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proteomics pathway analysis

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https://www.readbyqxmd.com/read/28109940/proteome-response-of-fish-under-multiple-stress-exposure-effects-of-pesticide-mixtures-and-temperature-increase
#1
Allison Gandar, Pascal Laffaille, Nathalie Marty-Gasset, Didier Viala, Caroline Molette, Séverine Jean
Aquatic systems can be subjected to multiple stressors, including pollutant cocktails and elevated temperature. Evaluating the combined effects of these stressors on organisms is a great challenge in environmental sciences. To the best of our knowledge, this is the first study to assess the molecular stress response of an aquatic fish species subjected to individual and combined pesticide mixtures and increased temperatures. For that, goldfish (Carassius auratus) were acclimated to two different temperatures (22 and 32°C) for 15 days...
January 15, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28109433/biotin-switch-assays-for-quantitation-of-reversible-cysteine-oxidation
#2
R Li, J Kast
Thiol groups in protein cysteine residues can be subjected to different oxidative modifications by reactive oxygen/nitrogen species. Reversible cysteine oxidation, including S-nitrosylation, S-sulfenylation, S-glutathionylation, and disulfide formation, modulate multiple biological functions, such as enzyme catalysis, antioxidant, and other signaling pathways. However, the biological relevance of reversible cysteine oxidation is typically underestimated, in part due to the low abundance and high reactivity of some of these modifications, and the lack of methods to enrich and quantify them...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28105855/analysis-of-a549-cell-proteome-alteration-in-response-to-recombinant-influenza-a-virus-nucleoprotein-and-its-interaction-with-cellular-proteins-a-preliminary-study
#3
D Kumar, K Tiwari, M S Rajala
 Influenza A virus undergoes frequent changes of antigenicity and contributes to seasonal epidemics or unpredictable pandemics. Nucleoprotein, encoded by gene segment 5, is an internal protein of the virus and is conserved among strains of different host origins. In the current study, we analyzed the differentially expressed proteins in A549 cells transiently transfected with the recombinant nucleoprotein of influenza A virus by 2D gel electrophoresis. The resolved protein spots on gel were identified by MALDI-TOF/Mass spectrometry analysis...
January 19, 2017: Acta Virologica
https://www.readbyqxmd.com/read/28104608/prothrombin-loading-of-vascular-smooth-muscle-cell-derived-exosomes-regulates-coagulation-and-calcification
#4
Alexander N Kapustin, Michael Schoppet, Leon J Schurgers, Joanne L Reynolds, Rosamund McNair, Alexander Heiss, Willi Jahnen-Dechent, Tilman M Hackeng, Georg Schlieper, Paul Harrison, Catherine M Shanahan
OBJECTIVE: The drug warfarin blocks carboxylation of vitamin K-dependent proteins and acts as an anticoagulant and an accelerant of vascular calcification. The calcification inhibitor MGP (matrix Gla [carboxyglutamic acid] protein), produced by vascular smooth muscle cells (VSMCs), is a key target of warfarin action in promoting calcification; however, it remains unclear whether proteins in the coagulation cascade also play a role in calcification. APPROACH AND RESULTS: Vascular calcification is initiated by exosomes, and proteomic analysis revealed that VSMC exosomes are loaded with Gla-containing coagulation factors: IX and X, PT (prothrombin), and proteins C and S...
January 19, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28104435/inhibition-of-nrf2-enhances-the-anticancer-effect-of-6-o-angeloylenolin-in-lung-adenocarcinoma
#5
Yang Wang, Ru-Yuan Yu, Jing Zhang, Wei-Xia Zhang, Zhi-Hao Huang, Hui-Fang Hu, Yao-Lan Li, Bin Li, Qing-Yu He
6-O-Angeloylenolin (6-OA), a sesquiterpene lactone isolated from Centipeda minima (L.) A. Br. (Compositae), has been used to treat respiratory diseases for centuries. However, whether and how 6-OA exerts anticancer effects against lung cancer remains to be elucidated. In this study, we showed that 6-OA markedly suppressed the cell viability and colony formation of lung cancer cells H1299 and A549, with no significant toxic effect on non-cancer cells HBE. Annexin V/7-AAD assay revealed that 6-OA induced cell apoptosis in dose- and time-dependent manners, which was further confirmed by the increased expression of cleaved caspase-3...
