areas involved with endorepellin anti-angiogenic mechanism of action. Further elucidation as such will ultimately provide useful in utilizing endorepellin as an anti-angiogenic therapy in humans. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1224961 Tue, 12 Feb 2008 05:00:00 +0100 1224961 http://www.medworm.com/index.php?rid=1189875&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F6 Background: Interrogation of chromatographic data for biomarker discovery becomes a tedious task due to stochastic variability in retention times arising from solvent and column performance. The difficulty is further compounded when the effects of exposure (e.g. to environmental contaminants) and biological variability result in varying numbers and intensities of peaks among chromatograms. Results: We developed a software tool to correct the stochastic time shifts in chromatographic data through iterative selection of landmark peaks and isometric interpolation to improve alignment of all chromatographic peaks. To illustrate application of the tool, plasma peptides from Fischer rats exposed for 4h to clean air or Ottawa urban particles (EHC-93) were separated by HPLC with autofluorescence d... Proteome Science journals http://www.medworm.com/rss/comments.php?id=1189875 Wed, 30 Jan 2008 05:00:00 +0100 1189875 http://www.medworm.com/index.php?rid=1182675&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F4 Conclusions: Soluble fusion proteins can be produced in E.coli in sufficient qualities and Aug/ml culture quantities for downstream applications like microarray-based assays, and studies on protein-protein interactions employing a fully automated protein expression and purification strategy. Future applications might include the optimization of experimental conditions for the large-scale production of soluble recombinant proteins from libraries of open reading frames. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1182675 Mon, 28 Jan 2008 05:00:00 +0100 1182675 http://www.medworm.com/index.php?rid=1182674&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F5 Conclusions: Collectively these results demonstrate that M. paratuberculosis proteins are detected by sera from experimentally infected cattle as early as 70 days after exposure. These data further suggest at least two antigens may be useful in the early diagnosis of M. paratuberculosis infections. Finally, the construction and use of a protein array in this pilot study has led to a novel approach for discovery of M. paratuberculosis antigens. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1182674 Mon, 28 Jan 2008 05:00:00 +0100 1182674 http://www.medworm.com/index.php?rid=1149528&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F6%2F1%2F1 Conclusions: This pilot study demonstrates the potential interest of protein expression signature in the identification of new potential biological markers that might be helpful for the rapid clinical management of high-risk pregnancies. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1149528 Fri, 11 Jan 2008 05:00:00 +0100 1149528 http://www.medworm.com/index.php?rid=1108375&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F20 Conclusions: Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at http://genomics.unibe.ch/dora. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=1108375 Thu, 20 Dec 2007 05:00:00 +0100 1108375 http://www.medworm.com/index.php?rid=847113&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F15 Conclusions: Based on these results, SELDI-TOF MS may be a suitable high-throughput candidate for HDL protein profiling and marker search. This approach may be used to i) investigate the underlying mechanisms that lead to increased atherothrombotic risk and ii) to investigate the atherothrombotic state of an individual. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=847113 Thu, 06 Sep 2007 04:00:00 +0100 847113 http://www.medworm.com/index.php?rid=843230&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F14 Conclusions: By removing poor-quality, outlier spectra, we were able to increase peak detection, and by reducing the variance introduced when samples are processed and analyzed in batches, we were able to increase the reproducibility of peak detection. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=843230 Wed, 05 Sep 2007 04:00:00 +0100 843230 http://www.medworm.com/index.php?rid=813840&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F13 Conclusion: We identified thirteen proteins whose expression is changed in EAAC-/- mice retinas. These proteins are known to regulate cell proliferation, death, transport, metabolism, cell organization and extracellular matrix. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=813840 Tue, 21 Aug 2007 04:00:00 +0100 813840 http://www.medworm.com/index.php?rid=792384&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F12 Conclusion: Our data demonstrate the broad array of proteins present in secretory vesicles that provides the PMN with the capacity for remarkable and rapid reorganization of its plasma membrane after exposure to proinflammatory agents or stimuli. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=792384 Fri, 10 Aug 2007 04:00:00 +0100 792384 http://www.medworm.com/index.php?rid=762886&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F11 Conclusions: This is the first description of the time course of protein secretion for the pathogen Bacillus anthracis. Time course studies of protein secretion and accumulation may be relevant in elucidation of the progression of pathogenicity, identification of therapeutics and diagnostic markers, and vaccine development. This study also adds to the continuously growing list of identified Bacillus anthracis secretome proteins. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=762886 Fri, 27 Jul 2007 04:00:00 +0100 762886 http://www.medworm.com/index.php?rid=708688&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F9 Conclusion: This report assesses the variation across fractionated sera processed over a one-month period. The optimizations reported decreased the variance and increased the number of peaks detected. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=708688 Mon, 02 Jul 2007 04:00:00 +0100 708688 http://www.medworm.com/index.php?rid=672237&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F8 Background: Technological advances in mass spectrometry and other detection methods are leading to larger and larger proteomics datasets. However, when papers describing such information are published the enormous volume of data can typically only be provided as supplementary data in a tabular form through the journal website. Several journals in the proteomics field, together with the Human Proteome Organization's (HUPO) Proteomics Standards Initiative and institutions such as the Institute for Systems Biology are working towards standardizing the reporting of proteomics data, but just defining standards is only a means towards an end for sharing data. Data repositories such as ProteomeCommons.org and the Open Proteomics Database allow for public access to proteomics data but provide litt... Proteome Science journals http://www.medworm.com/rss/comments.php?id=672237 Wed, 06 Jun 2007 04:00:00 +0100 672237 http://www.medworm.com/index.php?rid=619671&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F6 Conclusion: Our data provide evidence that deregulation of apoptosis and membrane trafficking proteins might be strongly implicated in the selection of carcinogen resistant cells. Some of these proteins might have potential as biomarkers of resistance and cancer risk. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=619671 Thu, 03 May 2007 04:00:00 +0100 619671 http://www.medworm.com/index.php?rid=440695&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F5 Conclusions: Retinal tissue in LCA is characterised by an up-regulation of alphaA-crystallin, triosephosphate isomerase, and ATP synthase (beta-chain fragment) and down-regulation of a fragment of beta-tubulin. These proteins/protein fragments may play a crucial role for the retinal degeneration processes in LCA and other retinal dystrophies. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=440695 Tue, 27 Feb 2007 05:00:00 +0100 440695 http://www.medworm.com/index.php?rid=390303&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F4 Conclusions: We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from http://www.mcisb.org/software/PrideWizard. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=390303 Thu, 01 Feb 2007 07:00:00 +0100 390303 http://www.medworm.com/index.php?rid=440696&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F4 Conclusion: We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQTM data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from http://www.mcisb.org/software/PrideWizard. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=440696 Thu, 01 Feb 2007 05:00:00 +0100 440696 http://www.medworm.com/index.php?rid=362854&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F5%2F1%2F3 Conclusions: Our results demonstrate that when combined, these methods can boost the sensitivity and specificity of spectral comparison. Therefore they are capable of enhancing and complementing existing tools for consistent and accurate peptide identification. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=362854 Tue, 16 Jan 2007 07:00:00 +0100 362854 http://www.medworm.com/index.php?rid=362855&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F4%2F1%2F23 Conclusion: A total of 45 proteins were identified, including proteins involved in cellular metabolism, cytoskeleton organization, vesicular trafficking, transcriptional and translational regulation, and cell signaling. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=362855 Thu, 21 Dec 2006 07:00:00 +0100 362855 http://www.medworm.com/index.php?rid=362856&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F4%2F1%2F22 Conclusion: Protocols for protein profiling by SELDI-TOF MS and protein identification by fractionation, SDS-PAGE and PMF were optimized for serum from humans with T2DM. With these protocols differentially expressed proteins were discovered and identified when serum from NGT- and T2DM-individuals was analyzed. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=362856 Tue, 12 Dec 2006 07:00:00 +0100 362856 http://www.medworm.com/index.php?rid=362858&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F4%2F1%2F19 High cell density cultivations were performed under identical conditions for two Bacillus megaterium strains (MS941 and WH320), both carrying a heterologous dextransucrase (dsrS) gene under the control of the xylA promoter. At characteristic points of the cultivations (end of batch, initial feeding, before and after induction) the proteome was analyzed based on two dimensional gel electrophoresis and mass spectrometric protein identification using the protein database "bmegMEC.v2" recently made available.High expression but no secretion of DsrS was found for the chemical mutant WH320 whereas for MS 941, a defined protease deficient mutant of the same parent strain (DSM319), not even expression of DsrS could be detected. The proteomic analysis resulted in the identification of proteins invo... Proteome Science journals http://www.medworm.com/rss/comments.php?id=362858 Thu, 05 Oct 2006 06:00:00 +0100 362858 http://www.medworm.com/index.php?rid=362857&cid=s_34089_79_f&fid=34089&url=http%3A%2F%2Fwww.proteomesci.com%2Fcontent%2F4%2F1%2F20 Conclusion: The combination of immunocapture and SELDI-TOF analysis opens new avenues into proteomic profiling for the discovery of blood biomarkers. (Source: Proteome Science) Proteome Science journals http://www.medworm.com/rss/comments.php?id=362857 Thu, 05 Oct 2006 06:00:00 +0100 362857