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proteomics pathway ontology

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https://www.readbyqxmd.com/read/28636987/combination-of-calr-and-pdia3-is-a-potential-prognostic-biomarker-for-non-small-cell-lung-cancer
#1
Ke Wang, Hao Li, Ruo Chen, Yang Zhang, Xiu-Xuan Sun, Wan Huang, Huijie Bian, Zhi-Nan Chen
Proteomic-based approaches for biomarker discovery are promising strategies used in cancer research. In this study, we performed quantitative proteomic analysis on 16 paired samples of non-small cell lung cancer (NSCLC) and adjacent non-tumor lung tissues using label-free quantitative proteomics and liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS) to identify differentially expressed proteins. A total of 91 proteins were differentially expressed in NSCLC compared with adjacent non-tumor lung tissues among 4047 identified proteins (fold change > 1...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28634367/proteomic-analysis-reveals-large-amounts-of-decomposition-enzymes-and-major-metabolic-pathways-involved-in-algicidal-process-of-trametes-versicolor-f21a
#2
Xueyan Gao, Congyan Wang, Wei Dai, Shenrong Ren, Fang Tao, Xingbing He, Guomin Han, Wei Wang
A recent algicidal mode indicates that fungal mycelia can wrap and eliminate almost all co-cultivated algal cells within a short time span. However, the underlying molecular mechanism is rarely understood. We applied proteomic analysis to investigate the algicidal process of Trametes versicolor F21a and identified 3,754 fungal proteins. Of these, 30 fungal enzymes with endo- or exoglycosidase activities such as β-1,3-glucanase, α-galactosidase, α-glucosidase, alginate lyase and chondroitin lyase were significantly up-regulated...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28626498/tubulin-beta-3-chain-as-a-new-candidate-protein-biomarker-of-human-skin-aging-a-preliminary-study
#3
Sylvia G Lehmann, Sandrine Bourgoin-Voillard, Michel Seve, Walid Rachidi
Skin aging is a complex process, and a lot of efforts have been made to identify new and specific targets that could help to diagnose, prevent, and treat skin aging. Several studies concerning skin aging have analyzed the changes in gene expression, and very few investigations have been performed at the protein level. Moreover, none of these proteomic studies has used a global quantitative labeled proteomic offgel approach that allows a more accurate description of aging phenotype. We applied such an approach on human primary keratinocytes obtained from sun-nonexposed skin biopsies of young and elderly women...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/28626452/proteomic-differences-between-developmental-stages-of-toxoplasma-gondii-revealed-by-itraq-based-quantitative-proteomics
#4
Ze-Xiang Wang, Chun-Xue Zhou, Hany M Elsheikha, Shuai He, Dong-Hui Zhou, Xing-Quan Zhu
Toxoplasma gondii has a complex two-host life-cycle between intermediate host and definitive host. Understanding proteomic variations across the life-cycle stages of T. gondii may improve the understanding of molecular adaption mechanism of T. gondii across life-cycle stages, and should have implications for the development of new treatment and prevention interventions against T. gondii infection. Here, we utilized LC-MS/MS coupled with iTRAQ labeling technology to identify differentially expressed proteins (DEPs) specific to tachyzoite (T), bradyzoites-containing cyst (C) and sporulated oocyst (O) stages of the cyst-forming T...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28601907/high-glucose-increases-the-formation-and-pro-oxidative-activity-of-endothelial-microparticles
#5
Dylan Burger, Maddison Turner, Fengxia Xiao, Mercedes N Munkonda, Shareef Akbari, Kevin D Burns
AIMS/HYPOTHESIS: Individuals with diabetes exhibit increases in circulating endothelial microparticles (eMPs, also referred to as endothelial microvesicles), which are associated with endothelial dysfunction and a heightened risk of cardiovascular complications. We have shown that eMPs are markers and mediators of vascular injury although their role in diabetes is unclear. We hypothesised that the composition and biological activity of eMPs are altered in response to high glucose exposure...
