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78 records returned

Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thalianaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - November 10, 2009 Category: Bioinformatics Authors: Jue-Liang HsuLan-Yu WangShu-Ying WangChing-Huang LinKuo-Chieh HoFong-Ku ShiIng-Feng Chang Source Type: journals

Enrichment and proteomic analysis of plasma membrane from rat dorsal root ganglionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - November 5, 2009 Category: Bioinformatics Authors: Xia XiongSha HuangHai ZhangJianjun LiJianying ShenYong LinJixian XiongLiping JiangXianchun WangSongping Liang Source Type: journals

Proteins related to lipoprotein profile were identified using a pharmaco-proteomic approach as markers for growth response to growth hormone (GH) treatment in short prepubertal childrenEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - November 2, 2009 Category: Bioinformatics Authors: Bjorn AnderssonGunnel HellgrenAndreas NieropZe'ev HochbergKerstin Albertsson-Wikland Source Type: journals

Plasma and urine biomarkers in acute viral hepatitis EEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Proteome Science - October 27, 2009 Category: Bioinformatics Authors: Shikha TanejaSomdutta SenVijay GuptaRakesh AggarwalShahid Jameel Source Type: journals

Proteome analysis of the Escherichia coli heat shock response under steady-state conditionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 st...
Source: Proteome Science - September 20, 2009 Category: Bioinformatics Authors: Svenja LudersClaas FalletEzequiel Franco-Lara Source Type: journals

Prediction of outcome of non-small cell lung cancer patients treated with chemotherapy and bortezomib by time-course MALDI-TOF-MS serum peptide profilingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - September 2, 2009 Category: Bioinformatics Authors: Johannes VoortmanThang PhamJaco KnolGiuseppe GiacconeConnie Jimenez Source Type: journals

Subcellular proteomic characterization of the high-temperature stress response of the cyanobacterium Spirulina platensisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 biolo...
Source: Proteome Science - September 1, 2009 Category: Bioinformatics Authors: Apiradee HongsthongMatura SirijuntarutRayakorn YutthanasirikulJittisak SenachakPavinee KurdridSupapon CheevadhanarakMorakot Tanticharoen Source Type: journals

Proteomic analysis of total cellular proteins of human neutrophilsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - August 30, 2009 Category: Bioinformatics Authors: Gisele TomazellaIdalete da SilvaHelen LaureJose RosaRoger ChammasHarald WikerGustavo de SouzaLewis Greene Source Type: journals

Transchromosomic cell model of Down syndrome shows aberrant migration, adhesion and proteome response to extracellular matrixEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - August 27, 2009 Category: Bioinformatics Authors: Frederic DelomEmma BurtAlex HoischenJoris VeltmanJurgen GroetFinbarr CotterDean Nizetic Source Type: journals

Large-scale analysis of protein expression changes in human keratinocytes immortalized by human papilloma virus type 16 E6 and E7 oncogenesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This large-scale analysis provides a framework for understanding the cooperation between E6 and E7 oncoproteins in HPV-driven carcinogenesis. (Source: Proteome Science)
Source: Proteome Science - August 22, 2009 Category: Bioinformatics Authors: Mark MerkleyEllen HildebrandtRobert PodolskyHilal ArnoukDaron FerrisWilliam DynanHubert Stoppler Source Type: journals

A fractionation method to identify qauntitative changes in protein expression mediated by IGF-1 on the proteome of murine C2C12 myoblastsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, expre...
Source: Proteome Science - August 10, 2009 Category: Bioinformatics Authors: Charles KingKathryn BouicTheodore Friedmann Source Type: journals

Identification of protein functions using a machine-learning approach based on sequence-derived propertiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 pred...
Source: Proteome Science - August 8, 2009 Category: Bioinformatics Authors: Bum Ju LeeMoon Sun ShinYoung Joon OhHae Seok OhKeun Ho Ryu Source Type: journals

Proteomic profiling of glucocorticoid-exposed myogenic cells: time series assessment of protein translocation and transcription of inactive mRNAsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - July 29, 2009 Category: Bioinformatics Authors: Erica ReevesHeather Gordish-DressmanEric HoffmanYetrib Hathout Source Type: journals

Altered proteolytic events in experimental autoimmune encephalomyelitis discovered by iTRAQ shotgun proteomics analysis of spinal cordEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - July 15, 2009 Category: Bioinformatics Authors: Mohit Raja JainShengjie BianTong LiuJun HuStella ElkabesHong Li Source Type: journals

Proteins altered by elevated levels of palmitate or glucose implicated in impaired glucose-stimulated insulin secretionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The identified altered proteins indicate mechanism important for altered beta-cell function in T2DM. (Source: Proteome Science)
Source: Proteome Science - July 15, 2009 Category: Bioinformatics Authors: E-ri SolMeri HovsepyanPeter Bergsten Source Type: journals

Enhanced detection method for corneal protein identification using shotgun proteomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - June 28, 2009 Category: Bioinformatics Authors: Mitchell MeadePavel ShiyanovJohn Schlager Source Type: journals

Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Proteome Science - June 28, 2009 Category: Bioinformatics Authors: Srilatha KuntumallaJohn BraistedShih-Ting HuangPrashanth ParmarDavid ClarkHamid AlamiQuanshun ZhangArthur Donohue-RolfeSaul TziporiRobert FleischmannScott PetersonRembert Pieper Source Type: journals

Proteins recruited by SH3 domains of Ruk/CIN85 adaptor identified by LC-MS/MSEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - June 15, 2009 Category: Bioinformatics Authors: Serhiy HavrylovYuriy RzhepetskyyAgata MalinowskaLyudmyla DrobotMaria Jolanta Redowicz Source Type: journals

Mitochondrial proteomics on human fibroblasts for identification of metabolic imbalance and cellular stressEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - May 28, 2009 Category: Bioinformatics Authors: Johan PalmfeldtSoren VangVibeke StenbroenChristina PedersenJane ChristensenPeter BrossNiels Gregersen Source Type: journals

Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasetsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Proteome Science - May 14, 2009 Category: Bioinformatics Authors: Wouter Wegdam, Perry D Moerland, Marrije R Buist, Emiel Ver Loren van Themaat, Boris Bleijlevens, Huub CJ Hoefsloot, Chris G de Koster and Johannes MFG Aerts Source Type: journals

Proteomic analysis of the response of the plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stressEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - May 7, 2009 Category: Bioinformatics Authors: Zhenyu Cheng, Yi-Yun C Wei, Wilson WL Sung, Bernard R Glick and Brendan J McConkey Source Type: journals

Comprehensive proteomic analysis of human cervical-vaginal fluid using colposcopy samplesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - April 17, 2009 Category: Bioinformatics Authors: Geert Zegels, Geert AA Van Raemdonck, Edmond P Coen, Wiebren AA Tjalma and Xaveer WM Van Ostade Source Type: journals

Proteomic study on gender differences in aging kidney of miceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - April 9, 2009 Category: Bioinformatics Authors: Hanna Amelina and Susana Cristobal Source Type: journals

Development of reverse phase protein microarrays for the validation of clusterin, a mid-abundant blood biomarkerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - April 6, 2009 Category: Bioinformatics Authors: Adriana Aguilar-Mahecha, Christiane Cantin, Maureen O'Connor-McCourt, Andre Nantel and Mark Basik Source Type: journals

Proteomic analysis of phosphoproteins sensitive to a phosphatidylinositol 3-kinase inhibitor, ZSTK474, by using SELDI-TOF MSEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - March 31, 2009 Category: Bioinformatics Authors: Tetsuyuki Akashi and Takao Yamori Source Type: journals

Proteome analysis of the hyaluronic acid-producing bacterium, Streptococcus zooepidemicusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - March 28, 2009 Category: Bioinformatics Authors: Esteban Marcellin, Christian W. Gruber, Colin Archer, David J. Craik and Lars K. Nielsen Source Type: journals

The impact of surfactant protein-A on ozone-induced changes in the mouse bronchoalveolar lavage proteomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - March 26, 2009 Category: Bioinformatics Authors: Rizwanul Haque, Todd M. Umstead, Willard M. Freeman, Joanna Floros and David S. Phelps Source Type: journals

Identification and bioinformatic analysis of the membrane proteins of synechocystis sp. PCC 6803Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - March 25, 2009 Category: Bioinformatics Authors: Yingchun Wang, Wu Xu and Parag Chitnis Source Type: journals

Two-dimensional gel proteome reference map of human small intestine.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - March 19, 2009 Category: Bioinformatics Authors: Maria Paola Simula, Renato Cannizzaro, Maria Dolores Marin, Alessandro Pavan, Giuseppe Toffoli, Vincenzo Canzonieri and Valli De Re Source Type: journals

A novel approach to denoising ion trap tandem mass spectraEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - March 17, 2009 Category: Bioinformatics Authors: Jiarui Ding, Jinhong Shi, Guy G. Poirier and Fang-Xiang Wu Source Type: journals

Discovery and identification of potential biomarkers of pediatric Acute Lymphoblastic LeukemiaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - March 16, 2009 Category: Bioinformatics Authors: Linan Shi, Jun Zhang, Peng Wu, Kai Feng, Jing Li, Zhensheng Xie, Peng Xue, Tanxi Cai, Ziyou Cui, Xiulan Chen, Junjie Hou, Jianzhong Zhang and Fuquan Yang Source Type: journals

GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - February 24, 2009 Category: Bioinformatics Authors: Paulo C Carvalho, Juliana SG Fischer, Emily I Chen, Gilberto B Domont, Maria GC Carvalho, Wim M Degrave, John R Yates and Valmir C Barbosa Source Type: journals

GO Explorer: A gene-ontology tool to aid in the interpretation of spectral counting data in shotgun proteomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - February 24, 2009 Category: Bioinformatics Authors: Paulo C Carvalho, Juliana S G Fischer, Emily I Chen, Gilberto B Domont, Maria G C Carvalho, Wim M Degrave, John R Yates and Valmir C Barbosa Source Type: journals