January 16, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28104103/comparative-proteomic-analysis-of-bleomycin-induced-pulmonary-fibrosis-based-on-isobaric-tag-for-quantitation
#6
Tiejun Yang, Yanlong Jia, Yongkang Ma, Liang Cao, Xiaobing Chen, Baoping Qiao
BACKGROUND: Pulmonary fibrosis (PF) is a destructive pulmonary disease and the molecular mechanisms underlying PF are unclear. This study investigated differentially expressed proteins associated with the occurrence and development of PF in rat lung tissue with bleomycin-induced PF. METHODS: Sixteen Sprague-Dawley rats were randomly divided into 2 groups: the PF model group (n = 8) and the control group (n = 8). After successfully establishing the rat PF model induced by bleomycin, the differentially expressed proteins in the 2 groups were identified through isobaric tag for relative and absolute quantitation coupled with liquid chromatography-mass spectrometry and bioinformatics analysis...
January 2017: American Journal of the Medical Sciences
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
#7
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/28100206/hypoglycemic-effects-of-trichosanthes-kirilowii-and-its-protein-constituent-in-diabetic-mice-the-involvement-of-insulin-receptor-pathway
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28097087/identification-of-the-vascular-endothelial-growth-factor-signalling-pathway-by-quantitative-proteomic-analysis-of-rat-condylar-cartilage
#11
Liting Jiang, Yinyin Xie, Li Wei, Qi Zhou, Xing Shen, Xinquan Jiang, Yiming Gao
Angiogenesis mediated by vascular endothelial growth factor (VEGF) is known to play an important role in regulating cartilage remodelling and endochondral ossification. However, the details of how VEGF signalling mechanisms affect condyle remodelling in response to alterations in functional loading remains unclear. To explore this, eighty 16-day-old male SD rats were divided into two equal groups which were fed either a soft/powdery diet or a hard diet for 4 weeks; the stiffness of the diet results in alteration of mastication force and hence temporomandibular joint (TMJ) development...
January 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28094349/proteomic-and-carbonylation-profile-analysis-at-the-critical-node-of-seed-ageing-in-oryza-sativa
#12
Guangkun Yin, Xia Xin, Shenzao Fu, Mengni An, Shuhua Wu, Xiaoling Chen, Jinmei Zhang, Juanjuan He, James Whelan, Xinxiong Lu
The critical node (CN), which is the transition from the plateau phase to the rapid decreasing phase of seed ageing, is extremely important for seed conservation. Although numerous studies have investigated the oxidative stress during seed ageing, information on the changes in protein abundance at the CN is limited. In this study, we aimed to investigate the abundance and carbonylation patterns of proteins at the CN of seed ageing in rice. The results showed that the germination rate of seeds decreased by less than 20% at the CN; however, the abundance of 112 proteins and the carbonylation levels of 68 proteins markedly changed, indicating oxidative damage...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093102/proteomic-changes-in-the-ileum-of-sheep-infected-with-mycobacterium-avium-subspecies-paratuberculosis
#13
S Pisanu, T Cubeddu, S Uzzau, S Rocca, M F Addis
Johne's disease (JD) is a chronic enteritis of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). To identify the processes activated in the sheep intestine during natural MAP infection, and to provide a panel of differential host and pathogen proteins with diagnostic and prognostic potential, a differential shotgun proteomics workflow, including mass spectrometry, label-free quantisation and pathway analysis, was applied to ileal tissues of ewes with and without JD. Out of 2889 total proteins identified, 384 were differentially expressed and 341 were expressed at a higher level in JD...
January 2017: Veterinary Journal
https://www.readbyqxmd.com/read/28089782/hepatic-co-cultures-in-vitro-reveal-suitable-to-detect-nrf2-mediated-oxidative-stress-responses-on-the-bladder-carcinogen-o-anisidine
#14
Franziska Wewering, Florent Jouy, Sükran Caliskan, Stefan Kalkhof, Martin von Bergen, Andreas Luch, Sebastian Zellmer
The azo dye o-anisidine is known as an industrial and environmental pollutant. Metabolites of o-anisidine remain in the liver for >24h. However, the toxicological impact of o-anisidine on the liver and its individual cell types, e.g., hepatocytes and immune cells, is currently poorly understood. A novel co-culture system, composed of HepG2 or Huh-7 cells, and differentiated THP-1 cells was used to study the metabolic capacity towards o-anisidine, and compared to primary murine hepatocytes which express high enzyme activities...