June 10, 2017: Diabetologia
https://www.readbyqxmd.com/read/28590090/motile-hepatocellular-carcinoma-cells-preferentially-secret-sugar-metabolism-regulatory-proteins-via-exosomes
#6
Jing Zhang, Shaohua Lu, Ye Zhou, Kun Meng, Zhipeng Chen, Yizhi Cui, Yunfeng Shi, Qing-Yu He, Tong Wang
Exosomes are deliverers of critically functional proteins, capable of transforming target cells in numerous cancers, including hepatocellular carcinoma (HCC). We hypothesize that the motility of HCC cells can be featured by comparative proteome of exosomes. Hence, we performed the super-SILAC-based MS analysis on the exosomes secreted by three human HCC cell lines, including the non-motile Hep3B cell, and the motile 97H and LM3 cells. Over 1400 exosomal proteins were confidently quantified in each MS analysis with highly biological reproducibility...
June 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28570707/de-novo-characterization-of-the-pine-aphid-cinara-pinitabulaeformis-zhang-et-zhang-transcriptome-and-analysis-of-genes-relevant-to-pesticides
#7
Songqing Wu, Zhicheng Huang, Carballar-Lejarazú Rebeca, Xiaoli Zhu, Yajie Guo, Qiannan Lin, Xia Hu, Rong Wang, Guanghong Liang, Xiong Guan, Feiping Zhang
The pine aphid Cinara pinitabulaeformis Zhang et Zhang is the main pine pest in China, it causes pine needles to produce dense dew (honeydew) which can lead to sooty mold (black filamentous saprophytic ascomycetes). Although common chemical and physical strategies are used to prevent the disease caused by C. pinitabulaeformis Zhang et Zhang, new strategies based on biological and/or genetic approaches are promising to control and eradicate the disease. However, there is no information about genomics, proteomics or transcriptomics to allow the design of new control strategies for this pine aphid...
2017: PloS One
https://www.readbyqxmd.com/read/28552634/itraq-based-quantitative-proteomic-analysis-reveals-bai-hu-tang-enhances-phagocytosis-and-cross-presentation-against-lps-fever-in-rabbit
#8
Shidong Zhang, Dongsheng Wang, Shuwei Dong, Zhiqiang Yang, Zuoting Yan
ETHNOPHARMACOLOGICAL RELEVANCE: Bai-Hu-Tang (BHT), a classical anti-febrile Chinese formula comprising of liquorice, anemarrhena rhizome, gypsum and rice, has been traditionally used to anti-febrile treatment and promote the production of body fluid to relieve thirst. In this paper, we aim to explore anti-febrile mechanism of BHT at protein level through analyzing alteration of differentially expressed proteins (DEPs) both lipopolysaccharide (LPS) fever syndrome and that was treated with BHT in rabbits...
May 24, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28510335/proteoforms-in-peripheral-blood-mononuclear-cells-as-novel-rejection-biomarkers-in-liver-transplant-recipients
#9
T K Toby, M Abecassis, K Kim, P M Thomas, R T Fellers, R D LeDuc, N L Kelleher, J Demetris, J Levitsky
Biomarker profiles of acute rejection in liver transplant recipients could enhance the diagnosis and management of recipients. Our aim was to identify diagnostic proteoform signatures of acute rejection in circulating immune cells, using an emergent "top down" proteomics methodology. We prepared differentially processed and cryopreserved cell lysates from 26 non-viral liver transplant recipients by molecular weight-based fractionation and analyzed them by mass spectrometry of whole proteins in three steps: 1) Nanocapillary liquid chromatography coupled with high-resolution tandem mass spectrometry; 2) database searching to identify and characterize intact proteoforms; 3) data processing through a hierarchical linear model matching the study design to quantify proteoform fold changes in patients with rejection vs...
May 16, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28472326/novel-insights-into-the-effect-of-nitrogen-on-storage-protein-biosynthesis-and-protein-body-development-in-wheat-caryopsis
#10
Xurun Yu, Xinyu Chen, Leilei Wang, Yang Yang, Xiaowei Zhu, Shanshan Shao, Wenxue Cui, Fei Xiong
Molecular and cytological mechanisms concerning the effects of nitrogen on wheat (Triticum aestivum L.) storage protein biosynthesis and protein body development remain largely elusive. We used transcriptome sequencing, proteomics techniques, and light microscopy to investigate these issues. In total, 2585 differentially expressed genes (DEGs) and 57 differentially expressed proteins (DEPs) were found 7 days after anthesis (DAA), and 2456 DEGs and 64 DEPs were detected 18 DAA after nitrogen treatment. Gene ontology terms related to protein biosynthesis processes enriched these numbers by 678 and 582 DEGs at 7 and 18 DAA, respectively...
