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proteomics pathway analysis

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https://www.readbyqxmd.com/read/28329269/proteomics-highlights-decrease-of-matricellular-proteins-in-left-ventricular-assist-device-therapy%C3%A2
#1
Jasmin Hasmik Shahinian, Bettina Mayer, Stefan Tholen, Kerstin Brehm, Martin L Biniossek, Hannah Füllgraf, Selina Kiefer, Ulrike Heizmann, Claudia Heilmann, Florian Rüter, Martin Grapow, Oliver Thomas Reuthebuch, Friedrich Eckstein, Friedhelm Beyersdorf, Oliver Schilling, Matthias Siepe
OBJECTIVES: We investigated the impact of mechanical unloading with a left ventricular assist device (LVAD) on the myocardial proteome. METHODS: We collected 11 patient-matched samples of myocardial left ventricular tissue of patients with non-ischaemic dilate cardiomyopathy, harvested at time of LVAD implant ('pre-LVAD') and heart transplant ('post-LVAD'). Samples were studied by quantitative proteomics. Further we performed histological assessment of deposited collagens and immune infiltration in both pre- and post-LVAD samples...
February 20, 2017: European Journal of Cardio-thoracic Surgery
https://www.readbyqxmd.com/read/28329008/insulin-and-diet-induced-changes-in-the-ubiquitin-modified-proteome-of-rat-liver
#2
Shilpa R Nagarajan, Amanda E Brandon, Jessie A McKenna, Harrison C Shtein, Thinh Q Nguyen, Eurwin Suryana, Philip Poronnik, Gregory J Cooney, Darren N Saunders, Andrew J Hoy
Ubiquitin is a crucial post-translational modification regulating numerous cellular processes, but its role in metabolic disease is not well characterized. In this study, we identified the in vivo ubiquitin-modified proteome in rat liver and determined changes in this ubiquitome under acute insulin stimulation and high-fat and sucrose diet-induced insulin resistance. We identified 1267 ubiquitinated proteins in rat liver across diet and insulin-stimulated conditions, with 882 proteins common to all conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28328971/mapping-the-n-linked-glycosites-of-rice-oryza-sativa-l-germinating-embryos
#3
Jiezheng Ying, Juan Zhao, Yuxuan Hou, Yifeng Wang, Jiehua Qiu, Zhiyong Li, Xiaohong Tong, Zhaomei Shi, Jun Zhu, Jian Zhang
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered...
2017: PloS One
https://www.readbyqxmd.com/read/28327085/a-shift-in-the-virulence-potential-of-corynebacterium-pseudotuberculosis-biovar-ovis-after-passage-in-a-murine-host-demonstrated-through-comparative-proteomics
#4
Wanderson M Silva, Fernanda A Dorella, Siomar C Soares, Gustavo H M F Souza, Thiago L P Castro, Núbia Seyffert, Henrique Figueiredo, Anderson Miyoshi, Yves Le Loir, Artur Silva, Vasco Azevedo
BACKGROUND: Corynebacterium pseudotuberculosis biovar ovis, a facultative intracellular pathogen, is the etiologic agent of caseous lymphadenitis in small ruminants. During the infection process, C. pseudotuberculosis changes its gene expression to resist different types of stresses and to evade the immune system of the host. However, factors contributing to the infectious process of this pathogen are still poorly documented. To better understand the C. pseudotuberculosis infection process and to identify potential factors which could be involved in its virulence, experimental infection was carried out in a murine model using the strain 1002_ovis and followed by a comparative proteomic analysis of the strain before and after passage...
