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https://www.readbyqxmd.com/read/28102936/unbiased-and-quantitative-proteomics-reveals-highly-increased-angiogenesis-induction-by-the-secretome-of-mesenchymal-stromal-cells-isolated-from-fetal-rather-than-adult-skin
#1
Massimiliano Gaetani, Cinzia Maria Chinnici, Anna Paola Carreca, Claudia Di Pasquale, Giandomenico Amico, Pier Giulio Conaldi
Scarless wound healing and functional regeneration are typical processes of the fetus, gradually lost during post-natal life, and maximally attributed to fetal skin tissue and induced by fetal skin fibroblasts. The latter have been successfully applied to post-natal wounds, with clear advantages compared with autologous dermis grafts or adult fibroblast applications. Our goal was to functionally identify and uncover key factors and mechanisms through the analysis of secretomes, the principal players in all cell therapies based on mesenchymal stromal cells (MSCs)...
January 19, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28102851/cellular-prion-protein-mediates-early-apoptotic-proteome-alternation-and-phospho-modification-in-human-neuroblastoma-cells
#2
Saima Zafar, Christina Behrens, Hassan Dihazi, Matthias Schmitz, Inga Zerr, Walter J Schulz-Schaeffer, Sanja Ramljak, Abdul R Asif
Anti-apoptotic properties of physiological and elevated levels of the cellular prion protein (PrP(c)) under stress conditions are well documented. Yet, detrimental effects of elevated PrP(c) levels under stress conditions, such as exposure to staurosporine (STS) have also been described. In the present study, we focused on discerning early apoptotic STS-induced proteome and phospho-proteome changes in SH-SY5Y human neuroblastoma cells stably transfected either with an empty or PRNP-containing vector, expressing physiological or supraphysiological levels of PrP(c), respectively...
January 19, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28102850/japanese-encephalitis-virus-induces-human-neural-stem-progenitor-cell-death-by-elevating-grp78-phb-and-hnrnpc-through-er-stress
#3
Sriparna Mukherjee, Noopur Singh, Nabonita Sengupta, Mahar Fatima, Pankaj Seth, Anita Mahadevan, Susarla Krishna Shankar, Arindam Bhattacharyya, Anirban Basu
Japanese encephalitis virus (JEV), which is a causative agent of sporadic encephalitis, harbours itself inside the neural stem/progenitor cells. It is a well-known fact that JEV infects neural stem/progenitor cells and decreases their proliferation capacity. With mass spectrometry-based quantitative proteomic study, it is possible to reveal the impact of virus on the stem cells at protein level. Our aim was to perceive the stem cell proteomic response upon viral challenge. We performed a two-dimensional gel electrophoresis-based proteomic study of the human neural stem cells (hNS1 cell line) post JEV infection and found that 13 proteins were differentially expressed...
January 19, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28102082/characterization-of-the-molecular-mechanisms-underlying-the-chronic-phase-of-stroke-in-a-cynomolgus-monkey-model-of-induced-cerebral-ischemia
#4
Henry C H Law, Samuel S W Szeto, Quan Quan, Yun Zhao, Zaijun Zhang, Olga Krakovska, Leong Ting Lui, Chengyou Zheng, Simon Ming Yuen Lee, K W Michael Siu, Yuqiang Wang, Ivan K Chu
Stroke is one of the main causes of mortality and long-term disability worldwide. The pathophysiological mechanisms underlying this disease are not well understood, particularly in the chronic phase after the initial ischemic episode. In this study, a Macaca fascicularis stroke model consisting of two sample groups, as determined by MRI-quantified infarct volumes as a measure of the stroke severity 28 days after the ischemic episode, was evaluated using qualitative and quantitative proteomics analyses. By using multiple online multidimensional liquid chromatography platforms, 8790 non-redundant proteins that condensed to 5223 protein groups at 1% global false discovery rate (FDR)...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102081/deep-coverage-of-global-protein-expression-and-phosphorylation-in-breast-tumor-cell-lines-using-tmt-10-plex-isobaric-labeling
#5
Fang-Ke Huang, Guoan Zhang, Kevin Lawlor, Arpi Nazarian, John Philip, Paul Tempst, Noah Dephoure, Thomas A Neubert