April 1, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28450823/proteomic-profiling-of-human-intraschisis-cavity-fluid
#11
Dhandayuthapani Sudha, Mahdokht Kohansal-Nodehi, Purnima Kovuri, Srikanth Srinivas Manda, Srividya Neriyanuri, Lingam Gopal, Pramod Bhende, Subbulakshmi Chidambaram, Jayamuruga Pandian Arunachalam
BACKGROUND: X-linked retinoschisis (XLRS) is a vitreoretinal degenerative disorder causing vision deterioration, due to structural defects in retina. The hallmark of this disease includes radial streaks arising from the fovea and splitting of inner retinal layers (schisis). Although these retinal changes are attributed to mutations in the retinoschisin gene, schisis is also observed in patients who do not carry mutations. In addition, the origin of intraschisis fluid, the triggering point of schisis formation and its progression are largely unknown still...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28431930/quantitative-proteomics-reveals-key-proteins-regulated-by-eicosapentaenoic-acid-in-endothelial-activation
#12
Lu Zhang, Kunhong Xiao, Xuyang Zhao, Xiaoli Sun, Jianshu Zhang, Xian Wang, Yi Zhu, Xu Zhang
Eicosapentaenoic acid (EPA), an n-3 polyunsaturated fatty acid (PUFA), has been shown to decrease the risk of atherosclerosis by attenuating endothelial activation. In this study, we used mass spectrometry-based label-free quantitative proteomics to study the protective mechanisms of EPA and to identify key proteins that regulated by EPA in endothelial activation. Arachidonic acid (AA) was used as a control. HUVECs were pretreated with each of the two PUFAs, and then stimulated with TNFα as a model of endothelial activation...
May 27, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28428745/decreased-levels-of-foldase-and-chaperone-proteins-are-associated-with-an-early-onset-amyotrophic-lateral-sclerosis
#13
Melania Filareti, Silvia Luotti, Laura Pasetto, Mauro Pignataro, Katia Paolella, Paolo Messina, Elisabetta Pupillo, Massimiliano Filosto, Christian Lunetta, Jessica Mandrioli, Giuseppe Fuda, Andrea Calvo, Adriano Chiò, Massimo Corbo, Caterina Bendotti, Ettore Beghi, Valentina Bonetto
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by a progressive upper and lower motor neuron degeneration. One of the peculiar clinical characteristics of ALS is the wide distribution in age of onset, which is probably caused by different combinations of intrinsic and exogenous factors. We investigated whether these modifying factors are converging into common pathogenic pathways leading either to an early or a late disease onset. This would imply the identification of phenotypic biomarkers, that can distinguish the two populations of ALS patients, and of relevant pathways to consider in a therapeutic intervention...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28420359/saikosaponins-induced-hepatotoxicity-in-mice-via-lipid-metabolism-dysregulation-and-oxidative-stress-a-proteomic-study
#14
Xiaoyu Li, Xiaojiaoyang Li, Junxian Lu, Youyi Huang, Lili Lv, Yongfu Luan, Runping Liu, Rong Sun
BACKGROUND: Radix Bupleuri (RB) has been popularly used for treating many liver diseases such as chronic hepatic inflammation and viral Hepatitis in China. Increasing clinical and experimental evidence indicates the potential hepatotoxicity of RB or prescriptions containing RB. Recently, Saikosaponins (SS) have been identified as major bioactive compounds isolated from RB, which may be also responsible for RB-induced liver injury. METHODS: Serum AST, ALT and LDH levels were determined to evaluate SS-induced liver injury in mice...
