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Journal of Proteomics

Jessica Brandi, Ilaria Dando, Elisa Dalla Pozza, Giulia Biondani, Rosalind Jenkins, Victoria Elliott, Kevin Park, Giuseppina Fanelli, Lello Zolla, Eithne Costello, Aldo Scarpa, Daniela Cecconi, Marta Palmieri
: Recently, we have shown that the secretome of pancreatic cancer stem cells (CSCs) is characterized by proteins that participate in cancer differentiation, invasion, and metastasis. However, the differentially expressed intracellular proteins that lead to the specific characteristics of pancreatic CSCs have not yet been identified, and as a consequence the deranged metabolic pathways are yet to be elucidated. To identify the modulated proteins of pancreatic CSCs, iTRAQ-based proteomic analysis was performed to compare the proteome of Panc1 CSCs and Panc1 parental cells, identifying 230 modulated proteins...
October 13, 2016: Journal of Proteomics
Jeovanis Gil, Alberto Ramírez-Torres, Sergio Encarnación-Guevara
Lysine acetylation is a reversible modification controlled by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs). Acetylated lysine residues are recognized by bromodomains, a family of evolutionarily conserved domains. The use of high-resolution mass spectrometry-based proteomics, in combination with the enrichment of acetylated peptides through immunoprecipitation with anti-acetyl-lysine antibodies, has expanded the number of acetylated proteins from histones and a few nuclear proteins to more than 2000 human proteins...
October 13, 2016: Journal of Proteomics
Kristien A Van Camp, Geert Baggerman, Ronny Blust, Steven J Husson
: (Neuro)peptides are small messenger molecules that are derived from larger, inactive precursor proteins by the highly controlled action of processing enzymes. These biologically active peptides can be found in all metazoan species where they orchestrate a wide variety of physiological processes. Obviously, detailed knowledge on the actual peptide sequences, including the potential existence of truncated versions or presence of post-translation modifications, is of high importance when studying their function...
October 2, 2016: Journal of Proteomics
Tomas Erban, Karel Harant, Julie Chalupnikova, Frantisek Kocourek, Jitka Stara
: Insecticide resistance is an increasingly global problem that hampers pest control. We sought the mechanism responsible for survival following pyrethroid treatment and the factors connected to paralysis/death of the pollen beetle Meligethes aeneus through a proteome-level analysis using nanoLC coupled with Orbitrap Fusion™ Tribrid™ mass spectrometry. A tolerant field population of beetles was treated with deltamethrin, and the ensuing proteome changes were observed in the survivors (resistant), dead (paralyzed) and control-treated beetles...
October 2, 2016: Journal of Proteomics
Wen Ma, Dan Zhang, Guoshun Li, Jingjing Liu, Gu He, Peng Zhang, Li Yang, Hongxia Zhu, Ningzhi Xu, Shufang Liang
: Daptomycin (DAP) is a novel lipopeptide antibiotic which exhibits excellent antibacterial activity against most clinically relevant Gram-positive bacteria, but the DAP-targeting protein molecules against host bacterial infection are far from clear. In order to discover bacterial protein response to DAP treatment, an iTRAQ-based quantitative proteomic analysis was applied to identify differential bacterial proteome profiling of Staphylococcus aureus (S. aureus) ATCC 25923 to 0.125μg/ml DAP exposure...
September 29, 2016: Journal of Proteomics
Yingchao Wang, Hongzhi Liu, Dong Liang, Yao Huang, Yongyi Zeng, Xiaohua Xing, Jiangbao Xia, Minjie Lin, Xiao Han, Naishun Liao, Xiaolong Liu, Jingfeng Liu
: Tumor size of hepatocellular carcinoma (HCC) is a key parameter for predicting prognosis of HCC patients. The biological behaviors of HCC, such as tumor growth, recurrence and metastasis are significantly associated with tumor size. However, the underlying molecular mechanisms remain unclear. Here, we applied iTRAQ-based proteomic strategy to analyze the proteome differences among small, media, large and huge primary HCC tissues. In brief,88 proteins in small HCC, 69 proteins in media HCC, 118 proteins in large HCC and 215 proteins in huge HCC, were identified by comparing the proteome of cancerous tissues with its corresponding non-cancerous tissues...
September 28, 2016: Journal of Proteomics
Bruna Marques Dos Santos, Tiago Santana Balbuena
: Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO2 concentrations. Growth under a high concentration of CO2 could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO2. Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species...
September 24, 2016: Journal of Proteomics
Bertrand Colignon, Edouard Delaive, Marc Dieu, Catherine Demazy, Yordan Muhovski, Cindy Wallon, Martine Raes, Sergio Mauro
: SUMOylation is a post-translational modification which regulates a number of critical biological processes in, for example mammals, yeast and plants. In order to fully understand the functional effects of SUMOylation an essential first step is the identification of endogenous targets for SUMOylation. Here we report the results of using a recently developed proteomic approach based on the use of 3D gels to identify the endogenous SUMO targets in leaves of Solanum tuberosum. By using 3D gels we avoid the problem of co-migration of proteins, which is a major limitation of 2D gels, and we enable the use of the highly sensitive CyDye DIGE fluor saturation dyes...
September 23, 2016: Journal of Proteomics
Christopher A Toth, Zsuzsanna Kuklenyik, Jeffrey I Jones, Bryan A Parks, Michael S Gardner, David M Schieltz, Jon C Rees, Michael L Andrews, Lisa G McWilliams, James L Pirkle, John R Barr
: Apolipoproteins measured in plasma or serum are potential biomarkers for assessing metabolic irregularities that are associated with the development of cardiovascular disease (CVD). LC-MS/MS allows quantitative measurement of multiple apolipoproteins in the same sample run. However, the accuracy and precision of the LC-MS/MS measurement depends on the reproducibility of the enzymatic protein digestion step. With the application of an immobilized enzyme reactor (IMER), the reproducibility of the trypsin digestion can be controlled with high precision via flow rate, column volume and temperature...
September 23, 2016: Journal of Proteomics
Xia Yang, Zichang Zhang, Tao Gu, Mingchao Dong, Qiong Peng, Lianyang Bai, Yongfeng Li
: Barnyardgrass (Echinochloa crus-galli) is one of the top 15 herbicide-resistant weeds around the world that interferes with rice growth, resulting in major losses of rice yield. Thus, multi-herbicide resistance in barnyardgrass presents a major threat, with the underlying mechanisms that contribute to resistance requiring elucidation. In an attempt to characterize this multi-herbicide resistance at the proteomic level, comparative analysis of resistant and susceptible barnyardgrasses was performed using iTRAQ, both with and without quinclorac, bispyribac-sodium and penoxsulam herbicidal treatment...
September 23, 2016: Journal of Proteomics
Davinia Pla, Benjamin W Bande, Ronelle E Welton, Owen K Paiva, Libia Sanz, Álvaro Segura, Christine E Wright, Juan J Calvete, José María Gutiérrez, David J Williams
: The Papuan black snake (Pseudechis papuanus Serpentes: Elapidae) is endemic to Papua New Guinea, Indonesian Papua and Australia's Torres Strait Islands. We have investigated the biological activity and proteomic composition of its venom. The P. papuanus venom proteome is dominated by a variety (n≥18) of PLA2s, which together account for ~90% of the venom proteins, and a set of low relative abundance proteins, including a short-neurotoxic 3FTx (3.1%), 3-4 PIII-SVMPs (2.8%), 3 cysteine-rich secretory proteins (CRISP; 2...
September 17, 2016: Journal of Proteomics
Petra Darebna, Petr Novak, Radek Kucera, Ondrej Topolcan, Miloslav Sanda, Radoslav Goldman, Petr Pompach
: Alternations in the glycosylation of proteins have been described in connection with several cancers, including hepatocellular carcinoma (HCC) and colorectal cancer. Analytical tools, which use combination of liquid chromatography and mass spectrometry, allow precise and sensitive description of these changes. In this study, we use MRM and FT-ICR operating in full-MS scan, to determine ratios of intensities of specific glycopeptides in HCC, colorectal cancer, and liver metastasis of colorectal cancer...
September 16, 2016: Journal of Proteomics
Suresh Jivan Gadher, Hana Kovarova
The Central and Eastern European Proteomic Conference (CEEPC), has reached a special milestone as it celebrates its 10th anniversary. Today, an expansive network of proteomics in Central and Eastern Europe stands established to facilitate scientific interactions and collaborations in and around Central and Eastern Europe, as well as with international research institutions worldwide. Currently, when many conferences are struggling to attract participants, CEEPC is thriving in its status and stature as well as expanding by attracting newer member countries...
September 13, 2016: Journal of Proteomics
Lina Sun, Huarong Chen, Wenxiong Lin, Xiangmin Lin
: Edwardsiella tarda is a virulent fish pathogen that causes extensive economic losses in the aquaculture industry worldwide. The antibiotic resistance status of E. tarda is high, especially in the biofilm status; however, the mechanisms underlying its resistance remain largely unknown. In this study, isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics methods were used to compare the differential expression of E. tarda in response to oxytetracycline (OXY) stress in biofilm...