March 22, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28326073/rhoptry-protein-5-rop5-is-a-key-virulence-factor-in-neospora-caninum
#5
Lei Ma, Jing Liu, Muzi Li, Yong Fu, Xiao Zhang, Qun Liu
Neospora caninum, of the Apicomplexa phylum, is a common cause of abortions in cattle and nervous system dysfunction in dogs. Rhoptry proteins of Apicomplexa play an important role in virulence. The objectives of this study were to study functions of NcROP5 in N. caninum by deleting the NcROP5 gene from the wild Nc-1 strain. We selected NcROP5 in ToxoDB and successfully constructed an NcROP5 gene-deleted vector, pTCR-NcROP5-CD KO. Then we screened the NcROP5 knockout strains (ΔNcROP5) at the gene, protein and transcription levels...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28323244/itraq-based-differential-proteomic-analysis-in-mongolian-gerbil-brains-chronically-infected-with-toxoplasma-gondii
#6
Lin Lv, Yapei Wang, Weili Feng, Jorge A Hernandez, Wanyi Huang, Yuxiang Zheng, Xue Zhou, Shumei Lv, Yajun Chen, Zi-Guo Yuan
The aim of our study was to detect differentially regulated proteins and specific signaling pathways in Mongolian gerbil brains during chronic Toxoplasma gondii (T.gondii) PRU strain infection. We use a iTRAQ-based strategy to detecte 4935 proteins, out of which 110 proteins were differentially expressed (>/=2.0-fold, p value <0.05) when the brain of gerbils infected with T.gondii was compared to control brain tissues. We confirmed the authenticity and the accuracy of iTRAQ results through quantitative real-time PCR and western blot (WB), which was consistent with mass spectrometry analysis...
March 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28322828/metabolic-characterization-of-human-aqueous-humor-in-relation-to-high-myopia
#7
Yinghong Ji, Jun Rao, Xianfang Rong, Shang Lou, Zhi Zheng, Yi Lu
High myopia is the common eye disorder worldwide, which may contribute to increase the risk of serious disorders including glaucoma and cataract. Although various studies including genomics, transcriptomics, and proteomics have been implicated to identify potential biomarkers (genes or proteins) for predicting high myopia and to reveal the underlying mechanisms, the comprehensive metabolomics in relation to high myopia is very limited. In this study, we identified 242 metabolites in aqueous humor (AH) from a set of 40 patients (including 20 with high myopia and 20 for controls), using a non-targeted metabolomic technology, gas chromatography coupled to time-of-flight mass spectrometer (GC/TOF MS)...
March 17, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28322315/quantitative-proteomic-analysis-on-activated-hepatic-stellate-cells-reversion-reveal-stat1-as-a-key-regulator-between-liver-fibrosis-and-recovery
#8
Hongyu Zhang, Fangyan Chen, Xu Fan, Cong Lin, Yunwei Hao, Handong Wei, Weiran Lin, Ying Jiang, Fuchu He
Understanding the changes of activated HSCs reversion is an essential step toward clarifying the potential roles of HSCs in the treatment of liver fibrosis. In this study, we chose adipocyte differentiation mixture to induce LX-2 cells for 2 days in vitro as reversion phase, comparing with normal cultured LX-2 cells as activation phase. Mass spectrometric-based SILAC technology was adopted to study differentially expressed proteome of LX-2 cells between reversion and activation. Compared with activated HSCs, 273 proteins showed significant differences in reverted HSCs...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28314371/intrauterine-growth-restriction-programs-the-hypothalamus-of-adult-male-rats-integrated-analysis-of-proteomic-and-metabolomic-data
#9
Amanda Paula Pedroso, Adriana Pereira de Souza, Ana Paula Segantine Dornellas, Lila Missae Oyama, Cláudia Maria Oller Nascimento, Gianni Mara Silva Santos, José C Rosa, Ricardo Pimenta Bertolla, Jelena Klawitter, Uwe Christians, Alexandre Keiji Tashima, Eliane Beraldi Ribeiro
Programming of hypothalamic functions regulating energy homeostasis may play a role in intrauterine growth restriction (IUGR)-induced adulthood obesity. The present study investigated the effects of IUGR on the hypothalamus proteome and metabolome of adult rats submitted to 50% protein-energy restriction throughout pregnancy. Proteomic and metabolomic analyzes were performed by data independent acquisition mass spectrometry and multiple reaction monitoring, respectively. At age 4 months, the restricted rats showed elevated adiposity, increased leptin and signs of insulin resistance...
March 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28306714/reconstruction-and-signal-propagation-analysis-of-the-syk-signaling-network-in-breast-cancer-cells
#10
Aurélien Naldi, Romain M Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J Coopman, Ovidiu Radulescu
The ability to build in-depth cell signaling networks from vast experimental data is a key objective of computational biology. The spleen tyrosine kinase (Syk) protein, a well-characterized key player in immune cell signaling, was surprisingly first shown by our group to exhibit an onco-suppressive function in mammary epithelial cells and corroborated by many other studies, but the molecular mechanisms of this function remain largely unsolved. Based on existing proteomic data, we report here the generation of an interaction-based network of signaling pathways controlled by Syk in breast cancer cells...