April 19, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28408942/identification-of-tengfu-jiangya-tablet-target-biomarkers-with-quantitative-proteomic-technique
#15
Jingwen Xu, Yunlun Li, Shijun Zhang, Haiqiang Jiang, Nan Wang, Haiqing Lin
Tengfu Jiangya Tablet (TJT) is a well accepted antihypertension drug in China and its major active components were Uncaria total alkaloids and Semen Raphani soluble alkaloid. To further explore treatment effects mechanism of TJT on essential hypertension, a serum proteomic study was performed. Potential biomarkers were quantified in serum of hypertension individuals before and after taking TJT with isobaric tags for relative and absolute quantitation (iTRAQ) coupled two-dimensional liquid chromatography followed electrospray ionization-tandem mass spectrometry (2D LC-MS/MS) proteomics technique...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28404795/dynamics-of-the-interaction-between-cotton-bollworm-helicoverpa-armigera-and-nucleopolyhedrovirus-as-revealed-by-integrated-transcriptomic-and-proteomic-analyses
#16
Longsheng Xing, Chuanfei Yuan, Manli Wang, Zhe Lin, Benchang Shen, Zhihong Hu, Zhen Zou
Over the past decades, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) has been widely used for biocontrol of cotton bollworm, which is one of the most destructive pest insects in agriculture worldwide. However, the molecular mechanism underlying the interaction between HearNPV and host insects remains poorly understood. In this study, high-throughput RNA-sequencing was integrated with label-free quantitative proteomics analysis to examine the dynamics of gene expression in the fat body of H. armigera larvae in response to challenge with HearNPV...
June 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28350350/differential-proteome-analysis-of-a-flor-yeast-strain-under-biofilm-formation
#17
Jaime Moreno-García, Juan Carlos Mauricio, Juan Moreno, Teresa García-Martínez
Several Saccharomyces cerevisiae strains (flor yeasts) form a biofilm (flor velum) on the surface of Sherry wines after fermentation, when glucose is depleted. This flor velum is fundamental to biological aging of these particular wines. In this study, we identify abundant proteins in the formation of the biofilm of an industrial flor yeast strain. A database search to enrich flor yeast "biological process" and "cellular component" according to Gene Ontology Terminology (GO Terms) and, "pathways" was carried out...
March 28, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28345649/proteomic-analysis-indicates-that-mitochondrial-energy-metabolism-in-skeletal-muscle-tissue-is-negatively-correlated-with-feed-efficiency-in-pigs
#18
Liangliang Fu, Yueyuan Xu, Ye Hou, Xiaolong Qi, Lian Zhou, Huiying Liu, Yu Luan, Lu Jing, Yuanxin Miao, Shuhong Zhao, Huazhen Liu, Xinyun Li
Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345336/proteomic-identification-of-eef1a1-as-a-molecular-target-of-curcumol-for-suppressing-metastasis-of-mda-mb-231-cells
#19
Hongyi Qi, Ling Ning, Zanyang Yu, Guojun Dou, Li Li
Curcumol, a major volatile component in Rhizoma Curcumae, exhibited potent anti-metastatic effect on breast cancer cells. However, its molecular mechanism remains poorly understood. In this study, we employed a 2-DE based proteomics to investigate the cellular targets of curcumol in MDA-MB-231 cells, and identified 10 differentially expressed proteins. Moreover, Gene Ontology analysis revealed that those proteins mainly get involved in 9 types of cellular components, 7 different biological processes and 9 kinds of molecular functions, and 35 pathways (p < 0...
March 27, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28344024/putative-model-based-on-itraq-proteomics-for-spirulina-morphogenesis-mechanisms
#20
Fu-Shuang Wang, Shi-Rui Dong, Hong-Yu Zhang, Su-Ying Wang
The morphology of Spirulina during cultivation is susceptible to external interferences, but the morphogenesis mechanism is still unclear. Here the proteomic changes of linear Spirulina and spiral Spirulina were comparatively investigated via isobaric tag for relative and absolute quantitation (iTRAQ). Totally 165 and 167 differences in proteins expression were screened out from the TJSD2/TJSD3 and TJBC4-1/TJBC4-2 groups, respectively. Gene ontology and metabolic pathway analysis of differences in proteins expression uncovered the metabolic pathways (photosynthesis, carbon fixation, sugar metabolism) that were significantly enriched with the proteins correlated with Spirulina morphogenesis...
March 23, 2017: Journal of Proteomics
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