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https://www.readbyqxmd.com/read/28328035/%C3%AE-elimination-coupled-with-strong-cation-exchange-chromatography-for-phosphopeptide-analysis
#1
Hansuk Buncherd, Winfried Roseboom, Daranee Chokchaichamnankit, Phannee Sawangareetrakul, Amornrat Phongdara, Chantragan Srisomsap, Luitzen de Jong, Jisnuson Svasti
RATIONALE: Since the last decade, mass spectrometry (MS) has become an essential technique for phosphoprotein analysis. Formidable analytical challenges of MS for phosphoprotein study are both the low abundance of phosphopeptides and the lack of an unambiguous diagnostic fragment ion for identification of phospho residues. These challenges can be met by a charge-based isolation of β-elimination products after tryptic digestion using diagonal strong cation-exchange chromatography. METHODS: β-Elimination combined with diagonal strong cation-exchange chromatography (BE/2SCX) was used for the enrichment of phosphorylated peptides prior to a mass spectrometric analysis by liquid chromatography/ion trap tandem mass spectrometry (MS/MS)...
July 30, 2016: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28327990/estimating-the-total-number-of-phosphoproteins-and-phosphorylation-sites-in-eukaryotic-proteomes
#2
Panayotis Vlastaridis, Pelagia Kyriakidou, Anargyros Chaliotis, Yves Van de Peer, Stephen G Oliver, Grigoris D Amoutzias
Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and phosphorylation sites (p-sites), for four eukaryotes (human, mouse, Arabidopsis, and yeast)...
January 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28326824/osteopontin-its-potential-role-in-cancer-of-children-and-young-adults
#3
Gabrielle Karpinsky, Aleksandra Fatyga, Malgorzata Anna Krawczyk, Madeleine Chamera, Natalia Sande, Dagmara Szmyd, Ewa Izycka-Swieszewska, Ewa Bien
OBJECTIVE: Osteopontin (OPN) is aglyco-phosphoprotein, involved in tissue remodeling, inflammation and boneresorption. In various adult neoplasms OPN was shown to correlate with cancer progression, invasiveness and metastasis. AIM: to define the role of OPN in malignancies of children and young adults. MATERIAL AND METHODS: a structured PubMed and Google Scholar literature analysis based on reports published in English between I'1995 and XII'2015...
March 14, 2017: Biomarkers in Medicine
https://www.readbyqxmd.com/read/28326315/genomewide-expression-and-functional-interactions-of-genes-under-drought-stress-in-maize
#4
Nepolean Thirunavukkarasu, Rinku Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta Kumar Dash, Firoz Hossain, Hari Shanker Gupta
A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28326294/the-eukaryote-like-serine-threonine-kinase-stk-regulates-the-growth-and-metabolism-of-zoonotic-streptococcus-suis
#5
Chunyan Zhang, Wen Sun, Meifang Tan, Mengmeng Dong, Wanquan Liu, Ting Gao, Lu Li, Zhuofei Xu, Rui Zhou
Like eukaryotes, bacteria express one or more serine/threonine kinases (STKs) that initiate diverse signaling networks. The STK from Streptococcus suis is encoded by a single-copy stk gene, which is crucial in stress response and virulence. To further understand the regulatory mechanism of STK in S. suis, a stk deletion strain (Δstk) and its complementary strain (CΔstk) were constructed to systematically decode STK characteristics by applying whole transcriptome RNA sequencing (RNA-Seq) and phosphoproteomic analysis...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28320969/ena-vasp-proteins-regulate-activated-t-cell-trafficking-by-promoting-diapedesis-during-transendothelial-migration
#6
Miriam L Estin, Scott B Thompson, Brianna Traxinger, Marlie H Fisher, Rachel S Friedman, Jordan Jacobelli
