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proteomics pathway ontology

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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
#1
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
#2
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/28290293/comparative-proteomic-analysis-of-milk-derived-exosomes-in-human-and-bovine-colostrum-and-mature-milk-samples-by-itraq-coupled-lc-ms-ms
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/28241430/the-importance-of-endophenotypes-to-evaluate-the-relationship-between-genotype-and-external-phenotype
#7
REVIEW
Marinus F W Te Pas, Ole Madsen, Mario P L Calus, Mari A Smits
With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment...
February 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28199731/proteomic-profiling-analysis-reveals-a-link-between-experimental-autoimmune-uveitis-and-complement-activation-in-rats
#8
Dadong Guo, Bing Hu, Hongying Tang, Yuanyuan Sun, Bin Liu, Qingmei Tian, Hongsheng Bi
Uveitis is an autoimmune disease that usually damages the vision function, leading to poor visual quality in patients. As an autoimmune ocular inflammatory disease, the pathogenesis of uveitis is associated with abnormal expression of some proteins and aberrant regulation of multiple signaling pathways. Nevertheless, the detailed mechanism remains unclear. In this study, we induced an experimental autoimmune uveitis (EAU) model in rats. We determined the levels of C3a and membrane attack complex C5b-9 (soluble C5b-9, sC5b-9) in both plasma and aqueous humor, identified the differentially expressed proteins in plasma by liquid chromatography-tandem mass spectrometry, and employed bioinformatics algorithms to analyze differentially expressed proteins in EAU rat plasma...
February 15, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28150236/bioinformatics-analysis-of-protein-phosphorylation-in-plant-systems-biology-using-p3db
#9
Qiuming Yao, Dong Xu
Protein phosphorylation is one of the most pervasive protein post-translational modification events in plant cells. It is involved in many plant biological processes, such as plant growth, organ development, and plant immunology, by regulating or switching signaling and metabolic pathways. High-throughput experimental methods like mass spectrometry can easily characterize hundreds to thousands of phosphorylation events in a single experiment. With the increasing volume of the data sets, Plant Protein Phosphorylation DataBase (P3DB, http://p3db...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28141873/proteomic-and-transcriptomic-study-of-brain-microvessels-in-neonatal-and-adult-mice
#10
Baptiste Porte, Clémence Chatelain, Julie Hardouin, Céline Derambure, Yasmine Zerdoumi, Michèle Hauchecorne, Nicolas Dupré, Soumeya Bekri, Bruno Gonzalez, Stéphane Marret, Pascal Cosette, Philippe Leroux
Infants born before 29 weeks gestation incur a major risk of preterm encephalopathy and subependymal/intracerebral/intraventricular haemorrhage. In mice, an ontogenic window of haemorrhage risk was recorded up to 5 days after birth in serpine1 knock-out animals. Using proteome and transcriptome approaches in mouse forebrain microvessels, we previously described the remodelling of extracellular matrix and integrins likely strengthening the vascular wall between postnatal day 5 (P5) and P10. Haemorrhage is the ultimate outcome of vessel damage (i...
2017: PloS One
https://www.readbyqxmd.com/read/28139890/pharmacogenomics-of-17-alpha-hydroxyprogesterone-caproate-for-recurrent-preterm-birth-a-case-control-study
#11
T A Manuck, W S Watkins, M S Esplin, J Biggio, R Bukowski, S Parry, H Zhan, H Huang, W Andrews, G Saade, Y Sadovsky, U M Reddy, J Ilekis, M Yandell, M W Varner, L B Jorde
OBJECTIVE: To compare maternal genotypes between women with and without significant prolongation of pregnancy in the setting of 17-alpha hydroxyprogesterone caproate (17-P) administration for the prevention of recurrent preterm birth (PTB). DESIGN: Case-control. SETTING: Three tertiary-care centres across the USA. POPULATION: Women (n = 99) with ≥ 1 prior singleton spontaneous PTB, receiving 17-P. METHODS: Women were classified as having successful prolongation of pregnancy during the 17-P treated pregnancy, in two ways: (1) Definition A: success/non-success based on difference in gestational age at delivery between 17-P-treated and untreated pregnancies (success: delivered ≥ 3 weeks later with 17-P) and (2) Definition B: success/non-success based on reaching term (success: delivered at term with 17-P)...
January 31, 2017: BJOG: An International Journal of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28126595/global-proteome-and-phospho-proteome-analysis-of-merlin-deficient-meningioma-and-schwannoma-identifies-pdlim2-as-a-novel-therapeutic-target
#12
Kayleigh Bassiri, Sara Ferluga, Vikram Sharma, Nelofer Syed, Claire L Adams, Edwin Lasonder, C Oliver Hanemann
Loss or mutation of the tumour suppressor Merlin predisposes individuals to develop multiple nervous system tumours, including schwannomas and meningiomas, sporadically or as part of the autosomal dominant inherited condition Neurofibromatosis 2 (NF2). These tumours display largely low grade features but their presence can lead to significant morbidity. Surgery and radiotherapy remain the only treatment options despite years of research, therefore an effective therapeutic is required. Unbiased omics studies have become pivotal in the identification of differentially expressed genes and proteins that may act as drug targets or biomarkers...