Labeling peptides with isobaric tags is a popular strategy in quantitative bottom-up proteomics. In this study, we labeled six breast tumor cell lysates (1.34 mg proteins per channel) using 10-plex tandem mass tag reagents and analyzed the samples on a Q Exactive HF Quadrupole-Orbitrap mass spectrometer. We identified a total of 8706 proteins and 28186 phosphopeptides, including 7394 proteins and 23739 phosphosites common to all channels. The majority of technical replicates correlated with a R2 ≥ 0.98, indicating minimum variability was introduced after labeling...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102078/on-peptide-selection-for-targeted-protein-quantitation
#6
Cristina Chiva, Eduard Sabidó
Targeted proteomics methods in their different flavors rely on the use of a few peptides as proxies for protein quantitation, which need to be specified either prior or after data acquisition. However, in contrast to discovery methods that use all identified peptides for a given protein to estimate its abundance, targeted proteomics methods are limited in the number of peptides that are used for protein quantitation. As only few peptides per protein are acquired or extracted in targeted experiments, the selection of peptides that are used for targeted protein quantitation becomes crucial...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28102076/kinobead-and-single-shot-lc-ms-profiling-identifies-selective-pkd-inhibitors
#7
Martin Golkowski, Rama Subba Rao Vidadala, Chloe K Lombard, Hyong Won Suh, Dustin J Maly, Shao-En Ong
ATP-competitive protein kinase inhibitors are important research tools and therapeutic agents. Because there are >500 human kinases that contain highly conserved active sites, the development of selective inhibitors is extremely challenging. Methods to rapidly and efficiently profile kinase inhibitor targets in cell lysates are urgently needed to discover selective compounds and to elucidate the mechanisms of action for polypharmacological inhibitors. Here, we describe a protocol for microgram-scale chemoproteomic profiling of ATP-competitive kinase inhibitors using kinobeads...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28101936/quantitative-itraq-based-proteomic-analysis-of-rice-grains-to-assess-high-night-temperature-stress
#8
Hong-Yu Zhang, Gang Lei, Hui-Wen Zhou, Chao He, Jiang-Lin Liao, Ying-Jin Huang
Rice yield and quality are adversely affected by increasing global surface temperature, and are strongly attributed to high night temperature (HNT) than high daytime temperature. However, the molecular mechanism underlying the heat-tolerant characteristics of rice remains unclear. In the present study, we compared the proteomes of heat-tolerant and -sensitive lines of rice at early milky stage using an iTRAQ method. We have identified 38 differentially expressed proteins between the two lines, of which 32 proteins have been functionally annotated in NCBI and/or the UniProt database...
January 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28101920/quantitative-proteomic-analysis-of-hiv-1-tat-induced-dysregulation-in-sh-sy5y-neuroblastoma-cells
#9
Tariq Ganief, Putuma Gqamana, Shaun Garnett, Jackie Hoare, Dan J Stein, John Joska, Nelson Soares, Jonathan M Blackburn
Despite affecting up to 70% of HIV-positivepatients and being the leading cause of dementia in patients under 40 years, the molecular mechanisms involved in the onset of HIV-associated neurocognitive disorders (HAND) are not well understood. To address this, we performed SILAC-based quantitative proteomic analysis on HIV-Tat treated SH-SY5Y neuroblastoma cells. Isolated protein was fractionated by SDS-PAGE and analysed by nLC-MS/MS on an Orbitrap Velos. Using MaxQuant, we identified and quantified 3077 unique protein groups, of which 407 were differentially regulated...
January 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28101531/osteopontin-is-a-blood-biomarker-for-microglial-activation-and-brain-injury-in-experimental-hypoxic-ischemic-encephalopathy
#10
Yikun Li, Eric B Dammer, Xiaohui Zhang-Brotzge, Scott Chen, Duc M Duong, Nicholas T Seyfried, Chia-Yi Kuan, Yu-Yo Sun
Clinical management of neonatal hypoxic-ischemic encephalopathy (HIE) suffers from the lack of reliable surrogate marker tests. Proteomic analysis may identify such biomarkers in blood, but there has been no proof-of-principle evidence to support this approach. Here we performed in-gel trypsin digestion of plasma proteins from four groups of 10-d-old mice [untouched and 24 h after low-dose lipopolysaccharide (LPS) exposure, hypoxia-ischemia (HI), or LPS/HI injury; n = 3 in each group) followed by liquid chromatography-tandem mass spectrometry and bioinformatics analysis to search for HI- and LPS/HI-associated brain injury biomarkers...
January 2017: ENeuro
https://www.readbyqxmd.com/read/28101252/identification-of-proteins-from-wild-cardoon-flowers-cynara-cardunculus-l-by-a-proteomic-approach
#11
Amal Ben Amira, Julien Bauwens, Edwin De Pauw, Souhail Besbes, Hamadi Attia, Frédéric Francis, Christophe Blecker
Proteomic approach was applied to identify total proteins, particularly the enzymatic content, from wild cardoon flowers. As the selection of an appropriate sample preparation method is the key for getting reliable results, two different extraction/precipitation methods (trichloroacetic acid and phenol/ammonium acetate) were tested on fresh and lyophilized flowers. After two-dimensional electrophoresis (2D-E) separations, a better protein pattern was obtained after phenol extraction from lyophilized flowers...
January 2017: Journal of Chemical Biology
https://www.readbyqxmd.com/read/28101236/identification-of-proteins-associated-with-pediatric-bilateral-wilms-tumor
#12
Zechen Yan, Qingjun Meng, Jinjian Yang, Junjie Zhang, Wei Zhao, Fei Guo, Dongjian Song, Yuxiao Zhan, Dandan Fan, Ruiyi Zhou, Shuqiang Zuo, Zehua Wang, Jiekai Yu, Shu Zheng, Jiaxiang Wang
Wilms tumor (WT) is the most common cancer that primarily develops in abdominal solid organ of children. It has no incipient symptom, and the most frequent symptoms are a painless, palpable abdominal mass. Proteomics technology was used to select the differentially expressed proteins of bilateral Wilms tumor (BWT). Ten serum samples of children with BWT were chosen, 20 serum samples of children with unilateral WT (UWT) and 20 serum samples of healthy children were selected, and proteomics technology was used to detect and collect data...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28100784/mitochondrial-o-glcnac-transferase-mogt-regulates-mitochondrial-structure-function-and-survival-in-hela-cells
#13
Juliana L Sacoman, Raul Y Dagda, Amanda R Burnham-Marusich, Ruben K Dagda, Patricia M Berninsone
O-linked N-acetylglucosamine transferase (OGT) catalyzes O-GlcNAcylation of target proteins and regulates numerous biological processes. OGT is encoded by a single gene that yields nucleocytosolic and mitochondrial isoforms. To date, the role of the mitochondrial isoform of OGT (mOGT) remains largely unknown. Using high-throughput proteomics, we identified 84 candidate mitochondrial glycoproteins, of which 44 are novel. Notably, two of the candidate glycoproteins identified (cytochrome oxidase 2 (COX2) and NADH: ubiquinone oxidoreductase core subunit 4 (MT-ND4)) are encoded by mitochondrial DNA...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100699/proteogenomics-produces-comprehensive-and-highly-accurate-protein-coding-gene-annotation-in-a-complete-genome-assembly-of-malassezia-sympodialis
#14
Yafeng Zhu, Pär G Engström, Christian Tellgren-Roth, Charles D Baudo, John C Kennell, Sheng Sun, R Blake Billmyre, Markus S Schröder, Anna Andersson, Tina Holm, Benjamin Sigurgeirsson, Guangxi Wu, Sundar Ram Sankaranarayanan, Rahul Siddharthan, Kaustuv Sanyal, Joakim Lundeberg, Björn Nystedt, Teun Boekhout, Thomas L Dawson, Joseph Heitman, Annika Scheynius, Janne Lehtiö
Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28100627/inflammatory-biomarkers-predict-heart-failure-severity-and-prognosis-in-patients-with-heart-failure-with-preserved-ejection-fraction-a-holistic-proteomic-approach
#15
Camilla Hage, Erik Michaëlsson, Cecilia Linde, Erwan Donal, Jean-Claude Daubert, Li-Ming Gan, Lars H Lund
BACKGROUND: Underlying mechanisms in heart failure (HF) with preserved ejection fraction remain unknown. We investigated cardiovascular plasma biomarkers in HF with preserved ejection fraction and their correlation to diastolic dysfunction, functional class, pathophysiological processes, and prognosis. METHODS AND RESULTS: In 86 stable patients with HF and EF ≥45% in the Karolinska Rennes (KaRen) biomarker substudy, biomarkers were quantified by a multiplex immunoassay...