Vasodilator-stimulated phosphoprotein (VASP) and Ena-VASP-like (EVL) are cytoskeletal effector proteins implicated in regulating cell morphology, adhesion, and migration in various cell types. However, the role of these proteins in T-cell motility, adhesion, and in vivo trafficking remains poorly understood. This study identifies a specific role for EVL and VASP in T-cell diapedesis and trafficking. We demonstrate that EVL and VASP are selectively required for activated T-cell trafficking but are not required for normal T-cell development or for naïve T-cell trafficking to lymph nodes and spleen...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320458/b-cell-epitope-of-human-cytomegalovirus-phosphoprotein-65-hcmv-pp65-induced-anti-dsdna-antibody-in-balb-c-mice
#7
Ao HoHsieh, Chin Man Wang, Yeong-Jian Jan Wu, Albert Chen, Ming-I Chang, Ji-Yih Chen
BACKGROUND: HCMV phosphoprotein 65 (HCMVpp65) is a putative immunogen that acts as an accelerator, inducing autoantibody and exacerbating autoimmune response in susceptible animals. The immunity to pp65336-439 instigates autoimmunity, suggesting that pp65336-439 contains crucial B cell epitope(s) for the development of nephritis. This study narrowed down the target epitope to pp65422-439 for immunization of BALB/c mice and mapping of B cell epitope. METHODS: The target epitope pp65422-439 reactivity and B cell epitope mapping was examined in serum from pp65422-439-immunized mice and patients with systemic lupus erythematosus (SLE)...
March 21, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28319142/microrna-32-promotes-calcification-in-vascular-smooth-muscle-cells-implications-as-a-novel-marker-for-coronary-artery-calcification
#8
Jianghua Liu, Xinhua Xiao, Yingying Shen, Ling Chen, Canxin Xu, Heng Zhao, Ying Wu, Qinghai Zhang, Jing Zhong, Zhenwang Tang, Changhui Liu, Qiang Zhao, Yi Zheng, Renxian Cao, Xuyu Zu
Cardiovascular calcification is one of the most severe outcomes associated with cardiovascular disease and often results in significant morbidity and mortality. Previous reports indicated that epigenomic regulation of microRNAs (miRNAs) might play important roles in vascular smooth muscle cell (VSMC) calcification. Here, we identified potential key miRNAs involved in vascular calcification in vivo and investigated the role of miR-32-5p (miR-32). According to microarray analysis, we observed increased expression of miR-125b, miR-30a, and miR-32 and decreased expression of miR-29a, miR-210, and miR-320 during the progression of vascularcalcification...
2017: PloS One
https://www.readbyqxmd.com/read/28314311/core-needle-biopsy-specimens-are-more-appropriate-than-surgical-specimens-for-evaluating-the-expression-of-phosphoproteins-as-biological-markers-in-invasive-breast-cancer
#9
Hyun-Ah Kim, Ji Hyun Kim, Hyang Suk Choi, Yun Gyoung Kim, Seok Joon Lee, Kang Hee Han, Min Ki Seong, Hye Sil Seol, Woo Chul Noh
BACKGROUND/AIM: To evaluate whether core needle biopsy specimens (CNBS) would be better than surgical specimens (SS) for evaluating phosphoproteins as biological markers in breast cancer. MATERIALS AND METHODS: This retrospective analysis included a total of 99 patients who had invasive breast cancer and were treated surgically between January 2012 and July 2013. The expression of phosphorylated ribosomal protein S6-kinase-1 (p-S6K1), phosphorylated protein kinase B (p-AKT), and estrogen receptor (ER) were assessed immunohistochemically on both CNBS and SS for each patient...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28306668/a-role-for-intracellular-and-extracellular-dek-in-regulating-hematopoiesis
#10
Maegan L Capitano, Hal E Broxmeyer
PURPOSE OF REVIEW: Hematopoietic stem/progenitor cell fate decision during hematopoiesis is regulated by intracellular and extracellular signals such as transcription factors, growth factors, and cell-to-cell interactions. In this review, we explore the function of DEK, a nuclear phosphoprotein, on gene regulation. We also examine how DEK is secreted and internalized by cells, and discuss how both endogenous and extracellular DEK regulates hematopoiesis. Finally, we explore what currently is known about the regulation of DEK during inflammation...