February 2017: EBioMedicine
https://www.readbyqxmd.com/read/28122643/identification-of-potential-saliva-and-tear-biomarkers-in-primary-sj%C3%A3-gren-s-syndrome-utilising-the-extraction-of-extracellular-vesicles-and-proteomics-analysis
#13
Lara A Aqrawi, Hilde Kanli Galtung, Beate Vestad, Reidun Øvstebø, Bernd Thiede, Shermin Rusthen, Alix Young, Eduarda M Guerreiro, Tor Paaske Utheim, Xiangjun Chen, Øygunn Aass Utheim, Øyvind Palm, Janicke Liaaen Jensen
BACKGROUND: There is a long-lasting need for non-invasive, more accurate diagnostic techniques when evaluating primary Sjögren's syndrome (pSS) patients. Incorporation of additional diagnostics involving screening for disease-specific biomarkers in biological fluid is a promising concept that requires further investigation. In the current study we aimed to explore novel disease biomarkers in saliva and tears from pSS patients. METHODS: Liquid chromatography-mass spectrometry (LC-MS) was performed on stimulated whole saliva and tears from 27 pSS patients and 32 healthy controls, and salivary and tear proteomic biomarker profiles were generated...
January 25, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28120393/proteomic-analyses-of-changes-in-synechococcus-sp-pcc7942-following-uv-c-stress
#14
Xi Peng, Jie Yang, Yang Gao
UV-C's effects on the physiological and biochemical processes of cyanobacteria have been well characterized. However, the molecular mechanisms of cyanobacteria's tolerance to UV-C still needs further investigation. This research attempts to decode the variation in protein abundances in cyanobacteria after UV-C stress. Different expression levels of proteins in the cytoplasm of Synechococcus sp. PCC7942 under UV-C stress were investigated by using a comparative proteomic approach. Forty-seven UV-C-regulated proteins were identified by MALDI-TOF analysis and classified by Gene Ontology (GO)...
January 25, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28116073/protein-profiling-of-plasma-proteins-in-dairy-cows-with-subclinical-hypocalcaemia
#15
Ziling Fan, Shi Shu, Chuchu Xu, Xinhuan Xiao, Gang Wang, Yunlong Bai, Cheng Xia, Ling Wu, Hongyou Zhang, Chuang Xu, Wei Yang
Subclinical hypocalcaemia (SH) is an important metabolic disease in dairy cows that has a serious impact on production performance. The objective of this study was to investigate novel aspects of pathogenesis using proteomics technology to identify proteins that are differentially expressed in diseased and healthy animals. Dairy cows were divided into an SH group (T, n = 10) and a control group (C, n = 10) based on plasma calcium concentration. A total of 398 differentially expressed proteins were identified, of which 265 proteins were overlapped in the two parallel experiments...
2017: Irish Veterinary Journal
https://www.readbyqxmd.com/read/28049027/an-integrated-shotgun-proteomics-and-bioinformatics-approach-for-analysis-of-brain-proteins-from-mcao-model-using-serial-affinity-chromatograph-with-four-active-ingredients-from-shengmai-preparations-as-ligands
#16
Xiao-Xue Fan, Fang Li, Yan-Ni Lv, Yu Zhang, Jun-Ping Kou, Bo-Yang Yu
Identification and validation of disease-relevant target proteins for natural products is an essential component of modern pharmaceutical research. In the present study, an integrated shotgun proteomics and bioinformatics approach was established to profile the interaction of active small molecules derived from ShengMai preparations (SMXZF) with hundreds of endogenously expressed proteins from middle cerebral artery occlusion (MCAO) model. Affinity-based proteomic strategies for isolation and identification of targets for the bioactive components is a classic, but still powerful approach...
February 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28039103/itraq-based-proteome-analysis-of-fluoroquinolone-resistant-staphylococcus-aureus
#17
Van Chi Thai, Teck Kwang Lim, Kim Phuong Uyen Le, Qingsong Lin, Thi Thu Hoai Nguyen
OBJECTIVES: The aim of this study was to compare global protein expression changes during fluoroquinolone (FQ) exposure of Staphylococcus aureus. METHODS: Total protein extracts of wild-type S. aureus ATCC 29213 and six multidrug-resistant (MDR) strains derived from the wild-type under different FQ exposures were analysed using the 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) method combined with LC-MS/MS analysis. Differentially expressed proteins were searched for their Gene Ontology (GO) annotation (UniProt database) and protein-protein interaction network (STRING v...
December 27, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28018404/functional-and-integrative-analysis-of-the-proteomic-profile-of-radish-root-under-pb-exposure
#18
Yan Wang, Liang Xu, Mingjia Tang, Haiyan Jiang, Wei Chen, Wei Zhang, Ronghua Wang, Liwang Liu
Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L(-1)(Pb500) and 1000 mg L(-1)(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification)...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27975291/a-systematic-bioinformatics-approach-to-identify-high-quality-mass-spectrometry-data-and-functionally-annotate-proteins-and-proteomes
#19
Mohammad Tawhidul Islam, Abidali Mohamedali, Seong Beom Ahn, Ishmam Nawar, Mark S Baker, Shoba Ranganathan
In the past decade, proteomics and mass spectrometry have taken tremendous strides forward, particularly in the life sciences, spurred on by rapid advances in technology resulting in generation and conglomeration of vast amounts of data. Though this has led to tremendous advancements in biology, the interpretation of the data poses serious challenges for many practitioners due to the immense size and complexity of the data. Furthermore, the lack of annotation means that a potential gold mine of relevant biological information may be hiding within this data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27941623/identification-of-potential-biomarkers-for-rhegmatogenous-retinal-detachment-associated-with-choroidal-detachment-by-vitreous-itraq-based-proteomic-profiling
#20
Zhifeng Wu, Nannan Ding, