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proteomics pathway ontology

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https://www.readbyqxmd.com/read/28510335/proteoforms-in-peripheral-blood-mononuclear-cells-as-novel-rejection-biomarkers-in-liver-transplant-recipients
#1
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
#2
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...
May 4, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28450823/proteomic-profiling-of-human-intraschisis-cavity-fluid
#3
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
#4
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...
April 18, 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
#5
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
#6
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
#7
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
#8
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...
April 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28350350/differential-proteome-analysis-of-a-flor-yeast-strain-under-biofilm-formation
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28343001/comprehensive-functional-analysis-of-large-lists-of-genes-and-proteins
#13
Bernhard Mlecnik, Jérôme Galon, Gabriela Bindea
The interpretation of high dimensional datasets resulting from genomic and proteomic experiments in a timely and efficient manner is challenging. ClueGO software is a Cytoscape App that extracts representative functional biological information for large lists of genes or proteins. The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO. Predefined settings for the selection of the terms are provided to facilitate the analysis...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28339073/identification-of-proteins-in-the-aqueous-humor-associated-with-cataract-development-using-itraq-methodology
#14
Minhong Xiang, Xingru Zhang, Qingsong Li, Hanmin Wang, Zhenyong Zhang, Zhumei Han, Meiqing Ke, Xingxing Chen
Proteins in the aqueous humor (AH) are important in the induction of cataract development. The identification of cataract-associated proteins assists in identifying patients and predisposed to the condition and improve treatment efficacy. Proteomics analysis has previously been used for identifying protein markers associated with eye diseases; however, few studies have examined the proteomic alterations in cataract development due to high myopia, glaucoma and diabetes. The present study, using the isobaric tagging for relative and absolute protein quantification methodology, aimed to examine cataract-associated proteins in the AH from patients with high myopia, glaucoma or diabetes, and controls...
May 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28333993/integrated-transcriptomic-and-proteomic-analysis-of-the-molecular-cargo-of-extracellular-vesicles-derived-from-porcine-adipose-tissue-derived-mesenchymal-stem-cells
#15
Alfonso Eirin, Xiang-Yang Zhu, Amrutesh S Puranik, John R Woollard, Hui Tang, Surendra Dasari, Amir Lerman, Andre J van Wijnen, Lilach O Lerman
BACKGROUND: Mesenchymal stromal/stem cell (MSC) transplantation is a promising therapy for tissue regeneration. Extracellular vesicles (EVs) released by MSCs act as their paracrine effectors by delivering proteins and genetic material to recipient cells. To assess how their cargo mediates biological processes that drive their therapeutic effects, we integrated miRNA, mRNA, and protein expression data of EVs from porcine adipose tissue-derived MSCs. METHODS: Simultaneous expression profiles of miRNAs, mRNAs, and proteins were obtained by high-throughput sequencing and LC-MS/MS proteomic analysis in porcine MSCs and their daughter EVs (n = 3 each)...
2017: PloS One
https://www.readbyqxmd.com/read/28323244/itraq-based-differential-proteomic-analysis-in-mongolian-gerbil-brains-chronically-infected-with-toxoplasma-gondii
#16
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 18, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28290293/comparative-proteomic-analysis-of-milk-derived-exosomes-in-human-and-bovine-colostrum-and-mature-milk-samples-by-itraq-coupled-lc-ms-ms
#17
Mei Yang, Dahe Song, Xueyan Cao, Rina Wu, Biao Liu, Wenhui Ye, Junrui Wu, Xiqing Yue
Exosomes are membranous vesicles found in biological fluids with important functions. However, milk-derived exosome proteins from humans and bovines have not been studied in detail. The advanced iTRAQ proteomic approach was used to analyze milk-derived exosomes in human and bovine colostrum and mature milk samples. A total of 920 milk exosome proteins were identified and quantified. Among these, 575 differentially expressed exosome proteins (P<0.05) were found. Multivariate analysis, gene ontology (GO) annotation and the KEGG pathway were used to interpret the identified proteins...
February 2017: Food Research International
https://www.readbyqxmd.com/read/28276902/comparative-proteomic-exploration-of-whey-proteins-in-human-and-bovine-colostrum-and-mature-milk-using-itraq-coupled-lc-ms-ms
#18
Mei Yang, Xueyan Cao, Rina Wu, Biao Liu, Wenhui Ye, Xiqing Yue, Junrui Wu
Whey, an essential source of dietary nutrients, is widely used in dairy foods for infants. A total of 584 whey proteins in human and bovine colostrum and mature milk were identified and quantified by the isobaric tag for relative and absolute quantification (iTRAQ) proteomic method. The 424 differentially expressed whey proteins were identified and analyzed according to gene ontology (GO) annotation, Kyoto encyclopedia of genes and genomes (KEGG) pathway, and multivariate statistical analysis. Biological processes principally involved biological regulation and response to stimulus...
February 20, 2017: International Journal of Food Sciences and Nutrition
https://www.readbyqxmd.com/read/28256566/aberrant-epicardial-adipose-tissue-extracellular-matrix-remodeling-in-patients-with-severe-ischemic-cardiomyopathy-insight-from-comparative-quantitative-proteomics
#19
Ding-Sheng Jiang, Hao-Long Zeng, Rui Li, Bo Huo, Yun-Shu Su, Jing Fang, Qing Yang, Li-Gang Liu, Min Hu, Cai Cheng, Xue-Hai Zhu, Xin Yi, Xiang Wei
There is ample evidence indicating that epicardial adipose tissue (EAT) volume and thickness is positively associated with coronary artery disease (CAD). However, the exact pathological changes in the human EAT after myocardial ischemia remains largely unclear. In the current study, we applied a comparative quantitative proteomics to elucidate the altered biological processes in the EAT of ischemic cardiomyopathy (ICM) patients. A total of 1649 proteins were successfully quantified in our study, among which 165 proteins were significantly changed (ratio <0...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28248240/global-proteome-changes-in-liver-tissue-6-weeks-after-folfox-treatment-of-colorectal-cancer-liver-metastases
#20
Jozef Urdzik, Anna Vildhede, Jacek R Wiśniewski, Frans Duraj, Ulf Haglund, Per Artursson, Agneta Norén
(1) Oxaliplatin-based chemotherapy for colorectal cancer liver metastasis is associated with sinusoidal injury of liver parenchyma. The effects of oxaliplatin-induced liver injury on the protein level remain unknown. (2) Protein expression in liver tissue was analyzed-from eight patients treated with FOLFOX (combination of fluorouracil, leucovorin, and oxaliplatin) and seven controls-by label-free liquid chromatography mass spectrometry. Recursive feature elimination-support vector machine and Welch t-test were used to identify classifying and relevantly changed proteins, respectively...
October 14, 2016: Proteomes
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