March 16, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28303482/extracellular-superoxide-dismutase-is-necessary-to-maintain-renal-blood-flow-during-sepsis-development
#11
Larissa Constantino, Letícia Selinger Galant, Francieli Vuolo, Karla Lorena Guarido, Luiza Wilges Kist, Giovanna Medeiros Tavares de Oliveira, Matheus Augusto de Bittencourt Pasquali, Cláudio Teodoro de Souza, José Eduardo da Silva-Santos, Maurício Reis Bogo, José Cláudio Fonseca Moreira, Cristiane Ritter, Felipe Dal-Pizzol
BACKGROUND: Extracellular superoxide dismutase (ECSOD) protects nitric oxide (NO) bioavailability by decreasing superoxide levels and preventing peroxynitrite generation, which is important in maintaining renal blood flow and in preventing acute kidney injury. However, the profile of ECSOD expression after sepsis is not fully understood. Therefore, we intended to evaluate the content and gene expression of superoxide dismutase (SOD) isoforms in the renal artery and their relation to renal blood flow...
December 2017: Intensive Care Medicine Experimental
https://www.readbyqxmd.com/read/28290473/phosphoproteomics-reveals-hmga1-a-ck2-substrate-as-a-drug-resistant-target-in-non-small-cell-lung-cancer
#12
Yi-Ting Wang, Szu-Hua Pan, Chia-Feng Tsai, Ting-Chun Kuo, Yuan-Ling Hsu, Hsin-Yung Yen, Wai-Kok Choong, Hsin-Yi Wu, Yen-Chen Liao, Tse-Ming Hong, Ting-Yi Sung, Pan-Chyr Yang, Yu-Ju Chen
Although EGFR tyrosine kinase inhibitors (TKIs) have demonstrated good efficacy in non-small-cell lung cancer (NSCLC) patients harboring EGFR mutations, most patients develop intrinsic and acquired resistance. We quantitatively profiled the phosphoproteome and proteome of drug-sensitive and drug-resistant NSCLC cells under gefitinib treatment. The construction of a dose-dependent responsive kinase-substrate network of 1548 phosphoproteins and 3834 proteins revealed CK2-centric modules as the dominant core network for the potential gefitinib resistance-associated proteins...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28288918/increased-carbon-dioxide-levels-stimulate-neutrophils-to-produce-microparticles-and-activate-the-nucleotide-binding-domain-like-receptor-3-inflammasome
#13
Stephen R Thom, Veena M Bhopale, JingPing Hu, Ming Yang
We hypothesized that elevations of carbon dioxide (CO2) commonly found in modern buildings will stimulate leukocytes to produce microparticles (MPs) and activate the nucleotide-binding domain-like receptor 3 (NLRP3) inflammasome due to mitochondrial oxidative stress. Human and murine neutrophils generate MPs with high interleukin-1β (IL-1β) content when incubated ex vivo in buffer equilibrated with 0.1-0.4% additional CO2. Enhanced MPs production requires mitochondrial reactive oxygen species production, which is mediated by activities of pyruvate carboxylase and phosphoenolpyruvate carboxykinase...
March 10, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28288883/insights-regarding-fungal-phosphoproteomic-analysis
#14
REVIEW
Liliane F C Ribeiro, Cynthia L Chelius, Steven D Harris, Mark R Marten
Protein phosphorylation is a major means of regulation for cellular processes, and is important in cell signaling, growth, and cell proliferation. To study phosphorylated proteins, high throughput phosphoproteomic technologies, such as reverse phase protein array, phospho-specific flow cytometry, and mass spectrometry (MS) based technologies, have been developed. Among them, mass spectrometry has become the primary tool employed for the identification of phosphoproteins and phosphosites in fungi, leading to an improved understanding of a number of signaling pathways...