March 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28304376/an-integrated-analysis-based-on-transcriptome-and-proteome-reveals-deastringency-related-genes-in-cpcna-persimmon
#11
Wenxing Chen, Yalou Xiong, Liqing Xu, Qinglin Zhang, Zhengrong Luo
Persimmon fruits accumulate a large amount of proanthocyanidins (PAs) during development. PAs cause a dry or puckering sensation due to its astringency. Pollination constant and non-astringent (PCNA) persimmon fruits can lose astringency during fruit ripening. However, little is known about the mechanism of natural de-astringency of Chinese PCNA (CPCNA). To gain insight into the molecular events of CPCNA natural de-astringency, we used mRNA-seq and iTRAQ-based quantitative proteomic analysis to measure changes in genes and proteins expression at two key stages of natural astringency removal (i...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28304171/proteome-analysis-using-itraq-reveals-the-alterations-in-stress-induced-dysfunctional-chicken-muscle
#12
Tong Xing, Chong Wang, Xue Zhao, Chen Dai, Guanghong Zhou, Xinglian Xu
The current study was designed to investigate the changes in the protein profiles of pale, soft and exudative (PSE)-like muscles of broilers subjected to transportation under high temperature conditions, using isobaric tags for relative and absolute analysis quantitation (iTRAQ). Arbor Acres chickens (n = 112) were randomly divided to two treatments: unstressed control (CON) and 0.5 h of transport (T). Birds were transported based on a designed protocol. Pectoralis major (PM) muscle samples in the T group were collected and classified as normal (T-NOR) or PSE-like (T-PSE)...
March 17, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28303955/differential-proteomic-analysis-by-itraq-reveals-the-mechanism-of-pyropia-haitanensis-responding-to-high-temperature-stress
#13
Jianzhi Shi, Yuting Chen, Yan Xu, Dehua Ji, Changsheng Chen, Chaotian Xie
Global warming increases sea temperature and leads to high temperature stress, which affects the yield and quality of Pyropia haitanensis. To understand the molecular mechanisms underlying high temperature stress in a high temperature tolerance strain Z-61, the iTRAQ technique was employed to reveal the global proteomic response of Z-61 under different durations of high temperature stress. We identified 151 differentially expressed proteins and classified them into 11 functional categories. The 4 major categories of these are protein synthesis and degradation, photosynthesis, defense response, and energy and carbohydrate metabolism...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28300637/integrated-mass-spectrometry-imaging-and-omics-workflows-on-the-same-tissue-section-using-grid-aided-parafilm-assisted-microdissection
#14
Jusal Quanico, Julien Franck, Maxence Wisztorski, Michel Salzet, Isabelle Fournier
BACKGROUND: In spite of the number of applications describing the use of MALDI MSI, one of its major drawbacks is the limited capability of identifying multiple compound classes directly on the same tissue section. METHODS: We demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting acid dye 25 using a piezoelectric microspotter, and this grid was used as a guide to locate regions of interest and as an aid during manual microdissection...
March 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28298630/proteomic-analysis-of-proteome-and-histone-post-translational-modifications-in-heat-shock-protein-90-inhibition-mediated-bladder-cancer-therapeutics
#15
Qingdi Quentin Li, Jian-Jiang Hao, Zheng Zhang, L Spencer Krane, Kai H Hammerich, Thomas Sanford, Jane B Trepel, Len Neckers, Piyush K Agarwal
Heat shock protein 90 (HSP90) inhibition is an attractive strategy for cancer treatment. Several HSP90 inhibitors have shown promising effects in clinical oncology trials. However, little is known about HSP90 inhibition-mediated bladder cancer therapy. Here, we report a quantitative proteomic study that evaluates alterations in protein expression and histone post-translational modifications (PTMs) in bladder carcinoma in response to HSP90 inhibition. We show that 5 HSP90 inhibitors (AUY922, ganetespib, SNX2112, AT13387, and CUDC305) potently inhibited the proliferation of bladder cancer 5637 cells in a dose- and time-dependent manner...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28298564/proteomic-analysis-of-sera-from-individuals-with-diffuse-cutaneous-systemic-sclerosis-reveals-a-multianalyte-signature-associated-with-clinical-improvement-during-imatinib-mesylate-treatment
#16
D James Haddon, Hannah E Wand, Justin A Jarrell, Robert F Spiera, Paul J Utz, Jessica K Gordon, Lorinda S Chung
OBJECTIVE: Imatinib has been investigated for the treatment of systemic sclerosis (SSc) because of its ability to inhibit the platelet-derived growth factor receptor and transforming growth factor-β signaling pathways, which have been implicated in SSc pathogenesis. In a 12-month open-label clinical trial assessing the safety and efficacy of imatinib in the treatment of diffuse cutaneous SSc (dcSSc), significant improvements in skin thickening were observed. Here, we report our analysis of sera collected during the clinical trial...