January 12, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28087761/proteomics-technologies-and-their-applications
#15
REVIEW
Bilal Aslam, Madiha Basit, Muhammad Atif Nisar, Mohsin Khurshid, Muhammad Hidayat Rasool
Proteomics involves the applications of technologies for the identification and quantification of overall proteins present content of a cell, tissue or an organism. It supplements the other "omics" technologies such as genomic and transcriptomics to expound the identity of proteins of an organism, and to cognize the structure and functions of a particular protein. Proteomics-based technologies are utilized in various capacities for different research settings such as detection of various diagnostic markers, candidates for vaccine production, understanding pathogenicity mechanisms, alteration of expression patterns in response to different signals and interpretation of functional protein pathways in different diseases...
February 2017: Journal of Chromatographic Science
https://www.readbyqxmd.com/read/28081246/nitrosothiol-trapping-based-proteomic-analysis-of-s-nitrosylation-in-human-lung-carcinoma-cells
#16
Shani Ben-Lulu, Tamar Ziv, Pnina Weisman-Shomer, Moran Benhar
Nitrosylation of cysteines residues (S-nitrosylation) mediates many of the cellular effects of nitric oxide in normal and diseased cells. Recent research indicates that S-nitrosylation of certain proteins could play a role in tumor progression and responsiveness to therapy. However, the protein targets of S-nitrosylation in cancer cells remain largely unidentified. In this study, we used our recently developed nitrosothiol trapping approach to explore the nitrosoproteome of human A549 lung carcinoma cells treated with S-nitrosocysteine or pro-inflammatory cytokines...
2017: PloS One
https://www.readbyqxmd.com/read/28081159/osmoregulation-in-the-halophilic-bacterium-halomonas-elongata-a-case-study-for-integrative-systems-biology
#17
Viktoria Kindzierski, Silvia Raschke, Nicole Knabe, Frank Siedler, Beatrix Scheffer, Katharina Pflüger-Grau, Friedhelm Pfeiffer, Dieter Oesterhelt, Alberto Marin-Sanguino, Hans-Jörg Kunte
Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem...
2017: PloS One
https://www.readbyqxmd.com/read/28079188/proteome-response-of-chicken-embryo-fibroblast-cells-to-recombinant-h5n1-avian-influenza-viruses-with-different-neuraminidase-stalk-lengths
#18
Yongtao Li, Fan Ming, Huimin Huang, Kelei Guo, Huanchun Chen, Meilin Jin, Hongbo Zhou
The variation on neuraminidase (NA) stalk region of highly pathogenic avian influenza H5N1 virus results in virulence change in animals. In our previous studies, the special NA stalk-motif of H5N1 viruses has been demonstrated to play a significant role in the high virulence and pathogenicity in chickens. However, the molecular mechanisms underlying the pathogenicity of viruses with different NA stalk remain poorly understood. This study presents a comprehensive characterization of the proteome response of chicken cells to recombinant H5N1 virus with stalk-short NA (rNA-wt) and the stalkless NA mutant virus (rSD20)...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28079125/establishment-of-a-integrative-multi-omics-expression-database-ckddb-in-the-context-of-chronic-kidney-disease-ckd
#19
Marco Fernandes, Holger Husi
Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078386/early-differences-in-islets-from-prediabetic-nod-mice-combined-microarray-and-proteomic-analysis
#20
Inne Crèvecoeur, Valborg Gudmundsdottir, Saurabh Vig, Fernanda Marques Câmara Sodré, Wannes D'Hertog, Ana Carolina Fierro, Leentje Van Lommel, Conny Gysemans, Kathleen Marchal, Etienne Waelkens, Frans Schuit, Søren Brunak, Lut Overbergh, Chantal Mathieu
AIMS/HYPOTHESIS: Type 1 diabetes is an endocrine disease where a long preclinical phase, characterised by immune cell infiltration in the islets of Langerhans, precedes elevated blood glucose levels and disease onset. Although several studies have investigated the role of the immune system in this process of insulitis, the importance of the beta cells themselves in the initiation of type 1 diabetes is less well understood. The aim of this study was to investigate intrinsic differences present in the islets from diabetes-prone NOD mice before the onset of insulitis...
January 12, 2017: Diabetologia
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