High resolution preparation of monocyte-derived-macrophages (MDM) protein fractions for clinical proteomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - February 19, 2009 Category: Bioinformatics Authors: Rita Polati, Annalisa Castagna, Alessandra Bossi, Natascia Campostrini, Federica Zaninotto, Anna Maria Timperio, Lello Zolla, Oliviero Olivieri, Roberto Corrocher and Domenico Girelli Source Type: journals

Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 peripher...
Source: Proteome Science - February 19, 2009 Category: Bioinformatics Authors: Rembert Pieper, Shih-Ting Huang, David J. Clark, Jeffrey M. Robinson, Hamid Alami, Prashanth P. Parmar, Moo-Jin Suh, Srilatha Kuntumalla, Christine L. Bunai, Robert D. Perry, Robert D. Fleischmann and Scott N. Peterson Source Type: journals

A proteomic approach identified growth hormone-dependent nutrition markers in children with idiopathic short statureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - December 11, 2008 Category: Bioinformatics Authors: Gunnel Hellgren, Björn Andersson, Andreas FM Nierop, Jovanna Dahlgren, Ze'ev Hochberg and Kerstin Albertsson-Wikland Source Type: journals

A proteomic approach identified growth hormone dependent nutrition markers in children with idiopathic short statureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - December 11, 2008 Category: Bioinformatics Authors: Gunnel Hellgren, Bjorn Andersson, Andreas FM Nierop, Jovanna Dahlgren, Ze'ev Hochberg and Kerstin Albertsson-Wikland Source Type: journals

In-depth, high-accuracy proteomics of sea urchin tooth matrixEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Proteome Science - December 9, 2008 Category: Bioinformatics Authors: Karlheinz Mann, Albert J Poustka and Matthias Mann Source Type: journals

Label-free detection of biomolecular interactions in real time with a nano-porous silicon-based detection methodEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - November 4, 2008 Category: Bioinformatics Authors: Martin Latterich and Jacques Corbeil Source Type: journals

Dramatic down-regulation of oxidoreductases in human hepatocellular carcinoma hepG2 cells: proteomics and gene ontology unveiling new frontiers in cancer enzymologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 - October 24, 2008 Category: Bioinformatics Authors: Lambert C. M. Ngoka Source Type: journals

Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - October 24, 2008 Category: Bioinformatics Authors: Lambert C. M. Ngoka Source Type: journals

Improved proteome coverage by using iTRAQ labelling and peptide OFFGEL fractionationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - October 13, 2008 Category: Bioinformatics Authors: Emilie Ernoult, Erick Gamelin and Catherine Guette Source Type: journals

A simple and reliable protocol for mouse serum proteome profiling studies by use of two-dimensional electrophoresis and MALDI TOF/TOF mass spectrometryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - September 12, 2008 Category: Bioinformatics Authors: Maria Stella Ritorto and Jürgen Borlak Source Type: journals

Multidimensional protein fractionation using ProteomeLab PF 2D™ for profiling amyotrophic lateral sclerosis immunity: A preliminary reportEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We offer some insight into the strengths and limitations of this emerging proteomic platform. (Source: Proteome Science)
Source: Proteome Science - September 12, 2008 Category: Bioinformatics Authors: Joshua D Schlautman, Wojciech Rozek, Robert Stetler, R Lee Mosley, Howard E Gendelman and Pawel Ciborowski Source Type: journals

Deciphering animal development through proteomics: requirements and prospectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Proteome Science - July 24, 2008 Category: Bioinformatics Authors: Wolfgang E Reintsch and Craig A Mandato Source Type: journals

Proteomic profiling of urine for the detection of colon cancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - June 16, 2008 Category: Bioinformatics Authors: Douglas G Ward, Stephen Nyangoma, Joy Howard, Hamilton Emma, Wenbin Wei, Chris Tselepis, Neil Steven, Michael J O Wakelam, Philip J Johnson, Tariq Ismail and Ashley Martin Source Type: journals

Identification of differentially expressed proteins in spontaneous thymic lymphomas from knockout mice with deletion of p53Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - June 10, 2008 Category: Bioinformatics Authors: Bent Honore, Soren Buus and Mogens H Claesson Source Type: journals

Protein profiling of the dimorphic, pathogenic fungus, Penicillium marneffeiEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - June 4, 2008 Category: Bioinformatics Authors: Julie M Chandler, Erin R Treece, Heather R Trenary, Jessica L Brenneman, Tressa J Flickner, Jonathan L Frommelt, Zaw M Oo, Megan M Patterson, William T Rundle, Olga V Valle, Thomas D Kim, Gary R Walker and Chester R Cooper Source Type: journals

Pooling serum samples may lead to loss of potential biomarkers in SELDI-ToF MS proteomic profiling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions Pooling sera results in significant potential biomarker loss when using SELDI-ToF MS. (Source: Proteome Science)
Source: Proteome Science - June 1, 2008 Category: Bioinformatics Authors: S Tariq Sadiq and Dan Agranoff Source Type: journals