March 15, 2017: Journal of Rheumatology
https://www.readbyqxmd.com/read/28298427/systematic-protein-protein-interaction-mapping-for-clinically-relevant-human-gpcrs
#17
Kate Sokolina, Saranya Kittanakom, Jamie Snider, Max Kotlyar, Pascal Maurice, Jorge Gandía, Abla Benleulmi-Chaachoua, Kenjiro Tadagaki, Atsuro Oishi, Victoria Wong, Ramy H Malty, Viktor Deineko, Hiroyuki Aoki, Shahreen Amin, Zhong Yao, Xavier Morató, David Otasek, Hiroyuki Kobayashi, Javier Menendez, Daniel Auerbach, Stephane Angers, Natasa Pržulj, Michel Bouvier, Mohan Babu, Francisco Ciruela, Ralf Jockers, Igor Jurisica, Igor Stagljar
G-protein-coupled receptors (GPCRs) are the largest family of integral membrane receptors with key roles in regulating signaling pathways targeted by therapeutics, but are difficult to study using existing proteomics technologies due to their complex biochemical features. To obtain a global view of GPCR-mediated signaling and to identify novel components of their pathways, we used a modified membrane yeast two-hybrid (MYTH) approach and identified interacting partners for 48 selected full-length human ligand-unoccupied GPCRs in their native membrane environment...
March 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28296247/comprehensive-proteome-analysis-of-human-skeletal-muscle-in-cachexia-and-sarcopenia-a-pilot-study
#18
H Alexander Ebhardt, Simone Degen, Valentina Tadini, Alain Schilb, Neil Johns, Carolyn A Greig, Kenneth C H Fearon, Ruedi Aebersold, Carsten Jacobi
BACKGROUND: Cancer cachexia (cancer-induced muscle wasting) is found in a subgroup of cancer patients leaving the patients with a poor prognosis for survival due to a lower tolerance of the chemotherapeutic drug. The cause of the muscle wasting in these patients is not fully understood, and no predictive biomarker exists to identify these patients early on. Skeletal muscle loss is an inevitable consequence of advancing age. As cancer frequently occurs in old age, identifying and differentiating the molecular mechanisms mediating muscle wasting in cancer cachexia vs...
March 15, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28295929/bex4-upregulation-alters-sertoli-cell-growth-properties-and-protein-expression-profiles-an-explanation-for-cadmium-induced-testicular-sertoli-cell-injury
#19
Wu Yu, Liu Yaping, Wu Mingjun, Hao Jie, Liao Xiaogang, Li Gang
Increasing evidence has demonstrated that cadmium (Cd) may induce testicular dysfunction by targeting genes that are expressed in the testis. Here, we demonstrated that BEX4 is expressed in testis Sertoli cells, and its expression was significantly upregulated by CdCl2 treatment through activating the p38 signaling pathway. To investigate whether augmented BEX4 expression affects Sertoli cell growth and function, BEX4-overexpressing TM4 Sertoli cells were established. Proteomics analysis identified 85 differentially expressed proteins in BEX4-overexpressing cells...
March 15, 2017: Journal of Biochemical and Molecular Toxicology
https://www.readbyqxmd.com/read/28293639/proteomic-analysis-of-liver-proteins-in-a-rat-model-of-chronic-restraint-stress-induced-depression
#20
Cong Li, Zhengguang Guo, Ronghua Zhao, Wei Sun, Ming Xie
Depression is a global mental disorder disease and greatly threatened human health and stress is considered to be one of the important factors that lead to depression. In this study, we used newly developed iTRAQ labeling and high performance liquid chromatography (HPLC) and mass spectrum united analysis technology obtained the 2176 accurate proteins. Successively, we used the GO analysis and IPA software to analyze the 98 differentially expressed proteins of liver in depression rats due to chronic restraint stress, showing a map of proteomics analysis of liver proteins from the aspects of related functions, disease and function analysis, canonical pathway analysis, and associated network...
2017: BioMed Research International
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