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 'Journal of Proteomics' source. Thu, 09 Feb 2012 13:38:40 +0100 http://www.medworm.com/index.php?rid=5654877&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22285629%26dopt%3DAbstract Authors: Huerta-Ocampo JA, Osuna-Castro JA, Lino-López GJ, Barrera-Pacheco A, Mendoza-Hernández G, De León-Rodríguez A, Barba de la Rosa AP Abstract Papaya (Carica papaya L.) is a climacteric fruit susceptible to postharvest losses due to the ethylene-induced ripening. The inhibitor of ethylene action, 1-methylcyclopropene (1-MCP), has been used worldwide as a safe postharvest non-toxic agent, but the physiological and biochemical modifications induced by 1-MCP are not well understood. Using the 2-DE analysis, we report the changes in the protein profiles after 6 and 18days of postharvest and the effect of 1-MCP on fruits treatment. Twenty seven protein spots showing differences in abundance during ripening were successfully identified by nano-LC-ESI/MS/MS. Some spots correspon... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5654877 Wed, 25 Jan 2012 05:00:00 +0100 5654877 http://www.medworm.com/index.php?rid=5654876&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22285630%26dopt%3DAbstract Authors: Nagaraj SH, Harsha HC, Reverter A, Colgrave ML, Sharma R, Andronicos N, Hunt P, Menzies M, Lees MS, Sekhar NR, Pandey A, Ingham A Abstract Sheep have a variable ability to resist gastrointestinal nematode infection, but the key factors mediating this response are poorly defined. Here we report the first large-scale application of quantitative proteomic technologies to define proteins that are differentially abundant between sheep selectively bred to have an enhanced (resistant) or reduced (susceptible) ability to eliminate nematodes. Samples were collected from the abomasal mucosa three days after experimental challenge with the nematode, Haemonchus contortus. This timing reflects the initial interaction of host and parasite, and the tissue represents the immediate interfa... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5654876 Wed, 25 Jan 2012 05:00:00 +0100 5654876 http://www.medworm.com/index.php?rid=5654874&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22296676%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22296676 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5654874 Tue, 24 Jan 2012 05:00:00 +0100 5654874 http://www.medworm.com/index.php?rid=5654875&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22285631%26dopt%3DAbstract Authors: Collado-Romero M, Martins RP, Arce C, Moreno A, Lucena C, Carvajal A, Garrido JJ Abstract The enteropathogen Salmonella Typhimurium is one of the main causes of porcine and human enterocolitis. We have used a 2-DE, MALDI-TOF/TOF-based approach to characterize in vivo proteome changes in porcine ileum mucosa after pathogen interaction. Ileum samples from non-infected and orally infected animals were collected at 2days post infection and S. Typhimurium presence was confirmed by immunohistochemistry. Fifty one proteins, involved in immune response (acute phase response, inflammation and immune response regulation), apoptosis and pathogen-mediated cell invasion, were identified as being differentially expressed after pathogen challenge. Overall, anti-inflammatory signals and a... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5654875 Fri, 20 Jan 2012 05:00:00 +0100 5654875 http://www.medworm.com/index.php?rid=5636661&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22270014%26dopt%3DAbstract Authors: Zellner M, Baureder M, Rappold E, Bugert P, Kotzailias N, Babeluk R, Baumgartner R, Attems J, Gerner C, Jellinger K, Roth E, Oehler R, Umlauf E Abstract Monoamine oxidase-B (Mao-B) catalysing the breakdown of the neurotransmitter dopamine, is known to be involved in the pathophysiology of Parkinson's (PD) and Alzheimer's disease (AD). Increased brain Mao-B activity is associated with AD. This alteration can also be seen in platelets, albeit the cause has hitherto remained elusive. To gain a deeper understanding of the etiology of AD, the platelet proteome was characterised, (2D DIGE pH6-9, including Mao-B) from 150 individuals: 34AD, 13 vascular dementia, 15 non-demented PD patients, 49 matched controls, 18 oldest old and 21 young individuals. One significant change was no... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636661 Tue, 17 Jan 2012 05:00:00 +0100 5636661 http://www.medworm.com/index.php?rid=5636660&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22270015%26dopt%3DAbstract Authors: Xu Y, Qian H, Feng X, Xiong Y, Lei M, Ren Z, Zuo B, Xu D, Ma Y, Yuan H Abstract To gain further insight into the molecular mechanism of porcine skeletal muscle development, we combined MS characterization of proteins with high-throughput screening of differential mRNAs obtained from purebred Meishan longissimus dorsi muscle (LM) at four stages of 65days post conception, 3, 60 and 120days after birth. Strikingly, the dramatic differences were observed in embryo and newborn pigs, whereas 60 and 120days pigs exhibited similar patterns in protein and mRNA expression. At the protein level, 66 differentially expressed proteins were identified. The development-dependent alterations in protein abundance indicated dramatic changes in metabolism, myofibrillar filaments, cytoskeleton... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636660 Tue, 17 Jan 2012 05:00:00 +0100 5636660 http://www.medworm.com/index.php?rid=5636658&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22282019%26dopt%3DAbstract Authors: Grigera PR, Ma L, Borgman CA, Pinto AF, Sherman NE, Parsons JT, Fox JW Abstract Cortactin is an F-actin binding protein that functions as a scaffold to regulate Arp2/3 mediated actin polymerization in lamellipodia and invadopodia formation as well as functioning in cell migration and endocytosis of many different cell types. In light of the fact that regulated actin polymerization is critical for many cellular processes we launched a search for novel cortactin interactions with cellular proteins that might indicate heretofore undescribed biological activities supported by cortactin. Using a modified stable isotope labeling in cell culture (SILAC) approach in HEK293 cells and Flag-tagged cortactin (F-cortactin) as bait, we identified a limited set of cortactin interactions ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636658 Tue, 17 Jan 2012 05:00:00 +0100 5636658 http://www.medworm.com/index.php?rid=5636667&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22266485%26dopt%3DAbstract Authors: Wang HY, Lin CY, Chien CC, Kan WC, Tian YF, Liao PC, Wu HY, Su SB Abstract Peritoneal morphology and function are abnormal in uremia patients, but the contributing mechanisms are unclear. Here we attempted to characterize the protein targets that may be related to peritoneal change in patients with uremia and have not exposed to peritoneal dialysis fluid. Protein profiles of peritoneal fluids collected from patients with uremia and patients with normal renal function receiving laparoscopic cholecystectomy were displayed by two-dimensional gel electrophoresis (2-DE). Altered protein spots were excised and subjected to tryptic digestion followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Sixteen 2-DE protein spots were altered between two groups. ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636667 Mon, 16 Jan 2012 05:00:00 +0100 5636667 http://www.medworm.com/index.php?rid=5636666&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22270009%26dopt%3DAbstract Authors: Schröder PC, Fernández-Irigoyen J, Bigaud E, Serna A, Hernández R, Lu SC, Mato JM, Prieto J, Corrales FJ Abstract Methionine adenosyltransferase I/III (MATI/III) synthesizes S-adenosylmethionine (SAM) in quiescent hepatocytes. Its activity is compromised in most liver diseases including liver cancer. Since SAM is a driver of hepatocytes fate we have studied the effect of re-expressing MAT1A in hepatoma Huh7 cells using proteomics. MAT1A expression leads to SAM levels close to those found in quiescent hepatocytes and induced apoptosis. Normalization of intracellular SAM induced alteration of 128 proteins identified by 2D-DIGE and gel-free methods, accounting for deregulation of central cellular functions including apoptosis, cell proliferation and survival. Human Dead-bo... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636666 Mon, 16 Jan 2012 05:00:00 +0100 5636666 http://www.medworm.com/index.php?rid=5636664&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22270011%26dopt%3DAbstract Authors: Wang L, Ma H, Song L, Shu Y, Gu W Abstract High temperature and humidity (HTH) stress during soybean seed development and maturity in the field easily leads seed to pre-harvest deterioration. However, how proteins and their involved pathways in developing soybean seed systematically cause deterioration is still not largely understood. To reveal it, we compared the proteome composition of developing seed (R(7) period) of a pre-harvest seed deterioration sensitive soybean cultivar at different HTH stress time points (24, 96 and 168h) with their corresponding controls by 2-DE. 42 protein spots were found to be differentially expressed and successfully identified by MALDI-TOF MS to match 31 diverse protein species. These proteins were involved in 13 cellular responses and meta... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636664 Mon, 16 Jan 2012 05:00:00 +0100 5636664 http://www.medworm.com/index.php?rid=5636663&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22270012%26dopt%3DAbstract Authors: Billing AM, Revets D, Hoffmann C, Turner JD, Vernocchi S, Muller CP Abstract In order to investigate rapid non-genomic effects of acute stress, rats were restrained for 15min which was sufficient to activate the hypothalamus-pituitary-adrenal (HPA) axis but too short to induce massive genomic effects of cortisol. Subcellular fractions of thymocytes (cytosol, nucleus, membrane) were investigated using quantitative 2D DIGE with MALDI-TOF/TOF mass spectrometry. In total, 108 proteins with differential subcellular localizations were identified. The specificity of the changes induced by psychological stress was reflected by the prominent modulation of proteins involved in the HPA and sympathoadrenal medullar (SAM) axis such as HMGB1 and NHERF1. Intracellular trafficking was cha... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636663 Mon, 16 Jan 2012 05:00:00 +0100 5636663 http://www.medworm.com/index.php?rid=5636662&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22270013%26dopt%3DAbstract This study compared protein profiles of mice small intestines at four time points (0, 3, 6 and 24h) after a single oral administration of 750μg/kg OA, and identified the differentially expressed proteins using 2-D DIGE and MALDI-TOF-TOF mass spectrometry. The results showed that the toxin content of the intestines reached its peak 3h after oral administration and then decreased rapidly. OA remarkably inhibited the intestinal PP activity but it recovered to the normal levels within 6 to 24h. Electron microscope revealed the collapse of the villous architecture and the intestinal microvilli fell off at 3h, but were repaired within 24h. Notable damage to the intestinal ultrastructure was observed after oral administration. Comparison of the small intestine protein profiles at four time point... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636662 Mon, 16 Jan 2012 05:00:00 +0100 5636662 http://www.medworm.com/index.php?rid=5636671&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22266101%26dopt%3DAbstract In this study, we performed a proteomic analysis of nucellus from two developmental stages of Ricinus communis seeds by a GeLC-MS/MS approach, using of a high resolution orbitrap mass spectrometer, which resulted in the identification of a total of 766 proteins that were grouped into 553 protein groups. The distribution of the identified proteins in stages III and IV into different Gene Ontology categories was similar, with a remarkable abundance of proteins associated with the protein synthesis machinery of cells, as well as several classes of proteins involved in protein degradation, particularly of peptidases associated with programmed cell death. Consistent with the role of the nucellus in mediating nutrient transfer from maternal tissues to the endosperm and embryo, a significant prop... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636671 Sat, 14 Jan 2012 05:00:00 +0100 5636671 http://www.medworm.com/index.php?rid=5636669&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22266103%26dopt%3DAbstract Authors: Capriotti AL, Caracciolo G, Cavaliere C, Foglia P, Pozzi D, Samperi R, Laganà A Abstract Cationic liposomes (CLs) are one of the most employed nonviral nanovector systems in gene therapy. However, their transfection efficiency is strongly affected by interactions with plasma components, that lead to the formation of a "protein corona" onto CL surface. The interactions between nanoparticles entering the body and biomolecules have an essential role for their biodistribution. Because the knowledge of proteins adsorbed onto vector surface could be useful in the screening of new, more efficient and more biocompatible liposomal formulations, the behavior of three CLs with different membrane charge densities was investigated. The proteins of the three coronas were identified by ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636669 Sat, 14 Jan 2012 05:00:00 +0100 5636669 http://www.medworm.com/index.php?rid=5636668&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22266484%26dopt%3DAbstract Authors: Herrera M, Fernández J, Vargas M, Villalta M, Segura A, León G, Angulo Y, Paiva O, Matainaho T, Jensen SD, Winkel KD, Calvete JJ, Williams DJ, Gutiérrez JM Abstract The venom proteomes of populations of the highly venomous taipan snake, Oxyuranus scutellatus, from Australia and Papua New Guinea (PNG), were characterized by reverse-phase HPLC fractionation, followed by analysis of chromatographic fractions by SDS-PAGE, N-terminal sequencing, MALDI-TOF mass fingerprinting, and collision-induced dissociation tandem mass spectrometry of tryptic peptides. Proteins belonging to the following eight protein families were identified in the two venoms: phospholipase A(2) (PLA(2)), Kunitz-type inhibitor, metalloproteinase (SVMP), three-finger toxin (3FTx), serine proteinase, cyste... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636668 Sat, 14 Jan 2012 05:00:00 +0100 5636668 http://www.medworm.com/index.php?rid=5636670&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22266102%26dopt%3DAbstract This report confirms that transferrin precursor/iron binding protein is the major component in reptile egg white. In egg white of Siamese crocodile, twenty isoforms of transferrin precursor were found. Iron binding protein was found in four species of turtle. In egg white of soft-shelled turtle, ten isoforms of lysozyme were found. Apart from well-known reptile egg white constituents, this study identified some reptile egg white proteins, such as the teneurin-2 (fragment), the interferon-induced GTP-binding protein Mx, the olfactory receptor 46 and the succinate dehydrogenase iron-sulfur subunit. PMID: 22266102 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636670 Fri, 13 Jan 2012 05:00:00 +0100 5636670 http://www.medworm.com/index.php?rid=5636665&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22270010%26dopt%3DAbstract Authors: Fonseca C, Planchon S, Renaut J, Oliveira MM, Batista R Abstract One of the main concerns about genetically modified foods and their potential impacts on human health is that the introduction of a new/ altered gene may putatively alter the expression of others, namely endogenous allergens. We intended to evaluate, and to compare, using quantitative real time RT-PCR technique, the expression of 5 already known maize allergens (Zea m14, Zea m25, Zea m27kD, 50kD Zein and trypsin inhibitor) in MON 810 vs. its non-transgenic counterpart, throughout seed development (10, 16 and 23days after pollination). We have shown that none of the tested allergen genes presented differential expression, with statistic significance, along all tested seed development stages, in MON810 vs. its ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636665 Fri, 13 Jan 2012 05:00:00 +0100 5636665 http://www.medworm.com/index.php?rid=5636659&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22282018%26dopt%3DAbstract We report on the simple application of a new nanostructured silicon (NanoSi) substrate as laser desorption/ionization (LDI)-promoting surface for high-throughput identification of protein tryptic digests by a rapid MS profiling and subsequent MS/MS analysis. The NanoSi substrate is easily prepared by chemical etching of crystalline silicon in NH(4)F/HNO(3)/AgNO(3) aqueous solution. To assess the LDI performances in terms of sensitivity, repeatability and robustness, the detection of small synthetic peptides (380-1700Da) was investigated. Moreover, peptide sequencing was tackled. Various tryptic synthetic peptide mixtures were first characterized in MS and MS/MS experiments carried out on a single deposit. Having illustrated the capability to achieve peptide detection and sequencing on thes... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5636659 Thu, 12 Jan 2012 05:00:00 +0100 5636659 http://www.medworm.com/index.php?rid=5618562&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245417%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22245417 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618562 Tue, 10 Jan 2012 05:00:00 +0100 5618562 http://www.medworm.com/index.php?rid=5618559&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245420%26dopt%3DAbstract Authors: Manivannan B, Jordan TW, Secor WE, La Flamme AC Abstract Chronic Schistosoma mansoni infection can present as a moderate or severe disease, termed intestinal or hepatosplenic schistosomiasis, respectively. Similarly, either moderate splenomegaly or hypersplenomegaly syndrome develops in CBA/J mice by 20weeks of infection and is similar to intestinal or hepatosplenic schistosomiasis respectively. Using this mouse model and two-dimensional differential in gel electrophoresis, the liver proteomic signatures of uninfected mice and mice infected for 6, 8, 12, or 20weeks were compared, and significant protein spots identified using mass spectrometry. We found the greatest number of changes at 12weeks suggesting that this period represents the peak time of change. Pathway analysi... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618559 Tue, 10 Jan 2012 05:00:00 +0100 5618559 http://www.medworm.com/index.php?rid=5618554&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22252011%26dopt%3DAbstract This study aimed to investigate changes in the abundance of protein species during cold pretreatment and subsequent cultivation of maize anthers on induction media using gel-based proteomics. Proteins upregulated on the third day of anther induction were identified and discussed here. Simultaneous microscopic observations revealed that the first division occurred in microspores within this period. Using 2-D electrophoresis combined with MALDI TOF/TOF MS/MS analysis 19 unique proteins were identified and classified into 8 functional groups. Proteins closely associated with metabolism, protein synthesis and cell structure were the most abundant ones. Importantly, ascorbate peroxidase, an enzyme decomposing hydrogen peroxide, was also upregulated. Isozyme analysis of peroxidases validated the... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618554 Mon, 09 Jan 2012 05:00:00 +0100 5618554 http://www.medworm.com/index.php?rid=5618561&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245418%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22245418 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618561 Sun, 08 Jan 2012 05:00:00 +0100 5618561 http://www.medworm.com/index.php?rid=5618560&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245419%26dopt%3DAbstract Authors: Mohammadi PP, Moieni A, Hiraga S, Komatsu S Abstract Changes in protein levels in drought-stressed soybean seedlings were analyzed using a proteomics approach. Three-day-old soybean seedlings were subjected to drought stress or treated with 10% polyethylene glycol (PEG) as osmotic stress. After treatment, the proteins were extracted from the leaf, hypocotyl, and root and separated using two-dimensional polyacrylamide gel electrophoresis. The root was the most drought-responsive organ, with the levels of 32, 13, and 12 proteins changing in response to drought stress, PEG treatment, and both, respectively. In the leaves of PEG-treated and drought-stressed seedlings, metabolism-related proteins increased and energy production- and protein synthesis-related proteins decreased.... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618560 Sun, 08 Jan 2012 05:00:00 +0100 5618560 http://www.medworm.com/index.php?rid=5618557&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245552%26dopt%3DAbstract This study presents a proteomic analysis on the change of egg white proteins during the first week of embryonic development. By using 2-DE, together with MALDI-TOF MS/MS, thirty protein spots representing eight proteins were identified showing significant changes in abundance during incubation. An accelerating degradation of ovalbumin was observed in a wide range of molecular weight. In addition, four protein complexes were predicted according to the detected molecular weight increase. Among these speculated protein complexes, an ovalbumin spot coupled with RNA-binding protein was detected. The absence of these protein complexes before incubation, followed by the constant increase in abundance during incubation indicates conceivable pivotal roles in embryonic development. To better underst... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618557 Fri, 06 Jan 2012 05:00:00 +0100 5618557 http://www.medworm.com/index.php?rid=5618563&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245046%26dopt%3DAbstract Authors: Guo G, Ge P, Ma C, Li X, Lv D, Wang S, Ma W, Yan Y Abstract A comparative proteomic analysis was made of salt response in seedling roots of wheat cultivars Jing-411 (salt tolerant) and Chinese Spring (salt sensitive) subjected to a range of salt stress concentrations (0.5%, 1.5% and 2.5%) for 2days. One hundred and ninety eight differentially expressed protein spots (DEPs) were located with at least two-fold differences in abundance on 2-DE maps, of which 144 were identified by MALDI-TOF-TOF MS. These proteins were involved primarily in carbon metabolism (31.9%), detoxification and defense (12.5%), chaperones (5.6%) and signal transduction (4.9%). Comparative analysis showed that 41 DEPs were salt responsive with significant expression changes in both varieties under salt ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618563 Thu, 05 Jan 2012 05:00:00 +0100 5618563 http://www.medworm.com/index.php?rid=5618558&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245551%26dopt%3DAbstract We describe an alternative, simple, rapid gel-free strategy to identify multiple immunogenic proteins from Bordetella pertussis (Bp). It couples immunoprecipitation to nano liquid chromatography- tandem mass spectrometry (IP-nLC-MS/MS) and is significantly both time- and labor-saving. We developed a gel-free magnetic bead-based immunoprecipitation (IP) method using different NP-40/PBS concentrations in which solubilized proteins of Bp Tohama I membrane fractions were precipitated with polyclonal rabbit anti-Bp whole cell immune sera. Immune complexes were analyzed by MS and Scaffold analysis (>95% protein identification probability). Total immunoproteins identified were 50, 63 and 49 for 0.90%, 0.45% and 0.22% NP-40/PBS buffer concentrations respectively. Known Bp proteins identified in... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618558 Thu, 05 Jan 2012 05:00:00 +0100 5618558 http://www.medworm.com/index.php?rid=5618556&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245553%26dopt%3DAbstract This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial Photosynthesis. PMID: 22245553 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618556 Thu, 05 Jan 2012 05:00:00 +0100 5618556 http://www.medworm.com/index.php?rid=5618555&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245554%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22245554 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5618555 Thu, 05 Jan 2012 05:00:00 +0100 5618555 http://www.medworm.com/index.php?rid=5595152&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22240297%26dopt%3DAbstract Authors: Svoboda DS, Kawaja MD Abstract Hypertension is a systemic disorder affecting numerous physiological processes throughout the body. As non-alcoholic fatty liver disorder (NAFLD) is a common comorbidity of hypertension in humans, we hypothesized that molecular hepatic physiology would be altered in a model of genetic hypertension. Despite the broad use of the spontaneous hypertensive rat (SHR) model, little is known regarding how hypertension influences hepatic function under basal conditions. In order to determine whether hypertension induces changes in the hepatic protein expression suggestive of early stages of NAFLD, we compared the whole tissue proteome of livers from SHR and Wistar Kyoto (WKY) 16week old rats using 2DGE and MALDI-TOF MS. Fifteen proteins were identifie... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595152 Thu, 05 Jan 2012 05:00:00 +0100 5595152 http://www.medworm.com/index.php?rid=5595158&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22234360%26dopt%3DAbstract This article is part of a Special Issue entitled: SI: Genome regulations and Genetic diversity. PMID: 22234360 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595158 Tue, 03 Jan 2012 05:00:00 +0100 5595158 http://www.medworm.com/index.php?rid=5595156&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22236518%26dopt%3DAbstract This article is part of a Special Issue entitled: Genome regulations and Genetic diversity. PMID: 22236518 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595156 Tue, 03 Jan 2012 05:00:00 +0100 5595156 http://www.medworm.com/index.php?rid=5595154&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22236520%26dopt%3DAbstract In conclusion, our study provided novel insights into Se response in rice at the proteome level, which are expected to be highly useful for dissecting the Se response pathways in higher plants and for producing Se enriched rice cultivars in the future. PMID: 22236520 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595154 Tue, 03 Jan 2012 05:00:00 +0100 5595154 http://www.medworm.com/index.php?rid=5595155&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22236519%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22236519 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595155 Mon, 02 Jan 2012 05:00:00 +0100 5595155 http://www.medworm.com/index.php?rid=5595153&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22240296%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22240296 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595153 Sat, 31 Dec 2011 05:00:00 +0100 5595153 http://www.medworm.com/index.php?rid=5595164&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22227400%26dopt%3DAbstract Authors: Zellner M, Graf A, Zehetmayer S, Winkler W, Staes A, Gevaert K, Vanderkerckhove J, Marchetti-Deschmann M, Miller I, Bauer P, Allmaier G, Oehler R Abstract Quantitative proteomic comparisons require a sufficient number of samples to reach an acceptable level of significance. But 2D gel electrophoresis commonly results in incomplete data sets due to spots with missing values reducing thereby the number of parallel measurements for individual proteins. Here we investigated how many missing values per spot can be tolerated. The number of spots in common between all gels was found to decrease with the number of parallel gels in a non-linear fashion. Increasing numbers of missing values were associated with a moderate increase in the quantitative variation of spot volumes. Based... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595164 Fri, 30 Dec 2011 05:00:00 +0100 5595164 http://www.medworm.com/index.php?rid=5595163&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22230806%26dopt%3DAbstract Authors: Mairesse J, Vercoutter-Edouart AS, Marrocco J, Zuena AR, Giovine A, Nicoletti F, Michalski JC, Maccari S, Morley-Fletcher S Abstract Rats exposed to early life stress are considered as a valuable model for the study of epigenetic programming leading to mood disorders and anxiety in the adult life. Rats submitted to prenatal restraint stress (PRS) are characterized by an anxious/depressive phenotype associated with neuroadaptive changes in the hippocampus. We used the model of PRS to identify proteins that are specifically affected by early life stress. We therefore performed a proteomic analysis in the hippocampus of adult male PRS rats. We found that PRS induced changes in the expression profile of a number of proteins, involved in the regulation of signal transduction, s... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595163 Fri, 30 Dec 2011 05:00:00 +0100 5595163 http://www.medworm.com/index.php?rid=5595162&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22230807%26dopt%3DAbstract Authors: Pavón EJ, García-Rodríguez S, Zumaquero E, Perandrés-López R, Rosal-Vela A, Lario A, Longobardo V, Carrascal M, Abián J, Callejas-Rubio JL, Ortego-Centeno N, Zubiaur M, Sancho J Abstract Proteins differentially expressed in peripheral blood mononuclear cells (PBMCs) from systemic lupus erythematosus (SLE) patients versus Normal controls were identified by 2-DE and MALDI-MS. Thus, S100A9 expression was significantly increased in SLE PBMCs relative to Normal PBMCs at both mRNA and protein levels. Increased S100A9 levels in SLE PBMCs correlated positively with the abnormal presence of low-density granulocytes (LDGs) detected by flow-cytometry in the mononuclear cell fractions. Another set of proteins that were differentially expressed in SLE PBMCs formed S100A9-independ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595162 Fri, 30 Dec 2011 05:00:00 +0100 5595162 http://www.medworm.com/index.php?rid=5595161&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22230808%26dopt%3DAbstract Authors: Fasoli E, D'Amato A, Citterio A, Righetti PG Abstract The trace proteome of a Ginger drink, stated to be produced with a ginger root extract, has been investigated via capture with combinatorial peptide ligand libraries (ProteoMiner). Although in traces, we could confirm the presence of five grape proteins and one apple protein, but not even the faintest trace of any ginger root proteins. The first two findings are correct, as the producer stated that this beverage had been reinforced with 12% grape juice and 6% apple juice, but the absence of even traces of ginger proteins does not permit the classification of this beverage as a ginger extract on a proteomics scale. However, organoleptic tasting has confirmed the presence of a ginger extract, due to its piquant and tongue... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595161 Fri, 30 Dec 2011 05:00:00 +0100 5595161 http://www.medworm.com/index.php?rid=5595160&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22234358%26dopt%3DAbstract Authors: Epiney M, Ribaux P, Arboit P, Irion O, Cohen M Abstract Preeclampsia (PE) is a pathology of pregnancy which represents the main cause of maternal and perinatal morbidity and mortality. Defective placentation is the first event of this pathology. The purpose of this study was to identify the proteins secreted by cytotrophoblastic cells (CTB) using proteomic approach that are associated with PE. Comparison of secreted proteins by mass spectrometry allowed us to identify 21 proteins which were significantly differentially secreted by control and PE CTB. One protein has been detected exclusively in supernatant of control CTB and was identified as factor XIII chain A. To determine if this observation is due to a difference of protein secretion or gene expression, its mRNA was q... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595160 Fri, 30 Dec 2011 05:00:00 +0100 5595160 http://www.medworm.com/index.php?rid=5595159&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22234359%26dopt%3DAbstract Authors: Ares-Carrasco S, Picatoste B, Camafeita E, Carrasco-Navarro S, Zubiri I, Ortiz A, Egido J, López JA, Tuñón J, Lorenzo O Abstract Diabetes with or without the presence of hypertension damages the heart. However, there is currently a lack of information about these associated pathologies and the alteration of linked proteins. For these reasons, we were interested in the potential synergistic interaction of diabetes and hypertension in the heart, focusing on the proteome characterization of the pathological phenotypes and the associated hypertrophic response. We treated normotensive and spontaneously hypertensive (SHR) rats with either streptozotocin or vehicle. After 22weeks, type-I diabetic (DM1), SHR, SHR/DM1 and control left-ventricles were studied using proteomic appr... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595159 Fri, 30 Dec 2011 05:00:00 +0100 5595159 http://www.medworm.com/index.php?rid=5595157&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22236517%26dopt%3DAbstract Authors: Tomazella GG, Risberg K, Mylvaganam H, Lindemann PC, Thiede B, de Souza GA, Wiker HG Abstract Horizontal transfer of gene clusters occurs in Escherichia coli (E. coli), which could lead to evolution of new pathovars and improve survival fitness. However, this genetic event results in genomic plasticity which is a hindrance for proteomic characterization of strains with unknown genetic backgrounds. To characterize such isolate with many specific genetic variations we used the recently in-house designed MSMSpdbb software which merges protein databases from several sources of E. coli including type strains and other commensal and pathogenic isolates. We selected a multidrug resistant clinical isolate in order to check the capacity of our approach to identify selected protein ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5595157 Fri, 30 Dec 2011 05:00:00 +0100 5595157 http://www.medworm.com/index.php?rid=5576505&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22212456%26dopt%3DAbstract In this study, the venom proteomes of Porthidium nasutum, P. ophryomegas, and Cerrophidion godmani from Costa Rica were analyzed, and correlated to their toxic and enzymatic activities. Their HPLC profiles revealed a higher similarity between the two Porthidium species than between these and C. godmani. Proteins belonging to nine (P. nasutum), eight (P. ophryomegas), and nine (C. godmani) families were identified by mass spectrometry or N-terminal sequencing. Final cataloging of proteins and their relative abundances confirmed the close relationship between venom of P. nasutum and P. ophryomegas, departing from that of C. godmani. Since the latter species had been taxonomically classified as Porthidium godmani previously, our venomic analyses agree with its current generic status. Venom of... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5576505 Fri, 23 Dec 2011 05:00:00 +0100 5576505 http://www.medworm.com/index.php?rid=5557854&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22200674%26dopt%3DAbstract This article is part of a Special Issue entitled: (Clinical Proteomics). PMID: 22200674 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557854 Tue, 20 Dec 2011 05:00:00 +0100 5557854 http://www.medworm.com/index.php?rid=5557853&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22200675%26dopt%3DAbstract In conclusion, our results indicate that overstimulation of cytochrome b(5) reductase associated with lipid rafts can account for the overshot of plasma membrane-focalized superoxide anion production that triggers the entry of CGN in the irreversible phase of apoptosis. PMID: 22200675 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557853 Tue, 20 Dec 2011 05:00:00 +0100 5557853 http://www.medworm.com/index.php?rid=5557852&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22200676%26dopt%3DAbstract Authors: Bond JJ, Dunne JC, Kwan FY, Li D, Zhang K, Leahy SC, Kelly WJ, Attwood GT, Jordan TW Abstract The research was aimed at finding which membrane proteins of the rumen bacterium Butyrivibrio proteoclasticus are involved in the uptake of carbohydrates resulting from extracellular enzymatic degradation of hemicellulose and fructan. The proteomic analysis of cells grown with fructose or xylan as the sole substrate identified 13 membrane proteins predicted to function as carbohydrate transporters. One protein detected was the membrane component of a fructose-specific phosphoenolpyruvate:sugar phosphotransferase system believed to be involved in the fructose uptake following extracellular fructan breakdown. The other 12 proteins were all ABC transport system substrate-binding prot... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557852 Tue, 20 Dec 2011 05:00:00 +0100 5557852 http://www.medworm.com/index.php?rid=5557851&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22200677%26dopt%3DAbstract This article is part of a Special Issue entitled: (Clinical Proteomics). PMID: 22200677 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557851 Tue, 20 Dec 2011 05:00:00 +0100 5557851 http://www.medworm.com/index.php?rid=5557850&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22202183%26dopt%3DAbstract Authors: Kailasa SK, Wu HF Abstract Functionalized quantum dots with dopamine dithiocarbamate (QDs-DDTC) were utilized for the first time as an efficient material for the quantification of efavirenz in human plasma of HIV infected patients and rapid identification of microwave tryptic digest proteins (cytochrome c, lysozyme and BSA) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The synthesized QDs-DDTC was characterized by using spectroscopic (UV-visible, FT-IR and (1)H NMR) and microscopic (SEM and TEM) techniques. Functionalized QDs-DDTC exhibited a high desorption/ionization efficiency for the rapid quantification of small molecules (efavirenz, tobramycin and aspartame) at low-mass region. QDs-DDTC has well ability to trap target... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557850 Tue, 20 Dec 2011 05:00:00 +0100 5557850 http://www.medworm.com/index.php?rid=5557849&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22202184%26dopt%3DAbstract In this study, we developed a combined chemical and enzymatic strategy as an alternative for the mass spectrometric analysis of aberrant glycosylation. Sialylated glycopeptides were enriched with reverse glycoblotting, cleaved by endoglycosidase F3 and analyzed by mass spectrometry with both neutral loss triggered MS(3) in collision induced dissociation (CID) and electron transfer dissociation (ETD). Interestingly, a great part of resulted glycopeptides were found with fucose attached to the N-acetylglucosamine (N-GlcNAc), which indicated that the aberrant glycosylation that is carrying both terminal sialylation and core fucosylation was identified. Totally, 69 aberrant N-glycosylation sites were identified in sera samples from hepatocellular carcinoma (HCC) patients. Following the identif... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557849 Tue, 20 Dec 2011 05:00:00 +0100 5557849 http://www.medworm.com/index.php?rid=5557848&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22202185%26dopt%3DAbstract This study provides insights into the biologic characteristics, potential virulence alteration and cross-species transmission mechanisms of the pandemic H1N1/2009. PMID: 22202185 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557848 Tue, 20 Dec 2011 05:00:00 +0100 5557848 http://www.medworm.com/index.php?rid=5557847&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22207155%26dopt%3DAbstract We present evidence that this shift corresponds to a hyxdroxymethylation of asparagine and glutamine residues. This known but poorly documented post-translational modification was only found in a few proteins of S. aureus grown under specific conditions. This specificity seemed to exclude the hypothesis of an artifact due to sample preparation. Altogether hydroxymethylation was observed in 35 peptides from 15 proteins in our dataset, which corresponded to 41 modified sites, 35 of them being univocally localized. While no function can currently be assigned to this post-translational modification, we hypothesize that it could be linked to modulation of virulence factors, since it was mostly found on some surface proteins of S. aureus. PMID: 22207155 [PubMed - as supplied by publisher] (S... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557847 Tue, 20 Dec 2011 05:00:00 +0100 5557847 http://www.medworm.com/index.php?rid=5557846&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22207156%26dopt%3DAbstract In this study, we performed iTRAQ proteome analysis of the amago salmon pituitary, with and without excess GH1 treatment, and found that the expression levels of proteins related to endocrine systems, metabolism, cell growth and proliferation were altered in the GH1-treated pituitary. Specifically, pituitary hormone prolactin (2.29 fold), and somatolactin α (0.14 fold) changed significantly. This result was confirmed by proteome and transcriptome analyses of pituitary from the GH1-transgenic (GH1-Tg) amago salmon. The dynamics of protein and gene expression in the pituitary of GH1-Tg amago salmon were similar to those of pituitary treated with excess GH1. Our findings suggest that not only excess GH1 hormone, but also the quantitative changes in other pituitary hormones, might be essentia... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5557846 Tue, 20 Dec 2011 05:00:00 +0100 5557846 http://www.medworm.com/index.php?rid=5544484&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22197968%26dopt%3DAbstract CONCLUSION: The study of tissue secretome reveals key proteins involved in atherosclerosis which have not been previously reported in plasma. Novel proteins are here highlighted which could be potential therapeutic targets in clinical practice. PMID: 22197968 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5544484 Fri, 16 Dec 2011 05:00:00 +0100 5544484 http://www.medworm.com/index.php?rid=5544485&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22193514%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22193514 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5544485 Tue, 13 Dec 2011 05:00:00 +0100 5544485 http://www.medworm.com/index.php?rid=5525480&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178444%26dopt%3DAbstract Authors: Li BQ, Hu LL, Niu S, Cai YD, Chou KC Abstract S-nitrosylation (SNO) is one of the most important and universal post-translational modifications (PTMs) which regulates various cellular functions and signaling events. Identification of the exact S-nitrosylation sites in proteins may facilitate the understanding of the molecular mechanisms and biological function of S-nitrosylation. Unfortunately, traditional experimental approaches used for detecting S-nitrosylation sites are often laborious and time-consuming. However, computational methods could overcome this demerit. In this work, we developed a novel predictor based on nearest neighbor algorithm (NNA) with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). The features... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5525480 Sun, 11 Dec 2011 05:00:00 +0100 5525480 http://www.medworm.com/index.php?rid=5525479&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178445%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22178445 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5525479 Sat, 10 Dec 2011 05:00:00 +0100 5525479 http://www.medworm.com/index.php?rid=5525476&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178446%26dopt%3DAbstract Authors: Lopitz-Otsoa F, Rodriguez-Suarez E, Aillet F, Casado-Vela J, Lang V, Matthiesen R, Elortza F, Rodriguez MS Abstract The successful use of proteasome inhibitors in clinical trials revealed the potential of the Ubiquitin Proteasome System for drug development. Protein remodeling through ubiquitylation is known to regulate the stability and activity of essential cellular factors through largely uncharacterized mechanisms. Here, we used Tandem repeated Ubiquitin Binding Entities (TUBEs) under non-denaturing conditions followed by mass spectrometry analysis to study global ubiquitylation events that may lead to the identification of potential drug targets. Using this approach we identified 643 proteins including known and unknown ubiquitin targets from human breast adenocarcino... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5525476 Sat, 10 Dec 2011 05:00:00 +0100 5525476 http://www.medworm.com/index.php?rid=5525481&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178302%26dopt%3DAbstract Authors: Nilo RP, Campos-Vargas R, Orellana A Abstract Fruit ripening in Prunus persica involves a number of physiological changes, being one of the most significant the mesocarp softening in melting varieties. In order to get a better understanding of the molecular processes involved in this phenomenon, the protein accumulation patterns in firm and soft fruit of three peach and two nectarine melting flesh varieties were assessed using 2D gel analysis. A General Linear Model (GLM) two-way analysis of variance determined that 164 of the 621 protein spots analyzed displayed a differential accumulation associated with the softening process. Among them, only 14 proteins changed their accumulation in all the varieties assessed, including proteins mostly involved in carbohydrates and cel... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5525481 Thu, 08 Dec 2011 05:00:00 +0100 5525481 http://www.medworm.com/index.php?rid=5525475&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178447%26dopt%3DAbstract Authors: Greenwood C, Metodieva G, Al-Janabi K, Lausen B, Alldridge L, Leng L, Bucala R, Fernandez N, Metodiev MV Abstract Triple-negative breast cancer is difficult to treat because of the lack of rationale-based therapies. There are no established markers and targets that can be used for stratification of patients and targeted therapy. Here we report the identification of novel molecular features, which appear to augment metastasis of triple negative breast tumors. We found that triple-negative breast tumors can be segregated into 2 phenotypes based on their genome-wide protein abundance profiles. The first is characterized by high expression of Stat1, Mx1, and CD74. Seven out of 9 tumors from this group had invaded at least 2 lymph nodes while only 1 out of 10 tumors in group 2 ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5525475 Thu, 08 Dec 2011 05:00:00 +0100 5525475 http://www.medworm.com/index.php?rid=5525474&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178735%26dopt%3DAbstract Authors: Gil-Dones F, Darde VM, Orgaz SA, Lopez-Almodovar LF, Mourino-Alvarez L, Padial LR, Vivanco F, Barderas MG Abstract Valvular aortic stenosis (AS) produces a slowly progressive obstruction in left ventricular outflow track. For this reason, aortic valve replacement is warranted when the valvular stenosis is hemodinamically significant, becoming the most common worldwide cause of aortic valve surgery. Recent epidemiologic studies have revealed an association between degenerative AS and cardiovascular risk factors for atherosclerosis, althought reducing the exposure to such factors and statin therapies both fail to delay or reverse the pathology. Hence, a deeper understanding of the pathophysiology of this disease is required to identify appropriate preventive measures. A prot... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5525474 Thu, 08 Dec 2011 05:00:00 +0100 5525474 http://www.medworm.com/index.php?rid=5506185&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155128%26dopt%3DAbstract Authors: Ma Y, He Y, Zhao R, Wu Y, Li W, Cao Z Abstract Venom is an important genetic development crucial to the survival of scorpions for over 400million years. We studied the evolution of the scorpion venom arsenal by means of comparative transcriptome analysis of venom glands and phylogenetic analysis of shared types of venom peptides and proteins between buthids and euscorpiids. Fifteen types of venom peptides and proteins were sequenced during the venom gland transcriptome analyses of two Buthidae species (Lychas mucronatus and Isometrus maculatus) and one Euscorpiidae species (Scorpiops margerisonae). Great diversity has been observed in translated amino acid sequences of these transcripts for venom peptides and proteins. Seven types of venom peptides and proteins were shared... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506185 Wed, 07 Dec 2011 05:00:00 +0100 5506185 http://www.medworm.com/index.php?rid=5506186&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155127%26dopt%3DAbstract This article is part of a Special Issue entitled: (Clinical Proteomics)." PMID: 22155127 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506186 Tue, 06 Dec 2011 05:00:00 +0100 5506186 http://www.medworm.com/index.php?rid=5506184&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155129%26dopt%3DAbstract In conclusion, CapG was identified as a novel candidate biomarker to predict response to gemcitabine treatment and survival in cholangiocarcinoma. PMID: 22155129 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506184 Tue, 06 Dec 2011 05:00:00 +0100 5506184 http://www.medworm.com/index.php?rid=5506230&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22146473%26dopt%3DAbstract Authors: Aryal BP, Paunesku T, Woloschak GE, He C, Jensen MP Abstract Plutonium can enter the body through different routes and remains there for decades; however its specific biochemical interactions are poorly defined. We, for the first time, have studied plutonium-binding proteins using a metalloproteomic approach with rat PC12 cells. A combination of immobilized metal ion chromatography, 2D gel electrophoresis, and mass spectrometry was employed to analyze potential plutonium-binding proteins. Our results show that several proteins from PC12 cells show affinity towards Pu(4+)-NTA (plutonium bound to nitrilotriacetic acid). Proteins from seven different spots in the 2D gel were identified. In contrast to the previously known plutonium-binding proteins transferrin and ferritin, w... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506230 Sat, 03 Dec 2011 05:00:00 +0100 5506230 http://www.medworm.com/index.php?rid=5506229&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22146474%26dopt%3DAbstract Authors: Buschow SI, Lasonder E, Szklarczyk R, Oud MM, de Vries IJ, Figdor CG Abstract Dendritic cells (DC) take up pathogens through phagocytosis and process them into protein and lipid fragments for presentation to T cells. So far, the proteome of the human DC phagosome, a detrimental compartment for antigen processing and presentation as well as for DC activation, remains largely uncharacterized. Here we have analyzed the protein composition of phagosomes from human monocyte-derived DC. For LC-MS/MS analysis we purified phagosomes from DC using latex beads targeted to DC-SIGN, and quantified proteins using a label-free method. We used organellar enrichment ranking (OER) to select proteins with a high potential to be relevant for phagosome function. The method compares phagosome ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506229 Sat, 03 Dec 2011 05:00:00 +0100 5506229 http://www.medworm.com/index.php?rid=5506228&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22146475%26dopt%3DAbstract Authors: D'Alessandro A, D'Aguanno S, Cencioni MT, Pieroni L, Diamantini A, Battistini L, Longone P, Spalloni A, De Laurenzi V, Bernardini S, Federici G, Urbani A Abstract The Ubiquitin-Proteasome System (UPS) and the Autophagy-Lysosome Pathways (ALP) are key mechanisms for cellular homeostasis sustenance and protein clearance. A wide number of Neurodegenerative Diseases (NDs) are tied with UPS impairment and have been also described as proteinopathies caused by aggregate-prone proteins, not efficiently removed by proteasome. Despite the large knowledge on proteasome biological role, molecular mechanisms associated with its impairment are still blur. We have pursued a comprehensive proteomic investigation to evaluate the phenotypic rearrangements in protein repertoires associated w... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506228 Fri, 02 Dec 2011 05:00:00 +0100 5506228 http://www.medworm.com/index.php?rid=5506189&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22154983%26dopt%3DAbstract In this study, hexapeptide ligands previously described for enrichment of low-abundance proteins in proteomics are evaluated for glycan analysis. A repeatable on-bead glycan release strategy was developed, and glycans were analyzed using capillary sieving electrophoresis on a DNA analyzer. Binding of proteins to the hexapeptide library occurred via the protein backbone. At neutral pH no discrimination between protein glycoforms was observed. Interestingly, glycan profiles of plasma with and without hexapeptide library enrichment revealed very similar patterns, despite the vast changes in protein concentrations in the samples. The most significant differences in glycosylation profiles were ascribed to a reduction in immunoglobulin-derived glycans. These results suggest that specific and sen... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506189 Fri, 02 Dec 2011 05:00:00 +0100 5506189 http://www.medworm.com/index.php?rid=5506188&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155126%26dopt%3DAbstract In this study, we used 2D-DIGE to compare the proteome of Acetobacter pasteurianus LMG 1262(T) when growing in glucose or ethanol and in the presence of acetic acid. Interesting protein spots were selected using the ANOVA p-value of 0.05 as threshold and 1.5-fold as the minimal level of differential expression, and a total of 53 proteins were successfully identified. Additionally, the size of AAB was reduced by approximately 30% in length as a consequence of the acidity. A modification in the membrane polysaccharides was also revealed by PATAg specific staining. PMID: 22155126 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506188 Fri, 02 Dec 2011 05:00:00 +0100 5506188 http://www.medworm.com/index.php?rid=5506183&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155469%26dopt%3DAbstract We report a systematic approach that addresses relevant contributing factors to PTN with particular focus on determining the effect of changing proximal amino acid side chain structure on tyrosine nitration yield. A trend was observed in which nitration yield tends to be greater when the tyrosine residue is surrounded by basic and/or uncharged polar residues compared to nitration levels observed when hydrophobic and possibly acidic residues are proximal to the tyrosine residue. Moreover, an electric dipole effect was observed where a higher degree of charge asymmetry surrounding the tyrosine residue appears to correlate with an increased tyrosine nitration yield in certain cases. The reported data are expected to facilitate site-specific prediction and validation of PTN, especially in case... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506183 Fri, 02 Dec 2011 05:00:00 +0100 5506183 http://www.medworm.com/index.php?rid=5506182&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22155470%26dopt%3DAbstract Authors: Ma H, Song L, Shu Y, Wang S, Niu J, Wang Z, Yu T, Gu W, Ma H Abstract Salinity is one of the major environmental constraints limiting yield of crop plants in many semi-arid and arid regions around the world. To understand responses in soybean seedling to salt stress at proteomic level, the extracted proteins from seedling leaves of salt-sensitive genotype Jackson and salt-tolerant genotype Lee 68 under 150mM NaCl stress for 1, 12, 72 and 144h, respectively, were analyzed by 2-DE. Approximately 800 protein spots were detected on 2-DE gels. Among them, 91 were found to be differently expressed, with 78 being successfully identified by MALDI-TOF-TOF. The identified proteins were involved in 14 metabolic pathways and cellular processes. Based on most of the 78 salt-responsive ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506182 Fri, 02 Dec 2011 05:00:00 +0100 5506182 http://www.medworm.com/index.php?rid=5506231&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22138257%26dopt%3DAbstract Authors: Zoega M, Ravnsborg T, Højrup P, Houen G, Schou C Abstract The neutrophil granulocyte is an important first line of defense against intruding pathogens and it contains a range of granules armed with antibacterial peptides and proteins. Proteinase 3 (PR3) is one among several serine proteases of the azurophilic granules in neutrophil granulocytes. Here, we characterize the glycosylation of PR3 and its association with antimicrobial human neutrophil peptides (HNPs, α-defensins) and the effect of these on the mechanism of inhibition of the major plasma inhibitor of PR3, α1-antitrypsin. The glycosylation of purified, mature PR3 showed some heterogeneity with carbohydrates at Asn 102 and 147 carrying unusual small moieties indicating heavy processing. Mass spectrometric analy... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506231 Wed, 30 Nov 2011 05:00:00 +0100 5506231 http://www.medworm.com/index.php?rid=5506181&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22166745%26dopt%3DAbstract We present a straightforward strategy applied to complex digests of human platelets, comprising (1) digest controls using a monolithic column HPLC-setup, (2) SCX enrichment of semitryptic/nonspecific peptides, (3) targeted MRM analysis of corresponding full cleavage/missed cleavage peptide pairs as well as (4) LC-MS analyses of complete digests with a three-step data interpretation. Thus, differences in digest performance can be readily assessed, rendering these procedures extremely beneficial to quality control not only the trypsin of choice, but also to effectively compare as well as optimize different digestion conditions and to evaluate the reproducibility of a dedicated digest protocol for all kinds of quantitative proteome studies. PMID: 22166745 [PubMed - as supplied by publishe... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506181 Wed, 30 Nov 2011 05:00:00 +0100 5506181 http://www.medworm.com/index.php?rid=5506211&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22146477%26dopt%3DAbstract Authors: Adav SS, Ravindran A, Sze SK Abstract Lignocellulosic biomass from agricultural crop residues and forest waste represents an abundant renewable resource for bioenergy and future biofuel. The current bottleneck of lignocellulosic biofuel production is the hydrolysis of biomass to sugar. To understand the enzymatic hydrolysis of complex biomasses, in this report, lignocellulolytic enzymes secretion by Phanerochaete chrysosporium cultivated in different natural lignocellulosic biomass such as corn stover, hay, sawdust, sugarcane baggase, wheat bran and wood chips were quantitatively analyzed with the iTRAQ technique using LC-MS/MS. A diverse groups of enzymes, including cellulases, glycoside hydrolases, hemicellulases, lignin degrading enzymes, peroxidases, esterases, lipases... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506211 Mon, 28 Nov 2011 05:00:00 +0100 5506211 http://www.medworm.com/index.php?rid=5506193&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22154982%26dopt%3DAbstract Authors: Daneshvar H, Wyllie S, Phillips S, Hagan P, Burchmore R Abstract We have previously described an attenuated line of Leishmania infantum (H-line), selected by culturing promastigotes in vitro in the presence of gentamicin. To elucidate the molecular basis for this attenuation, we undertook a comparative proteomic analysis using multiplex 2-dimensional (2D) difference gel electrophoresis. Eighteen proteins that showed significant and reproducible changes in expression were identified. Many of these were components of the thiol-redox control system in Leishmania and this observation, validated by Western blot, prompted us to investigate the sensitivity of the attenuated line to oxidative stress. The attenuated line was found to be significantly more susceptible to hydrogen pe... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506193 Mon, 28 Nov 2011 05:00:00 +0100 5506193 http://www.medworm.com/index.php?rid=5506234&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22134357%26dopt%3DAbstract Authors: Nogueira SB, Labate CA, Gozzo FC, Pilau EJ, Lajolo FM, Oliveira do Nascimento JR Abstract Papayas have a very short green life as a result of their rapid pulp softening as well as their susceptibility to physical injury and mold growth. The ripening-related changes take place very quickly, and there is a continued interest in the reduction of postharvest losses. Proteins have a central role in biological processes, and differential proteomics enables the discrimination of proteins affected during papaya ripening. A comparative analysis of the proteomes of climacteric and pre-climacteric papayas was performed using 2DE-DIGE. Third seven proteins corresponding to spots with significant differences in abundance during ripening were submitted to MS analysis, and 27 proteins we... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506234 Sun, 27 Nov 2011 05:00:00 +0100 5506234 http://www.medworm.com/index.php?rid=5506222&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22146476%26dopt%3DAbstract In this study we demonstrate the use of a multiplexed MRM-based assay to distinguish among normal (NL) and iron-metabolism disorder mouse models, particularly, iron-deficiency anemia (IDA), inflammation (INFL), and inflammation and anemia (INFL+IDA). Our initial panel of potential biomarkers was based on the analysis of 14 proteins expressed by candidate genes involved in iron transport and metabolism. Based on this study, we were able to identify a panel of 8 biomarker proteins: apolipoprotein A4 (APO4), transferring, transferrin receptor 1, ceruloplasmin, haptoglobin, lactoferrin, hemopexin, and matrix metalloproteinase-8 (MMP8) that clearly distinguish among the normal and disease models. Within this set of proteins, transferrin showed the best individual classification accuracy over al... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506222 Sat, 26 Nov 2011 05:00:00 +0100 5506222 http://www.medworm.com/index.php?rid=5506205&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22154799%26dopt%3DAbstract Authors: Kang UB, Yeom J, Kim HJ, Kim H, Lee C Abstract An efficient means of identifying protein biomarkers is essential to proper cancer management. A well-characterized proteome resource holds special promise for the discovery of novel biomarkers. However, quantification of the differences between physiological conditions together with deep down profiling has become increasingly challenging in proteomics. Here, we perform expression profiling of the colorectal cancer (CRC) proteome by stable isotope labeling and mass spectrometry. Quantitative analysis included performing mTRAQ and cICAT labeling in a pooled sample of three microsatellite stable (MSS) type CRC tissues and a pooled sample of their matched normal tissues. We identified and quantified a total of 3688 proteins. Amon... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506205 Sat, 26 Nov 2011 05:00:00 +0100 5506205 http://www.medworm.com/index.php?rid=5506236&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22129587%26dopt%3DAbstract Authors: Reinhardt TA, Lippolis JD, Nonnecke BJ, Sacco RE Abstract Exosomes are 40-100nm membrane vesicles of endocytic origin, secreted by cells and are found in biological fluids including milk. These exosomes are extracellular organelles important in intracellular communication, and immune function. Therefore, the proteome of bovine milk exosomes may provide insight into the complex processes of milk production. Exosomes were isolated from the milk of mid-lactation cows. Purified exosomes were trypsin digested, subjected offline high pH reverse phase chromatography and further fractionated on a nanoLC connected to tandem mass spectrometer. This resulted in identification of 2107 proteins that included all of the major exosome protein markers. The major milk fat globule membrane ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506236 Wed, 23 Nov 2011 05:00:00 +0100 5506236 http://www.medworm.com/index.php?rid=5506255&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22119885%26dopt%3DAbstract Authors: Gong Y, Li M, Xu D, Wang H, He J, Wu D, Chen D, Qiu N, Bao Q, Sun M, Yu Z Abstract B. thuringiensis strain YBT-1520 is highly toxic to some Lepidopteran pests and is used to control pests in southern part of China. The aim of this work is to uncover the metabolic changes associated with the ICP synthesis. A comparative proteomic analysis on the strain was performed with 2-DE and MALDI-TOF-MS methods with the bacterial culture grown in a modified defined minimal medium. Transcriptional expression of some key enzymes for carbohydrate metabolism was also investigated with qPCR. Seventy-two proteins differentially expressed at least two folds were identified. Significant changes were observed in metabolisms when comparing stationary growth phase to mid-log phase. In late-stati... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506255 Sun, 20 Nov 2011 05:00:00 +0100 5506255 http://www.medworm.com/index.php?rid=5506249&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22123078%26dopt%3DAbstract In conclusion, we identified HSPA1A as a possible therapeutic target, in combination with HDACi, for lymphoid neoplasms. PMID: 22123078 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506249 Sun, 20 Nov 2011 05:00:00 +0100 5506249 http://www.medworm.com/index.php?rid=5506237&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22123080%26dopt%3DAbstract Authors: Wang H, Zhang W, Zhao J, Zhang L, Liu M, Yan G, Yao J, Yu H, Yang P Abstract The membrane glycoprotein CD82 (KAI1) has attracted increasing attention as a suppressor of cell migration, related tumor invasion, as well as metastasis. The glycosylation of CD82 has been shown to be involved in a correlative cell adhesion and motility. However, the N-glycosylation pattern of CD82 has not been described yet. In the current study, a detailed characterization of the recombinant human CD82 N-linked glycosylation pattern was conducted by employing an integrative proteomic and glycomic approach, including glycosidase and protease digestions, glycan permethylation, MS analyses, site-directed mutagenesis, and lectin blots. The results reveal three N-glycosylation sites, and further dem... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506237 Sun, 20 Nov 2011 05:00:00 +0100 5506237 http://www.medworm.com/index.php?rid=5506235&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22134356%26dopt%3DAbstract In conclusion, the proteins negatively (ITIH3, FGG, TUBB5, and ZAG) or positively (Hp, ITIH4, and RBP) correlated with obesity found in this study could be used for selection of new targets for gender specific-medical treatment of obesity. PMID: 22134356 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506235 Sun, 20 Nov 2011 05:00:00 +0100 5506235 http://www.medworm.com/index.php?rid=5506233&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22134358%26dopt%3DAbstract Authors: Wang X, Yang B, Zhang A, Sun H, Yan G Abstract Potential metabolites from the metabolic pathways could be therapeutic targets and useful for the discovery of broad spectrum drugs. UPLC/ESI-SYNAPT-HDMS coupled with pattern recognition methods including PCA, PLS-DA, OPLS-DA and Heatmap were integrated to examine the global metabolic signature of insomnia and intervention effects of Jujuboside A (JuA). Six unique pathways of the insomnia were identified using Ingenuity Pathway Analysis (IPA) software. The VIP-value threshold cutoff of the metabolites was set to 10, above this threshold, were filtered out as potential target biomarkers. Sixteen distinct metabolites were identified from these pathways, and 6 of them can be considered for rational drug design. It was further exp... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506233 Sun, 20 Nov 2011 05:00:00 +0100 5506233 http://www.medworm.com/index.php?rid=5506232&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22137900%26dopt%3DAbstract Authors: Wang C, Liu Y, Li H, Xu WJ, Zhang H, Peng XX Abstract We have used differential sub-proteomic methodologies to detect Edwardsiella tarda outer membrane (OM) protein expression regulation during interaction with fish and human plasma, which is the critical step of the bacterial invasion internal organs via blood circulation. Seven and nine OM proteins were differentially expressed in response to fish and human plasma stress, respectively. Six proteins, TolB2, ETAE_2935, ETAE_0245, EvpA, ETAE_2675 and OmpA, were the shared proteins with the similar changes between the two plasma treatments. Except for EvpA, which was a known protein involved in bacterial pathogenesis and stress sensing, the others were first reported here to be related to bacterial invasion and infection. Ou... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506232 Sun, 20 Nov 2011 05:00:00 +0100 5506232 http://www.medworm.com/index.php?rid=5506257&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22119545%26dopt%3DAbstract This article is part of a Special Issue entitled: Clinical Proteomics. PMID: 22119545 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506257 Thu, 17 Nov 2011 05:00:00 +0100 5506257 http://www.medworm.com/index.php?rid=5506259&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22119543%26dopt%3DAbstract Authors: da Silva Batista JS, Hungria M Abstract The rhizobia-legume symbiosis requires a coordinated molecular interaction between the symbionts, initiated by seed and root exudation of several compounds, mainly flavonoids, that trigger the expression of nodulation genes in the bacteria. Since the role of flavonoids seems to be broader than the induction of nodulation genes, we aimed at characterizing genistein-induced proteins of Bradyrhizobium japonicum CPAC 15 (=SEMIA 5079), used in commercial soybean inoculants in Brazil, and of two genetically related strains grown in vitro. Whole-cell proteins were extracted both from induced (1μM genistein) and from non-induced cultures of the three strains, and separated by two-dimensional electrophoresis. Spot profiles were compared betw... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506259 Wed, 16 Nov 2011 05:00:00 +0100 5506259 http://www.medworm.com/index.php?rid=5506258&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22119544%26dopt%3DAbstract In this study, the global proteome responses of the probiotic lactic acid bacterium Lactobacillus rhamnosus GG to two physiologically relevant pH conditions (pH 4.8 and pH 5.8) were studied by 2-D DIGE. The proteomics data were complemented with transcriptome analyses by whole-genome DNA microarrays. The cells were cultured in industrial-type whey medium under strictly defined bioreactor conditions. In total, 2-D DIGE revealed the pH-dependent formation of 92 protein spots. In response to lower pH conditions, the strongest up-regulation of all proteins was detected for a predicted surface antigen, LGG_02016. In addition, the acid pH was found to up-regulate the expression of F(0)F(1)-ATP synthase genes whereas the abundance of proteins participating in nucleotide biosynthesis and protein s... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506258 Wed, 16 Nov 2011 05:00:00 +0100 5506258 http://www.medworm.com/index.php?rid=5506256&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22119884%26dopt%3DAbstract Authors: Gilad O, Hjernø K, Osterlund EC, Margolles A, Svensson B, Stuer-Lauridsen B, Møller AL, Jacobsen S Abstract Bifidobacterium animalis subsp. lactis BB-12 is a widely used probiotic strain associated with a variety of health-promoting traits. There is, however, only limited knowledge available regarding the membrane proteome and the proteins involved in oligosaccharide transport in BB-12. We applied two enrichment strategies to improve the identification of membrane proteins from BB-12 cultures grown on glucose and on xylo-oligosaccharides, the latter being an emerging prebiotic substrate recently reported to be fermented by BB-12. Our approach encompassed consecutive steps of detergent- and carbonate-treatment in order to generate inside-out membrane vesicles and to inter... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506256 Wed, 16 Nov 2011 05:00:00 +0100 5506256 http://www.medworm.com/index.php?rid=5506248&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22123079%26dopt%3DAbstract Authors: Bu Q, Yang Y, Yan G, Hu Z, Hu C, Duan J, Lv L, Zhou J, Zhao J, Shao X, Deng Y, Li Y, Li H, Zhu R, Zhao Y, Cen X Abstract It has been known that the reinforcing effects and long-term consequences of morphine are closely associated with nucleus accumbens (NAc) in the brain, a key region of the mesolimbic dopamine pathway. However, the proteins involved in neuroadaptive processes and withdrawal symptom in primates of morphine dependence have not been well explored. In the present study, we performed proteomes in the NAc of rhesus monkeys of morphine dependence and withdrawal intervention with clonidine or methadone. Two-dimensional electrophoresis was used to compare changes in cytosolic protein abundance in the NAc. We found a total of 46 proteins differentially expressed, w... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506248 Wed, 16 Nov 2011 05:00:00 +0100 5506248 http://www.medworm.com/index.php?rid=5506268&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22115752%26dopt%3DAbstract CONCLUSIONS: For the first time, antibody microarrays have been used to identify proteins associated with chemotherapy resistance using fresh breast cancer tissue. We propose a potential role for 14-3-3 theta/tau and tBID as predictive biomarkers of neoadjuvant chemotherapy resistance in breast cancer. Further validation in a larger sample series is now required. PMID: 22115752 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506268 Tue, 15 Nov 2011 05:00:00 +0100 5506268 http://www.medworm.com/index.php?rid=5506260&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22115753%26dopt%3DAbstract Authors: Weber C, Schreiber TB, Daub H Abstract Small molecule inhibitors of protein kinases have emerged as a major class of therapeutic agents for the treatment of hematological malignancies. Both in vitro studies and patient case reports suggest therapeutic potential of the clinical kinase inhibitors erlotinib and gefitinib in acute myeloid leukemia (AML). The drugs' cellular modes of action in AML warrant further investigation as their primary therapeutic target, the epidermal growth factor receptor, is not expressed. We therefore performed SILAC-based quantitative mass spectrometry analyses to a depth of 10,975 distinct phosphorylation sites to characterize the phosphoproteome of KG1 AML cells and its regulation upon erlotinib and gefitinib treatment. Less than 50 site-specifi... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506260 Tue, 15 Nov 2011 05:00:00 +0100 5506260 http://www.medworm.com/index.php?rid=5506254&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22120120%26dopt%3DAbstract Authors: Florentinus AK, Bowden P, Sardana G, Diamandis EP, Marshall JG Abstract The proteins secreted by prostate cancer cells (PC3(AR)6) were separated by strong anion exchange chromatography, digested with trypsin and analyzed by unbiased liquid chromatography tandem mass spectrometry with an ion trap. The spectra were matched to peptides within proteins using a goodness of fit algorithm that showed a low false positive rate. The parent ions for MS/MS were randomly and independently sampled from a log-normal population and therefore could be analyzed by ANOVA. Normal distribution analysis confirmed that the parent and fragment ion intensity distributions were sampled over 99.9% of their range that was above the background noise. Arranging the ion intensity data with the identifi... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506254 Tue, 15 Nov 2011 05:00:00 +0100 5506254 http://www.medworm.com/index.php?rid=5506253&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22120121%26dopt%3DAbstract Authors: Milli A, Cecconi D, Bortesi L, Persi A, Rinalducci S, Zamboni A, Zoccatelli G, Lovato A, Zolla L, Polverari A Abstract We analyzed the proteome of grapevine (Vitis vinifera) leaves 24, 48 and 96h post infection (hpi) with the downy mildew pathogen Plasmopara viticola. Total proteins were separated on 2-DE gels. By MS analysis, we identified 82 unique grapevine proteins differentially expressed after infection. Upregulated proteins were often included in the functional categories of general metabolism and stress response, while proteins related to photosynthesis and energy production were mostly downregulated. As expected, the activation of a defense reaction was observed more often at the late time point, consistent with the establishment of a compatible interaction. Most ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506253 Tue, 15 Nov 2011 05:00:00 +0100 5506253 http://www.medworm.com/index.php?rid=5506250&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22120122%26dopt%3DAbstract Authors: Selman MH, Derks RJ, Bondt A, Palmblad M, Schoenmaker B, Koeleman CA, van de Geijn FE, Dolhain RJ, Deelder AM, Wuhrer M Abstract Biological activities of immunoglobulin G such as effector functions via Fc receptor interactions are influenced by Fc-linked N-glycans. Here we describe a fast, robust and sensitive nano-LC-ESI-MS method for detailed subclass specific analysis of IgG Fc N-glycosylation. A sheath-flow ESI sprayer was used as a sensitive zero dead volume plug-and-play interface for online MS coupling, generating a very constant spray and ionization over the entire LC gradient. The propionic acid containing sheath-liquid effectively suppressed TFA gas-phase ion-pairing, enabling the use of TFA containing mobile phases. The fixed position of the sheath-flow ESI spra... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5506250 Tue, 15 Nov 2011 05:00:00 +0100 5506250 http://www.medworm.com/index.php?rid=5436362&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100381%26dopt%3DAbstract Authors: Lincet H, Guével B, Pineau C, Allouche S, Lemoisson E, Poulain L, Gauduchon P Abstract Ovarian cancer is the fifth most frequent cause of cancer death in women. Emergence of chemoresistance in the course of treatments with platinum drugs is in part responsible for therapeutic failures. In order to improve the understanding of the complex mechanisms involved in acquired platinum chemoresistance, we decided to compare the basal protein expression profile of the platinum-sensitive cell line OAW42 and that of its resistant counterpart OAW42-R by a proteomic approach. Reversed-phase HPLC pre-fractionated extracts from both cell lines were subjected to 2D-DIGE coupled to mass spectrometry (MS). Forty eight differentially expressed proteins were identified, 39 being up-regulated... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5436362 Sat, 12 Nov 2011 05:00:00 +0100 5436362 http://www.medworm.com/index.php?rid=5436365&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22086082%26dopt%3DAbstract Authors: Shui HA, Hsia CW, Chen HM, Chang TC, Wang CY Abstract Lovastatin (lova), a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor, can induce differentiation in cancer cells at low concentration, thus having potential to be used as an auxiliary agent in cancer therapy. However, biological networks associated with the differentiation effect of lova have not been elucidated. To investigate molecular mechanisms of lova, the present study was aimed at proteomics and bioinformatics analyses on anaplastic thyroid cancer cell line ARO differentiated with low concentration of lova. Thyroid differentiation was induced by treating ARO cells with 25μM of lova and confirmed by checking upregulation of some thyroid differentiation markers. Gel-based proteomics analysis was then per... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5436365 Mon, 07 Nov 2011 05:00:00 +0100 5436365 http://www.medworm.com/index.php?rid=5436364&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22086083%26dopt%3DAbstract Authors: Ray S, Kamath KS, Srivastava R, Raghu D, Gollapalli K, Jain R, Gupta SV, Ray S, Taur S, Dhali S, Gogtay N, Thatte U, Srikanth R, Patankar S, Srivastava S Abstract Vivax malaria is the most widely distributed human malaria resulting in 80-300million clinical cases every year. It causes severe infection and mortality but is generally regarded as a benign disease and has not been investigated in detail. The present study aimed to perform human serum proteome analysis in a malaria endemic area in India to identify potential serum biomarkers for vivax malaria and understand host response. The proteomic analysis was performed on 16 age and gender matched subjects (vivax patients and control) in duplicate. Protein extraction protocols were optimized for large coverage of the seru... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5436364 Mon, 07 Nov 2011 05:00:00 +0100 5436364 http://www.medworm.com/index.php?rid=5436363&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22094879%26dopt%3DAbstract This study examines the proteomes of DSC and NDSC larvae to assess proteins that may contribute to or inhibit the DSC trait. Using high throughput proteomics, we identified 138 proteins and 513 Gene Ontology categories in the DSC group and 104 proteins and 573 GO categories in the NDSC group. GO categories enriched in DSC include alcohol metabolic process, cellular component morphogenesis, monosaccharide metabolic process, regulation of biological quality, extracellular region, structural molecule activity, and antioxidant activity. Proteins unique to DSC include alpha casein precursor, alpha-actinin, vimentin, tropomyosin, beta-lactoglobulin, immunoglobulins, tubulin, cuticle proteins and endothelins. PMID: 22094879 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5436363 Mon, 07 Nov 2011 05:00:00 +0100 5436363 http://www.medworm.com/index.php?rid=5436361&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100410%26dopt%3DAbstract In this study, the gene clusters and pathways for the degradation of benzoate (via benzoyl-CoA), phenylacetate (via phenylacetyl-CoA), 4-hydroxyphenylacetate (via 3,4-dihydroxyphenylacetate) and anthranilate (via 3-hydroxyanthranilate) were confirmed using combined in silico analysis and proteomics approaches. It was observed that synthesis of the enzymes catalyzing initial activation, ring oxidation and ring cleavage reactions were generally induced specifically by their respective substrates, while many of the enzymes catalyzing downstream reactions exhibited broader substrate specificities. Novel genes encoding benzoyl-CoA epoxidase and 3,4-dihydroxyphenylacetate 2,3-dioxygenase, and a paaX homologue that serves as a positive regulator of benzoate degradation were proposed. Downregulati... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5436361 Mon, 07 Nov 2011 05:00:00 +0100 5436361 http://www.medworm.com/index.php?rid=5436360&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100459%26dopt%3DAbstract Authors: You X, Wang L, Liang W, Gai Y, Wang X, Chen W Abstract Two-dimensional gel electrophoresis (2-DE) was used to analyze the proteins related to floral reversion in Dimocarpus longan Lour. Proteins were extracted from buds undergoing the normal process of flowering and from those undergoing floral reversion in three developing stages in D. longan. Differentially expressed proteins were identified from the gels after 2-DE analysis, which were confirmed using matrix-assisted laser desorption/ionization-time of flying-mass spectroscopy and protein database search. A total of 39 proteins, including 16 up-regulated and 23 down-regulated proteins, were classified into different categories, such as energy and substance metabolism, protein translation, secondary metabolism, phytohorm... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5436360 Mon, 07 Nov 2011 05:00:00 +0100 5436360 http://www.medworm.com/index.php?rid=5411597&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079248%26dopt%3DAbstract Authors: Bièche C, de Lamballerie M, Chevret D, Federighi M, Tresse O Abstract Campylobacter jejuni is one of the most intriguing human foodborne bacterial pathogen. Its survival throughout the food processing chain and its pathogenesis mechanisms in humans remain enigmatic. Living in the animal guts and particularly in avian intestine as a commensal bacterium, this microorganism is frequently isolated from meat products. Ultra high pressure (HP) is a promising alternative to thermal technology for microbial safety of foodstuffs with less organoleptic and nutritional alterations. Its application could be extended to meat products potentially contaminated by C. jejuni. To evaluate the response of Campylobacter to this technological stress and subsequent recovery at a molecular leve... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411597 Mon, 07 Nov 2011 05:00:00 +0100 5411597 http://www.medworm.com/index.php?rid=5411601&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079244%26dopt%3DAbstract Authors: Zhang A, Sun H, Wang P, Han Y, Wang X Abstract Metabolomics, one of the 'omic' sciences in systems biology, is the global assessment and validation of endogenous small-molecule metabolites within a biologic system. Analysis of these key metabolites in body fluids has become an important role to monitor the state of biological organisms and is a widely used diagnostic tool for disease. A majority of these metabolites are being applied to metabolic profiling of the biological samples, for example, plasma and whole blood, serum, urine, saliva, cerebrospinal fluid, synovial fluid, semen, and tissue homogenates. However, the recognition of the need for a holistic approach to metabolism led to the application of metabolomics to biological fluids for disease diagnostics. A recent... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411601 Fri, 04 Nov 2011 04:00:00 +0100 5411601 http://www.medworm.com/index.php?rid=5411599&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079246%26dopt%3DAbstract This study highlights the possible contribution of such proteomic approach in the field of toxicology. PMID: 22079246 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411599 Fri, 04 Nov 2011 04:00:00 +0100 5411599 http://www.medworm.com/index.php?rid=5411598&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079247%26dopt%3DAbstract Authors: Immel F, Renaut J, Masfaraud JF Abstract Derelict contaminated sites are often colonized spontaneously by plant species leading to a vegetal cover thought to limit particle dispersal and polluted water infiltration. Those plants must cope with soil pollutants through tolerance mechanisms that are not yet fully understood. Here, we focused our attention on a particular Asteraceae plant, Solidago canadensis, considered as invasive in Europe. S. canadensis spontaneously growing on either polluted (NM soil) or control soils dumped on experimental plots were studied for their physiological status, oxidative stress and 2D-DIGE of leaf extracts. S. canadensis tolerance to soil pollutants was demonstrated since growth rates, allocation to reproduction ratios and Fv/Fm ratios were ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411598 Fri, 04 Nov 2011 04:00:00 +0100 5411598 http://www.medworm.com/index.php?rid=5411602&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22075168%26dopt%3DAbstract In conclusion, exploiting non-targeted UPLC-MS based approach for the investigation of UTI related changes in urine, we have identified and structurally characterized unique O-glycopeptides, which are, to our knowledge, the first demonstration of O-glycosylation of human fibrinogen alpha 1-chain. PMID: 22075168 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411602 Mon, 31 Oct 2011 04:00:00 +0100 5411602 http://www.medworm.com/index.php?rid=5411596&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079874%26dopt%3DAbstract In this study, fish gill and bacterial pull-down approaches were used to isolate both bacterial outer membrane proteins that bind to gills and fish gill proteins that interact with bacterial cells, respectively. Eight interacting bacterial proteins and twelve interacting fish proteins were obtained. The genes of seven bacterial proteins were cloned and expressed for preparation of antibodies. The prepared antibodies were used to investigate protein-protein interactions between bacterial cells and fish gills. Five heterogeneous protein-protein interactions were determined. Moreover, the protective ability of three of the bacterial recombinant proteins, selected at random, was investigated in a mouse model where they showed significant protection. The gill proteins were highly homologous pro... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411596 Mon, 31 Oct 2011 04:00:00 +0100 5411596 http://www.medworm.com/index.php?rid=5411610&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22061663%26dopt%3DAbstract Authors: Penque D, Simões T, Amado F PMID: 22061663 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411610 Sun, 30 Oct 2011 04:00:00 +0100 5411610 http://www.medworm.com/index.php?rid=5411603&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22075167%26dopt%3DAbstract Authors: Zheng P, Zhong Q, Xiong Q, Yang M, Zhang J, Li C, Bi LJ, Ge F Abstract Signal transducers and activators of transcription 3 (Stat3) has been reported to be involved in the pathogenesis of various human diseases and is constitutively active in human multiple myeloma (MM) U266 cells. The Stat3-regulated mechanisms involved in these processes, however, are not fully defined. To further understand the regulation of Stat3 activity, we performed a systematic proteomic analysis of Stat3 interacting proteins in U266 cells. This analysis, termed quantitative immunoprecipitation combined with knockdown (QUICK), combines RNAi, stable isotope labeling with amino acids in cell culture (SILAC), immunoprecipitation, and quantitative MS. As a result, quantitative mass spectrometry analysi... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411603 Sun, 30 Oct 2011 04:00:00 +0100 5411603 http://www.medworm.com/index.php?rid=5411606&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22062160%26dopt%3DAbstract Authors: Magherini F, Abruzzo PM, Puglia M, Bini L, Gamberi T, Esposito F, Veicsteinas A, Marini M, Fiorillo C, Gulisano M, Modesti A Abstract Understanding the relationship between physical exercise, reactive oxygen species and skeletal muscle modification is important in order to better identify the benefits or the damages that appropriate or inappropriate exercise can induce. Unbalanced ROS levels can lead to oxidation of cellular macromolecules and a major class of protein oxidative modification is carbonylation. The aim of this investigation was to study muscle protein expression and carbonylation patterns in trained and untrained animal models. We analyzed two muscles characterized by different metabolisms: tibialis anterior and soleus. Whilst tibialis anterior is mostly comp... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411606 Sat, 29 Oct 2011 04:00:00 +0100 5411606 http://www.medworm.com/index.php?rid=5411605&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22067702%26dopt%3DAbstract This study provides evidence for the first time that SEY contains higher levels of Pyruvate Kinase, HSP70, and Elongation factor 2 and lower levels of Eukaryotic Translation Initiation Factor 5A-2 and Triosephosphate Isomerase than those found in RY. PMID: 22067702 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411605 Sat, 29 Oct 2011 04:00:00 +0100 5411605 http://www.medworm.com/index.php?rid=5411604&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22075166%26dopt%3DAbstract Authors: Louarn S, Nawrocki A, Edelenbos M, Jensen DF, Jensen ON, Collinge DB, Jensen B Abstract Many carrots are discarded during post harvest cold storage due to development of fungal infections, caused by, e.g., Mycocentrospora acerina (liquorice rot). We compared the susceptibility of carrots grown under conventional and organic agricultural practices. In one year, organically cultivated carrots showed 3× to 7× more symptoms than conventionally cultivated, when studying naturally occurring disease at 4 and 6months, respectively. On the other hand, we have developed a bioassay for infection studies of M. acerina on carrots and observed that organic roots were more susceptible after one month of storage than conventional ones, but no differences were apparent after four or six ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411604 Sat, 29 Oct 2011 04:00:00 +0100 5411604 http://www.medworm.com/index.php?rid=5411600&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079245%26dopt%3DAbstract Authors: Ponnudurai RP, Basak T, Ahmad S, Bhardwaj G, Chauhan RK, Singh RA, Lalwani MK, Sivasubbu S, Sengupta S Abstract Cyclosporine A, a potent immunosuppressive agent extensively used to prevent allograft rejections, is under scrutiny due to severe toxic effects. CsA therapy is often continued during pregnancy in conditions such as organ transplantations and autoimmune diseases. Herein, we investigated the effects of CsA on early morphogenesis of zebrafish and identified a spectrum of proteins whose expression was altered in the drug treated embryos. Time-lapse fluorescence imaging of germ-line double transgenic zebrafish embryos treated with CsA revealed severe blood regurgitation in heart chambers, absence of blood circulation in vessels, pericardial and yolk sac edema. We als... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411600 Sat, 29 Oct 2011 04:00:00 +0100 5411600 http://www.medworm.com/index.php?rid=5411609&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22061664%26dopt%3DAbstract Authors: Gondret F, Guével B, Com E, Vincent A, Lebret B Abstract Subcutaneous fat tissues from an indigenous fat-type breed and an intensively-lean selected breed were studied in juvenile pigs. Combining DIGE with bioinformatics and target analyses of key genes, enzymes or terminal routes, this study identifies metabolic and homeostatic processes, response to organic substances, and acute-phase responses as the main pathways whose proteins were regulated in association with adiposity. Breed-related differences in abundance and activities of malic enzyme and glucose-6-phosphate dehydrogenase NADPH-supplying enzymes suggested up-regulation of the lipogenic pathway to dispose for a greater adiposity. Over-abundance in the lipolytic protein carboxylesterase-1 was revealed in fat-type... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411609 Fri, 28 Oct 2011 04:00:00 +0100 5411609 http://www.medworm.com/index.php?rid=5411608&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22062158%26dopt%3DAbstract Authors: Koziol AG, Marquez BK, Huebsch MP, Smith JC, Altosaar I Abstract Commercially available reference materials are integral components of many experimental protocols, as it is critical to compare one's results to those derived from well-characterized standards. Most reference materials are well defined, with all their components being cataloged. However, certain reference materials, such as commercially prepared starch samples, can have undefined components, potentially limiting their usefulness as standards. The proteome of commercially prepared starch has not been documented, and to that end, we initiated a mass spectrometry-based survey of the proteins associated with starch granules in commercially prepared rice and maize starch samples. We performed direct trypsin treatm... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411608 Fri, 28 Oct 2011 04:00:00 +0100 5411608 http://www.medworm.com/index.php?rid=5411607&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22062159%26dopt%3DAbstract Authors: Chantratita N, Tandhavanant S, Wikraiphat C, Trunck LA, Rholl DA, Thanwisai A, Saiprom N, Limmathurotsakul D, Korbsrisate S, Day NP, Schweizer HP, Peacock SJ Abstract Colony morphology variation of Burkholderia pseudomallei is a notable feature of a proportion of primary clinical cultures from patients with melioidosis. Here, we examined the hypothesis that colony morphology switching results in phenotypic changes associated with enhanced survival under adverse conditions. We generated isogenic colony morphology types II and III from B. pseudomallei strain 153 type I, and compared their protein expression profiles using 2D gel electrophoresis. Numerous proteins were differentially expressed, the most prominent of which were flagellin, arginine deiminase (AD) and carbamate ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411607 Fri, 28 Oct 2011 04:00:00 +0100 5411607 http://www.medworm.com/index.php?rid=5411611&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22057045%26dopt%3DAbstract Authors: Lemeer S, Bluwstein A, Wu Z, Leberfinger J, Müller K, Kramer K, Kuster B Abstract The receptor tyrosine kinase DDR1 has been implicated in multiple human cancers and fibrosis and is targeted by the leukemia drug Gleevec. This suggests that DDR1 might be a new therapeutic target. However, further insight into the DDR1 signaling pathway is required in order to support its further development. Here, we investigated DDR1 proximal signaling by the analysis of protein-protein interactions using proteomic approaches. All known interactors of DDR1 were identified and localized to specific phosphotyrosine residues on the receptor. In addition, we identified numerous signaling proteins as new putative phosphotyrosine mediated interactors including RasGAP, SHIP1, SHIP2, STATs, PI3K ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411611 Wed, 26 Oct 2011 04:00:00 +0100 5411611 http://www.medworm.com/index.php?rid=5411612&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22057044%26dopt%3DAbstract Authors: Pandey S, Rai R, Rai LC Abstract Proteomics in conjunction with morphological, physiological and biochemical variables has been employed for the first time to unravel survival strategies of the diazotrophic cyanobacterium Anabaena sp. PCC7120. Significant reduction in growth, carbon fixation, nitrogenase activity and chlorophyll content after 1day (1d) and recovery after 15days (15d) of As exposure indicates the acclimation of the test organism against As stress. The formation of akinete like structures is a novel observation never reported before in Anabaena sp. PCC7120. Proteomic characterization using 2-DE showed average 537, 422 and 439 spots in control, 1 and 15d treatment respectively. MALDI-TOF and LC-MS of As-treated Anabaena revealed a total of 45 differentially e... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5411612 Tue, 25 Oct 2011 04:00:00 +0100 5411612 http://www.medworm.com/index.php?rid=5376534&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22040741%26dopt%3DAbstract In this report, we carried out the in-depth proteomic analysis of Yersinia pestis strain 91001 under in vitro flea-simulated condition using three technique routes, SDS-PAGE combined with LTQ-FT, two-dimensional liquid chromatography peptide (2D-LC peptide) separation combined with LTQ-FT and intact protein separation followed by 2D-LC peptide separation combined with LTQ-FT. Totally, 1926 proteins (13082 peptides) were identified, covering 46.50% (1926/4142) of the predicted proteome. Transcriptome analysis based on a whole genome DNA microarray of Y. pestis defined 1655 genes with the coincidence of 56.65% to the proteomic results. Through analyzing the identifications of virulence factors involving in the life cycle of Y. pestis, it was found that Hms system and murine toxin, which are ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5376534 Tue, 25 Oct 2011 04:00:00 +0100 5376534 http://www.medworm.com/index.php?rid=5376529&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22040742%26dopt%3DAbstract Authors: Ferret-Bernard S, Castro-Borges W, Dowle AA, Sanin DE, Cook PC, Turner JD, Macdonald AS, Thomas JR, Mountford AP Abstract Dendritic cells (DCs) play a pivotal role in polarising Th lymphocyte subsets but it is unclear what molecular events occur when DCs generate Th2-type responses. Here, we analysed plasma membrane-enriched fractions from immature, pro-Th1 and pro-Th2 DCs and used a combination of iTRAQ labelling and LC-MS/MS to quantify changes in the proteomes. Analysis was performed on triplicate biological samples and changes verified by flow cytometry. MHC class II molecules and CD29 were up-regulated in pro-Th1 DCs whilst CD18 and CD44 were up-regulated in pro-Th2 DCs. One of the most down-regulated molecules in pro-Th1 DCs was YM-1 whilst the greatest decrease in p... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5376529 Tue, 25 Oct 2011 04:00:00 +0100 5376529 http://www.medworm.com/index.php?rid=5376543&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22037230%26dopt%3DAbstract Authors: O'Neil SE, Lundbäck B, Lötvall J Abstract The application of proteomics to respiratory diseases, such as asthma and COPD, has been limited compared to other fields, like cancer. Both asthma and COPD are recognised to be multi-factorial and complex diseases, both consisting of clusters of multiple disease phenotypes. The complexity of these diseases combined with the inaccessibility and invasiveness of disease relevant samples have provided a hurdle to the progress of respiratory proteomics. Advances in proteomic instrumentation and methodology have led to the possibility to identify proteomes in much smaller quantities of biological material. This review focuses on the efforts in respiratory proteomics in relation to asthma and COPD, and the importance of identifying sub... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5376543 Thu, 20 Oct 2011 04:00:00 +0100 5376543 http://www.medworm.com/index.php?rid=5376541&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22037231%26dopt%3DAbstract Authors: D'Amato A, Fasoli E, Righetti PG Abstract The proteome of coconut milk has been extensively mapped via capture at three pH values with combinatorial peptide ligand libraries (CPLL). A grand total of 307 unique gene products could be listed, 200 discovered via CPLL capture, 137 detected in the control, untreated material and 30 species in common between the two sets of data. This is by far the most extensive mapping of coconut milk, in which, up to the present, only a dozen proteins were known, those belonging to the high- to very-high abundance class. The database of coconut contains only 106 proteins: of those, only six are listed in our table. The vast majority of the classified proteins, thus, has been identified only by homologies with sequences deposited in the genera... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5376541 Thu, 20 Oct 2011 04:00:00 +0100 5376541 http://www.medworm.com/index.php?rid=5376537&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22037232%26dopt%3DAbstract Authors: Salavati A, Khatoon A, Nanjo Y, Komatsu S Abstract A proteomic approach was used to identify proteins involved in post-flooding recovery in soybean roots. Two-day-old soybean seedlings were flooded with water for up to 3days. After the flooding treatment, seedlings were grown until 7days after sowing and root proteins were then extracted and separated using two-dimensional polyacrylamide gel electrophoresis (2-DE). Comparative analysis of 2-D gels of control and 3day flooding-experienced soybean root samples revealed 70 differentially expressed protein spots, from which 80 proteins were identified. Many of the differentially expressed proteins are involved in protein destination/storage and metabolic processes. Clustering analysis based on the expression profiles of the 70... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5376537 Thu, 13 Oct 2011 04:00:00 +0100 5376537 http://www.medworm.com/index.php?rid=5376544&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22036931%26dopt%3DAbstract Authors: Luo R, Zhou C, Lin J, Yang D, Shi Y, Cheng G Abstract Schistosome is the causative agent of human schistosomiasis and related animal disease. Reversible protein phosphorylation plays a key role in signaling processing that are vital for a cell and organism. However, it remains to be undercharacterized in schistosomes. In the present study, we characterized in vivo protein phosphorylation events in different developmental stages (schistosomula and adult worms) of Schistosoma japonicum by using microvolume immobilized metal-ion affinity chromatography (IMAC) pipette tips coupled to nanoLC-ESI-MS/MS. In total, 127 distinct phosphorylation sites were identified in 92 proteins in S. japonicum. A comparison of the phosphopeptides identified between the schistosomula and the adul... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5376544 Tue, 11 Oct 2011 04:00:00 +0100 5376544 http://www.medworm.com/index.php?rid=5358255&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22005398%26dopt%3DAbstract Authors: Salavati A, Bushehri AA, Taleei A, Hiraga S, Komatsu S Abstract To reveal the processes involved in the early stages of symbiosis between soybean plants and root nodule bacteria, we conducted a proteomic analysis of the response to bacterial inoculation in the roots of supernodulating (En-b0-1) and non-nodulating (En1282) varieties, and their parental normal-nodulating variety (Enrei). A total of 56 proteins were identified from 48 differentially expressed protein spots in normal-nodulating variety after bacterial inoculation. Among 56 proteins, metabolism- and energy production-related proteins were upregulated in supernodulating and downregulated in non-nodulating varieties compared to normal-nodulating variety. The supernodulating and non-nodulating varieties responded ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5358255 Sat, 08 Oct 2011 04:00:00 +0100 5358255 http://www.medworm.com/index.php?rid=5358254&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22008608%26dopt%3DAbstract Authors: Tambor V, Hunter CL, Seymour SL, Kacerovsky M, Stulik J, Lenco J Abstract Shotgun proteomics is capable of characterizing differences in both protein quality and quantity, and has been applied in various biomedical applications. Unfortunately, the high complexity and dynamic range of proteins in studied samples, clinical in particular, often hinders the identification of relevant proteins. Indeed, information-rich, low abundance proteins often remain undetected, whereas repeatedly reported altered concentrations in high abundance proteins are often ambiguous and insignificant. Several techniques have therefore been developed to overcome this obstacle and provide a deeper insight into the proteome. Here we report a novel approach, which enables iTRAQ reagent quantitation of... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5358254 Sat, 08 Oct 2011 04:00:00 +0100 5358254 http://www.medworm.com/index.php?rid=5358253&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22015715%26dopt%3DAbstract Authors: Yu LR PMID: 22015715 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5358253 Sat, 08 Oct 2011 04:00:00 +0100 5358253 http://www.medworm.com/index.php?rid=5358252&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22015716%26dopt%3DAbstract Authors: Liu K, Han M, Yao L, Sun J, Zhang T, Li F Abstract Cotton fibers are single-celled seed trichomes and provide an ideal model for studying plant cell patterning. At present, the molecular mechanisms of fiber differentiation and initiation are unclear. To determine the proteins involved in these processes, a comparative proteomic analysis based on 2-DE and MS/MS technology was conducted between the fuzzless-lintless mutant (fl) and its parental wild type (WT). Forty-six differentially expressed proteins were identified in ovules at -3 and 0days post-anthesis (DPA), at the times of cotton fiber differentiation and initiation, respectively. Most of the proteins (72%) were expressed at lower levels in the fl mutant than in the WT, suggesting deleterious effects of the mutant ge... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5358252 Sat, 08 Oct 2011 04:00:00 +0100 5358252 http://www.medworm.com/index.php?rid=5323967&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21985938%26dopt%3DAbstract Authors: Righetti PG, Lomonte B, Calvete JJ Abstract A 26-year-old dried polyacrylamide gel, cast in presence of an immobilized pH gradient and containing focused proteins from the venoms of a northern black-tailed rattlesnake (Crotalus molossus molossus), and of a western diamondback rattlesnake (Crotalus atrox) has been screened in order to see the feasibility of extracting the proteins, analyzing them by mass spectrometry (MS) and assessing their integrity. Nine gel bands were excised along the pH 3-10 gradient and the gel segments reswollen in warm acetonitrile. Upon digestion and MS analysis, all the bands could be identified and attributed to the respective venoms of the two rattlesnake species. Although a few peptides exhibited modified amino acids, the proteins were found t... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323967 Sun, 02 Oct 2011 04:00:00 +0100 5323967 http://www.medworm.com/index.php?rid=5323965&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21989265%26dopt%3DAbstract Authors: George J, Shukla Y Abstract Humans are often exposed to a variety of pollutants that contribute to an individual's risk for diseases including cancer. Animal, cell cultures and epidemiological lines of evidence demonstrate that exposure to various environmental pollutants including pesticides are associated with increasing frequency of cancers. Organophosphates, organochlorines, carbamates, pyrethroids, the major groups of pesticides, have been reported to be carcinogenic in various models. However, the results of these studies are still controversial, nevertheless, their mechanism of action is clear. Therefore, new strategies in toxicological research are needed for efficient screening for adverse effects of pesticides on complex living systems. Biomarkers can be employed... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323965 Sun, 02 Oct 2011 04:00:00 +0100 5323965 http://www.medworm.com/index.php?rid=5323964&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21989266%26dopt%3DAbstract Authors: Chen PH, Wang CY, Hsia CW, Ho MY, Chen A, Tseng MJ, Wu YF, Chen HM, Huang TH, Liu HT, Shui HA Abstract Dermal papilla (DP) cells play a regulatory role in hair growth, and also play a role in alopecia (hair loss). However, effects of taxol, which is a wildly used chemotherapy drug, on DP cells remain unclear, despite that theoretically taxol can impact on DP cells to contribute to taxol-induced alopecia. To better understand pathophysiology of taxol-induced damage in DP cells, morphological and biochemical analyses were performed to check whether taxol can cause apoptosis in cultured DP cells or not. If it can, proteomics and bioinformatics analyses were then performed to investigate the protein networks which are impacted by the taxol treatment. Our data showed that taxol... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323964 Sun, 02 Oct 2011 04:00:00 +0100 5323964 http://www.medworm.com/index.php?rid=5323962&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21989268%26dopt%3DAbstract Authors: Sakai A, Otani M, Miyamoto A, Yoshida H, Furuya E, Tanigawa N Abstract To identify the proteins involved in 5-Fluorouracil (5-FU) resistance, a comparison of the total and phosphorylated proteins between the human colorectal cancer (CRC) cell line DLD-1 and its 5-FU-resistant subclone DLD-1/5-FU was performed. Using 2-DE and MALDI-TOF/TOF-based proteomics, 17 up-regulated and 19 down-regulated protein spots were identified in the 5-FU-resistant DLD-1/5-FU cells compared with the parent cell lines. In DLD-1/5-FU cells, 7 anti-apoptotic proteins (HSPB1, proteasome subunit α-5, transitional endoplasmic reticulum ATPase, 14-3-3 β, 14-3-3 γ, 14-3-3 σ, and phosphoglycerate kinase 1) were up-regulated and 4 proapoptotic proteins (cofilin-1, pyruvate kinase M2, glyceraldehyde-... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323962 Sun, 02 Oct 2011 04:00:00 +0100 5323962 http://www.medworm.com/index.php?rid=5323961&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21989269%26dopt%3DAbstract Authors: Galiacy SD, Froment C, Mouton-Barbosa E, Erraud A, Chaoui K, Desjardins L, Monsarrat B, Malecaze F, Burlet-Schiltz O Abstract The cornea is a transparent, avascular, and highly specialized connective tissue that provides the majority of light refraction in the optical system of the eye. The human cornea is composed of several layers interacting in a complex manner and possessing specific functions, like eye protection and optical clearness. Only few proteomic studies of mammalian cornea have been performed leading to the identification of less than 200 proteins in human corneas. The present study explores the proteome of the intact normal human cornea using a shot-gun nanoLC-MS/MS strategy and an LTQ Orbitrap mass spectrometer. A total of 2070 distinct corneal proteins wer... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323961 Sun, 02 Oct 2011 04:00:00 +0100 5323961 http://www.medworm.com/index.php?rid=5323979&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21982829%26dopt%3DAbstract "Cheek-to-cheek" urinary proteome profiling via combinatorial peptide ligand libraries: A novel, unexpected elution system. J Proteomics. 2011 Oct 1; Authors: Candiano G, Santucci L, Bruschi M, Pedretto A, Ambrosio CD, Scaloni A, Righetti PG, Ghiggeri GM Abstract A new method is here reported for facile elution of the human urinary proteome after being captured with combinatorial peptide ligand libraries (CPLL, ProteoMiner). It consists in challenging the beads with 100mM Tris, pH 7.4, or with 100mM Lys, pH 7.4 or even better with a mixture of Lys-Arg-Asp-Glu (150mM final concentration). These elutions permit recovery of species in a native form, for monitoring any biological activity of the eluted species, while avoiding the noxious presence of sodium dodecyl sulphate (SDS... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323979 Sat, 01 Oct 2011 04:00:00 +0100 5323979 http://www.medworm.com/index.php?rid=5323966&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21989264%26dopt%3DAbstract Authors: Pérez-Pérez R, García-Santos E, Ortega-Delgado FJ, López JA, Camafeita E, Ricart W, Fernández-Real JM, Peral B Abstract Obesity is recognized as an epidemic health problem worldwide. In humans, the accumulation of omental rather than subcutaneous fat appears to be tightly linked to insulin resistance, type 2 diabetes and cardiovascular disease. Differences in gene expression profiles in the adipose tissue comparing non-obese and obese subjects have been well documented. However, to date, no comparative proteomic studies based on omental fat have investigated the influence of obesity in protein expression. In this work, we searched for proteins differentially expressed in the omental fat of non-obese and obese subjects using 2D-DIGE and MS. Forty-four proteins, several... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323966 Sat, 01 Oct 2011 04:00:00 +0100 5323966 http://www.medworm.com/index.php?rid=5323963&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21989267%26dopt%3DAbstract In this study we explored the composition of the N-glycome released from newborn and adult B. jararaca venom proteins. We used an ion trap mass spectrometer (IT-MS) to disassemble glycan structures based on the use of several pathways of MS (MSn) and demonstrate the presence of some structural isomers in both newborn and adult venom B. jararaca N-glycans. The main N-glycans identified in both venoms are of the hybrid/complex type however some mannose-rich type structures were also detected. The N-glycan composition of newborn and adult venoms did not vary indicating that differences in the utilization of the N-glycosylation motif could be the explanation for the differences in the glycosylation levels indicated by the differential electrophoretic profiles previously reported for B. jararac... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323963 Sat, 01 Oct 2011 04:00:00 +0100 5323963 http://www.medworm.com/index.php?rid=5323980&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21982827%26dopt%3DAbstract Authors: Fang Y, Song F, Zhang L, Aleku DW, Han B, Feng M, Li J Abstract To understand the olfactory mechanism of honeybee antennae in detecting specific volatile compounds in the atmosphere, antennal proteome differences of drone, worker and queen were compared using 2-DE, mass spectrometry and bioinformatics. Therefore, 107 proteins were altered their expressions in the antennae of drone, worker and queen bees. There were 54, 21 and 32 up-regulated proteins in the antennae of drone, worker and queen, respectively. Proteins upregulated in the drone antennae were involved in fatty acid metabolism, antioxidation, carbohydrate metabolism and energy production, protein folding and cytoskeleton. Proteins upregulated in the antennae of worker and queen bees were related to carbohydrate ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323980 Thu, 29 Sep 2011 04:00:00 +0100 5323980 http://www.medworm.com/index.php?rid=5323978&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21982830%26dopt%3DAbstract Authors: Wetzel C, Limbach PA Abstract Transfer ribonucleic acid (tRNA) is the non-coding RNA that links the processes of gene transcription with protein translation. While tRNAs have, individually, been studied for many years, few approaches exist for the global identification of tRNAs at the RNA and posttranscriptional RNA levels. Previously our lab introduced the concept of signature enzymatic digestion products (SDPs) for tRNA identification using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). SDPs enable the direct determination of tRNA identity based on mass spectrometry detection of unique m/z values from enzymatic digestion products. Here we have examined the applicability of liquid chromatography-mass spectrometry (LC-MS) and liquid chromatograph... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323978 Thu, 29 Sep 2011 04:00:00 +0100 5323978 http://www.medworm.com/index.php?rid=5323977&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21982977%26dopt%3DAbstract Authors: Xie N, Huang K, Zhang T, Lei Y, Liu R, Wang K, Zhou S, Li J, Wu J, Wu H, Deng C, Nice EC, Huang C Abstract Lipid rafts are cholesterol- and sphingolipid-rich membrane microdomains that have been shown to participate in the entry, assembly and budding of various viruses. However, their involvement in HBV replication remains poorly characterized. In a preliminary study, we observed that HBV release could be markedly impaired by methyl-β-cyclodextrin mediated depletion of cholesterol in lipid rafts, and that this effect could be reversed by replenishment of exogenous cholesterol, suggesting that lipid rafts play an important role in the HBV life cycle. To further understanding how HBV exploited host cell lipid rafts to benefit replication, comprehensive proteomic approaches ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323977 Thu, 29 Sep 2011 04:00:00 +0100 5323977 http://www.medworm.com/index.php?rid=5323974&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21983555%26dopt%3DAbstract Authors: Izquierdo-Álvarez A, Martínez-Ruiz A Abstract There is increasing evidence that several reversible oxidative post-translational modifications of protein cysteines participate in cell signalling. Specific proteomic techniques are required to identify these modifications and to study their regulation in different cell processes, that are collectively known as thiol redox proteomics. Recently, fluorescence derivatization methods have been developed that enable these post-translational modifications to be studied using proteomic workflows based on two-dimensional electrophoresis, which is a relatively accessible and affordable technique. As well as enabling a large number of samples to be processed, two-dimensional electrophoresis has the advantage that it does not rely on t... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323974 Thu, 29 Sep 2011 04:00:00 +0100 5323974 http://www.medworm.com/index.php?rid=5323971&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21983556%26dopt%3DAbstract This article intends to provide a comprehensive overview of various PTM databases, software tools, and analyze critical information available from these resources to study PTMs in various biological organisms. PMID: 21983556 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5323971 Thu, 29 Sep 2011 04:00:00 +0100 5323971 http://www.medworm.com/index.php?rid=5293633&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21968429%26dopt%3DAbstract Authors: Paulo JA, Urrutia R, Banks PA, Conwell DL, Steen H Abstract Pancreatic stellate cells (PaSC) are emerging as key mediators in chronic pancreatitis and pancreatic cancer pathogenesis. Proteins regulating the biomolecular pathways involved in the conversion of quiescent to activated PaSC may have a significant influence in the development of chronic pancreatitis. We aim to compare differentially expressed proteins in activated and serum-starved non-proliferating PaSC using a mass spectrometry-based proteomics strategy. We cultured an immortalized rat PaSC cell line in media supplemented with 10% fetal bovine serum and in serum-free media. Using gel-based mass spectrometry (GeLC-MS/MS), we identified nearly 1500 proteins. Qualitative and quantitative proteomic analysis reveal... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5293633 Sun, 25 Sep 2011 04:00:00 +0100 5293633 http://www.medworm.com/index.php?rid=5293634&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21968428%26dopt%3DAbstract Authors: Aguilar-Melero P, Ferrín G, Muntané J Abstract Hepatocarcinoma is the fifth most common neoplasm and the third cause of cancer-related death. The development of genetic- and/or molecular-based therapies is urgently required. The administration of high doses of nitric oxide (NO) promotes cell death in hepatocytes. NO contributes to cell signaling by inducing oxidative/nitrosative-dependent post-translational modifications. The aim of the present study was to investigate protein modifications and its relation with alteration of cell proliferation and death in hepatoma cells. Increased intracellular NO production was achieved by stable nitric oxide synthase-3 (NOS-3) overexpression in HepG2 cells. We assessed the pattern of nitration, nitrosylation and carbonylation of prot... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5293634 Sat, 24 Sep 2011 04:00:00 +0100 5293634 http://www.medworm.com/index.php?rid=5293638&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21963438%26dopt%3DAbstract Authors: Rey-Suárez P, Núñez V, Gutiérrez JM, Lomonte B Abstract Venoms of the redtail coral snake Micrurus mipartitus from Colombia and Costa Rica were analyzed by "venomics", a proteomic strategy to determine their composition. Proteins were separated by RP-HPLC, followed by SDS-PAGE, in-gel tryptic digestion, identification by MALDI or ESI tandem mass spectrometry, and assignment to known protein families by similarity. These analyses were complemented with a characterization of venom activities in vitro and in vivo. Proteins belonging to seven families were found in Colombian M. mipartitus venom, including abundant three-finger toxins (3FTx; ~60% of total proteins) and phospholipases A(2) (PLA(2); ~30%), with the remaining ~10% distributed among l-amino acid oxidase, P-III ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5293638 Fri, 23 Sep 2011 04:00:00 +0100 5293638 http://www.medworm.com/index.php?rid=5293635&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21964283%26dopt%3DAbstract Authors: Li XH, Li C, Xiao ZQ Abstract A major problem in chemotherapy of cancer patients is drug resistance as well as unpredictable response to treatment. During chemotherapy, multiple alterations of genetics and epigenetics that contribute to chemoresistance take place, eventually impacting on disease outcome. A more complex picture of the mechanisms of drug resistance is now emerging through application of high-throughput proteomics technology. We have entered an exciting time where proteomics are being applied to characterize the mechanisms of drug resistance, and to identify biomarkers for predicting response to chemotherapy, thereby leading to personalized therapeutic strategies of cancer patients. Comparative proteomics have identified a large number of differentially expre... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5293635 Tue, 20 Sep 2011 04:00:00 +0100 5293635 http://www.medworm.com/index.php?rid=5293637&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21964257%26dopt%3DAbstract Authors: Lamoureux F, Mestre E, Essig M, Sauvage FL, Marquet P, Gastinel LN Abstract The calcineurin-inhibitors (CNIs) cyclosporine (CsA) and tacrolimus (TAC) remain the pillars of modern immunosuppression regimens used in solid organ transplantation. Nephrotoxicity is an adverse effect that limits their successful use. The precise molecular mechanisms underlying this nephrotoxicity remain unclear. Using SILAC together with LC-MALDI-TOF/TOF, we investigated the CNIs-induced proteomic perturbations in renal cells. Among the 495 proteins quantifiable in both forward and reverse SILAC, 69 displayed CsA-induced perturbations: proteins involved in ER-stress/protein folding, apoptosis, metabolism/transport or cytoskeleton pathways were up-regulated, while cyclophilin B as well as nuclear... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5293637 Sun, 18 Sep 2011 04:00:00 +0100 5293637 http://www.medworm.com/index.php?rid=5293636&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21964258%26dopt%3DAbstract Authors: Pereira SB, Ow SY, Barrios-Llerena ME, Wright PC, Moradas-Ferreira P, Tamagnini P Abstract Gloeothece sp. PCC 6909 is a unicellular N(2)-fixing cyanobacterium with a well defined and highly developed sheath surrounding its cells. A sheathless mutant of this strain was previously obtained by chemical mutagenesis and, although lacking the sheath, it releases large amounts of polysaccharides into the culture medium. To provide a global understanding on the metabolic differences between the two phenotypes, the proteomes of the wild type and mutant were analyzed using a cross-species proteomics approach coupled with iTRAQ isobaric tagging technology, since their genome sequences are not yet available. Effects arising from the presence/absence of nitrate and sulfur are presented... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5293636 Sat, 17 Sep 2011 04:00:00 +0100 5293636 http://www.medworm.com/index.php?rid=5293632&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21964256%26dopt%3DAbstract Authors: Yan GR, Yin XF, Xiao CL, Tan ZL, Xu SH, He QY Abstract Isolated from soybeans, genistein is an isoflavonoid that exhibits anti-carcinogenic effects. Genistein could induce G2/M arrest and apoptosis of various cancer cells in vivo and in vitro. Although ERK1/2, AKT, p90RSK and NFκB were previously found to be regulated by genistein, most of signaling components in genistein-inhibited signaling pathways were still unknown. Here, we used SILAC quantitative phosphoproteomics to globally identify the phosphoproteins and their regulatory sites in signaling pathways mediated by genistein. We detected 1177 phosphorylation sites on 635 unique proteins; among them, 320 phosphorylation sites on 222 unique phosphopeptides representing 215 non-redundant proteins were modulated at leas... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5293632 Sat, 17 Sep 2011 04:00:00 +0100 5293632 http://www.medworm.com/index.php?rid=5272702&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21945729%26dopt%3DAbstract Authors: Fan Y, Wang L, Zhou F, Zhang Y, Li H, Shan L, Yuan Z Abstract Neural tube defects (NTDs) are complex congenital anomalies of the central nervous system, with a prevalence of 5 per 10,000 worldwide. However, current therapeutics for NTDs are unsatisfactory. The neurological complications remain the main problem for therapy. Neurological dysfunction could result from the primary defect or injuries to the uncovered neural tissue in the uterus. However, the pathological changes in the uncovered neural tissue have not been described. Here, we present our comparative proteomics study of the spinal cord from rat fetuses with all-trans retinoic-acid-induced spina bifida aperta. Proteins from spinal cords were subjected to 2-D gel electrophoresis, then protein identification by mas... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5272702 Sat, 17 Sep 2011 04:00:00 +0100 5272702 http://www.medworm.com/index.php?rid=5272703&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21945728%26dopt%3DAbstract This study explored cellulose, hemicellulose, pectin and lignin degrading enzymes of P. chrysosporium that are valuable for lignocellulosic bioenergy. PMID: 21945728 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5272703 Tue, 13 Sep 2011 04:00:00 +0100 5272703 http://www.medworm.com/index.php?rid=5225582&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21920477%26dopt%3DAbstract Authors: D΄alessandro A, Marrocco C, Zolla V, D΄andrea MS, Zolla L Abstract Longissimus lumborum muscles from high fat-deposing Casertana and lean meat Large White pigs were assayed for meat quality parameters, including early and ultimate post mortem pH, water holding capacity and Minolta L*a*b*values. These parameters were correlated to results from differential proteomic and targeted metabolomic analyses. Higher levels of glycolytic enzymes and lactate accumulation were related to slow pH drop in Casertana pigs, albeit not to rapid pH lowering in LW counterparts. On the other hand, the individuation of pyruvate kinaseM1 and tropomyosin levels in LW were related to water holding capacity and Minolta values at 24h after slaughter. Bioinformatic analyses strengthened the correlat... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5225582 Thu, 08 Sep 2011 04:00:00 +0100 5225582 http://www.medworm.com/index.php?rid=5225585&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21920474%26dopt%3DAbstract Authors: Grifantini R, Pagani M, Pierleoni A, Grandi A, Parri M, Campagnoli S, Pileri P, Cattaneo D, Canidio E, Pontillo A, De Camilli E, Bresciani A, Marinoni F, Pedrazzoli E, Nogarotto R, Abrignani S, Viale G, Sarmientos P, Grandi G Abstract The YOMICS™ antibody library (http://www.yomics.com/) presented in this article is a new collection of 1559 murine polyclonal antibodies specific for 1287 distinct human proteins. This antibody library is designed to target marginally characterized membrane-associated and secreted proteins. It was generated against human proteins annotated as transmembrane or secreted in GenBank, EnsEMBL, Vega and Uniprot genome databases, described in no or very few dedicated PubMed-linked publications. The selected proteins/protein regions were expressed ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=5225585 Mon, 05 Sep 2011 04:00:00 +0100 5225585