March 10, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28286322/secreted-phosphoprotein-24kd-spp24-inhibits-growth-of-hepatocellular-carcinoma-in-vivo
#15
Lifeng Lao, Jia Shen, Haijun Tian, Guibin Zhong, Samuel S Murray, Jeffrey C Wang
Several studies have shown that secreted phosphoprotein 24kD (Spp24) inhibits tumor growth. However, the effects of spp24 on hepatocellular carcinoma are not quite clear. In this study, we observed the inhibitory effect of spp24 on hepatocellular carcinoma in vivo. A subcutaneous hepatocellular carcinoma mice model was established by using Hep G2 cells. After sacrifice at day 40, tumor growth was assessed and tumor cell apoptosis and tumor cells proliferation were assessed by TUNEL assay and immunochemical analysis, respectively...
March 4, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28283928/estimating-the-efficiency-of-phosphopeptide-identification-by-tandem-mass-spectrometry
#16
Chuan-Chih Hsu, Liang Xue, Justine V Arrington, Pengcheng Wang, Juan Sebastian Paez Paez, Yuan Zhou, Jian-Kang Zhu, W Andy Tao
Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events...
March 10, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28280819/microchip-based-single-cell-functional-proteomics-for-biomedical-applications
#17
REVIEW
Yao Lu, Liu Yang, Wei Wei, Qihui Shi
Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that traditional population-based methods fail to address. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical frameworks to extract new biology...
March 10, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28278256/activation-of-g-protein-coupled-estrogen-receptor-1-induces-coronary-artery-relaxation-via-epac-rap1-mediated-inhibition-of-rhoa-rho-kinase-pathway-in-parallel-with-pka
#18
Xuan Yu, Qiao Zhang, Yan Zhao, Benjamin J Schwarz, John N Stallone, Cristine L Heaps, Guichun Han
Previously, we reported that cAMP/PKA signaling is involved in GPER-mediated coronary relaxation by activating MLCP via inhibition of RhoA pathway. In the current study, we tested the hypothesis that activation of GPER induces coronary artery relaxation via inhibition of RhoA/Rho kinase pathway by cAMP downstream targets, exchange proteins directly activated by cAMP (Epac) as well as PKA. Our results show that Epac inhibitors, brefeldin A (BFA, 50 μM), or ESI-09 (20 μM), or CE3F4 (100 μM), all partially inhibited porcine coronary artery relaxation response to the selective GPER agonist, G-1 (0...
2017: PloS One
https://www.readbyqxmd.com/read/28272699/alteration-of-endothelial-nitric-oxide-synthase-expression-in-acute-pulmonary-embolism-a-study-from-bench-to-bioinformatics
#19
R Miao, D Leng, M Liu, X-X Huang, J-F Li, J-N Gong, Y Liang, Z-G Zhai, Y-H Yang, Y Wang, J Wan
OBJECTIVE: This study sought to explore endothelial nitric oxide synthase (eNOS) expression in acute pulmonary thromboembolism (APE). MATERIALS AND METHODS: eNOS expression in lung tissue and bone marrow-derived endothelial progenitor cells (BM-EPCs) from APE mouse models was assessed by immunohistochemistry and real-time PCR. A gene expression profile meta-analysis was performed on human venous thromboembolism (VTE) whole blood samples recorded in the Gene Expression Omnibus (GEO) repository...
February 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28270605/phosphoproteins-in-extracellular-vesicles-as-candidate-markers-for-breast-cancer
#20
I-Hsuan Chen, Liang Xue, Chuan-Chih Hsu, Juan Sebastian Paez Paez, Li Pan, Hillary Andaluz, Michael K Wendt, Anton B Iliuk, Jian-Kang Zhu, W Andy Tao
The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
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