February 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28100513/loss-of-ranbp2-in-motor-neurons-causes-the-disruption-of-nucleocytoplasmic-and-chemokine-signaling-and-proteostasis-of-hnrnph3-and-mmp28-and-the-development-of-amyotrophic-lateral-sclerosis-als-like-syndromes
#16
Kyoung-In Cho, Dosuk Yoon, Sunny Qiu, Zachary Danziger, Warren M Grill, William C Wetsel, Paulo A Ferreira
The pathogenic drivers of sporadic and familial motor neuron disease (MND), such ALS, are unknown. MND impair the Ran GTPase cycle, which controls nucleocytoplasmic transport, ribostasis and proteostasis; however, cause-effect mechanisms of Ran GTPase modulators in motoneuron pathobiology are heretofore elusive. The cytosolic and peripheral nucleoporin, Ranbp2, is a critical regulator of the Ran GTPase cycle and proteostasis of neurological disease-prone substrates, but the roles of Ranbp2 in motoneuron biology and disease remain unknown...
January 18, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28100303/ethanol-glycogen-and-glucosylglycerol-represent-competing-carbon-pools-in-ethanol-producing-cells-of-synechocystis-sp-pcc-6803-under-high-salt-conditions
#17
Nadin Pade, Stefan Mikkat, Martin Hagemann
Cyanobacteria are photoautotrophic microorganisms, which are increasingly being used as microbial cell factories to produce for example ethanol directly from solar energy and CO2. Here we analyzed the effects of different salt concentrations on an ethanol-producing strain of Synechocystis sp. PCC 6803 that over-expresses the pyruvate decarboxylase (pdc) from Zymomonas mobilis and the native alcohol dehydrogenase (adhA). Moderate salinities of 2% NaCl had no negative impact on ethanol production, whereas the addition of 4% NaCl resulted in significantly decreased ethanol yields compared to low salt conditions...
January 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28100206/hypoglycemic-effects-of-trichosanthes-kirilowii-and-its-protein-constituent-in-diabetic-mice-the-involvement-of-insulin-receptor-pathway
#18
Hsin-Yi Lo, Tsai-Chung Li, Tse-Yen Yang, Chia-Cheng Li, Jen-Huai Chiang, Chien-Yun Hsiang, Tin-Yun Ho
BACKGROUND: Diabetes is a serious chronic metabolic disorder. Trichosanthes kirilowii Maxim. (TK) is traditionally used for the treatment of diabetes in traditional Chinese medicine (TCM). However, the clinical application of TK on diabetic patients and the hypoglycemic efficacies of TK are still unclear. METHODS: A retrospective cohort study was conducted to analyze the usage of Chinese herbs in patients with type 2 diabetes in Taiwan. Glucose tolerance test was performed to analyze the hypoglycemic effect of TK...
January 18, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28099887/comparative-proteomics-of-paired-vocal-fold-and-oral-mucosa-fibroblasts
#19
Michael Karbiener, Barbara Darnhofer, Marie-Therese Frisch, Beate Rinner, Ruth Birner-Gruenberger, Markus Gugatschka
: Injuries of the vocal folds frequently heal with scar formation, which can have lifelong detrimental impact on voice quality. Current treatments to prevent or resolve scars of the vocal fold mucosa are highly unsatisfactory. In contrast, the adjacent oral mucosa is mostly resistant to scarring. These differences in healing tendency might relate to distinct properties of the fibroblasts populating oral and vocal fold mucosae. We thus established the in vitro cultivation of paired, near-primary vocal fold fibroblasts (VFF) and oral mucosa fibroblasts (OMF) to perform a basic cellular characterization and comparative cellular proteomics...
January 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28099886/itraq-based-quantitative-proteome-revealed-metabolic-changes-of-flammulina-velutipes-mycelia-in-response-to-cold-stress
#20
Jing-Yu Liu, Jun-Long Men, Ming-Chang Chang, Cui-Ping Feng, Ling-Gang Yuan
: Temperature is one of the pivotal factors influencing mycelium growth and fruit-body formation of Flammulina velutipes. To gain insights into hyphae growth and fruit-body formation events and facilitate the identification of potential stage-specific biomarker candidates, we investigated the proteome response of F. velutipes mycelia to cold stresses using iTRAQ-coupled two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) technique. Among 1198 proteins identified with high confidence, a total of 63 displayed altered expression level after cold stress treatments...
January 15, 2017: Journal of Proteomics
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