September 13, 2016: Journal of Proteomics
Lina Zhang, Giacomo Lanzoni, Matteo Battarra, Luca Inverardi, Qibin Zhang
: The etiology of Type 1 Diabetes (T1D) remains elusive. Enzymatically isolated and cultured (EIC) islets cannot fully reflect the natural protein composition and disease process of in vivo islets, because of the stress from isolation procedures. In order to study islet protein composition in conditions close to the natural environment, we performed proteomic analysis of EIC islets, and laser capture microdissected (LCM) human islets and acinar tissue from fresh-frozen pancreas sections of three cadaveric donors...
September 13, 2016: Journal of Proteomics
Jesús Mateos, Isabel Carneiro, Fernando Corrales, Felix Elortza, Alberto Paradela, Manuel Sánchez Del Pino, Ibon Iloro, Miguel Marcilla, Maria Isabel Mora, Luz Valero, Sergio Ciordia, Verónica Fernández, Maria Antonia Fortuño, Isabel García-Sánchez, Rosario Martínez, Maria Angeles Muñoz, Clara Rodriguez, Nieves Doménech
: Analytical proteomics has experienced exponential progress in the last decade and can be expected to lead research studies on diagnostic and therapeutic biomarkers in the near future. Because the development of this type of analysis requires the use of a large number of human samples with a minimum of quality requirements, our objective was to identify appropriate indicators for quality control of plasma samples stored in biobanks for research in proteomics. To accomplish this, plasma samples from 100 healthy donors were obtained and processed according to the pre-analytical variables of: a) time delay for the first centrifugation of the original blood sample (4 or 24h) and b) number of freeze/thaw cycles (1, 2 or 3) of the processed plasma samples...
September 9, 2016: Journal of Proteomics
Gourav Bhardwaj, Marcus Dörr, Praveen Kumar Sappa, Sabine Ameling, Vishnu Dhople, Leif Steil, Karin Klingel, Klaus Empen, Daniel Beug, Uwe Völker, Stephan B Felix, Elke Hammer
: Dilated cardiomyopathy (DCM) is a disease of the myocardium with reduced left ventricular ejection fraction (LVEF). Cardiac autoantibodies (AAbs) play a causal role in the development and progression of DCM. Removal of AAbs using immunoadsorption (IA/IgG) has been shown as a therapeutic option to improve cardiac function. However, the response to therapy differs significantly among patients. The reasons for this variability are not completely understood. Hitherto, no potential biomarker is available to predict improvement of cardiac function after therapy accurately...
September 9, 2016: Journal of Proteomics
Anja M Billing, Hisham Ben Hamidane, Aditya M Bhagwat, Richard J Cotton, Shaima S Dib, Pankaj Kumar, Shahina Hayat, Neha Goswami, Karsten Suhre, Arash Rafii, Johannes Graumann
: Dynamic range limitations are challenging to proteomics, particularly in clinical samples. Affinity proteomics partially overcomes this, yet suffers from dependence on reagent quality. SOMAscan, an aptamer-based platform for over 1000 proteins, avoids that issue using nucleic acid binders. Targets include low expressed proteins not easily accessible by other approaches. Here we report on the potential of SOMAscan for the study of differently sourced mesenchymal stem cells (MSC) in comparison to LC-MS/MS and RNA sequencing...
September 6, 2016: Journal of Proteomics
Jinzhi Han, Peng Gao, Shengming Zhao, Xiaomei Bie, Zhaoxin Lu, Chong Zhang, Fengxia Lv
: LI-F type peptides (AMP-jsa9) produced by Paenibacillus polymyxa JSa-9 are a group of cyclic lipodepsipeptide antibiotics that exhibit a broad antimicrobial spectrum against Gram-positive bacteria and filamentous fungi, especially Bacillus cereus and Fusarium moniliforme. In this study, to better understand the antibacterial mechanism of AMP-jsa9 against B. cereus, the ultrastructure of AMP-jsa9-treated B. cereus cells was observed by both atomic force microscopy and transmission electron microscopy, and quantitative proteomic analysis was performed on proteins extracted from treated and untreated bacterial cells by using isobaric tag for relative and absolute quantitation (iTRAQ) labeling and LC-MS/MS analysis to access differentially expressed proteins...
September 5, 2016: Journal of Proteomics
Line P Lauridsen, Andreas H Laustsen, Bruno Lomonte, José María Gutiérrez
: A toxicovenomic analysis of the venom of the forest cobra, N. melanoleuca, was performed, revealing the presence of a total of 52 proteins by proteomics analysis. The most abundant proteins belong to the three-finger toxins (3FTx) (57.1wt%), which includes post-synaptically acting α-neurotoxins. Phospholipases A2 (PLA2) were the second most abundant group of proteins (12.9wt%), followed by metalloproteinases (SVMPs) (9.7wt%), cysteine-rich secretory proteins (CRISPs) (7.6wt%), and Kunitz-type serine proteinase inhibitors (3...
September 1, 2016: Journal of Proteomics
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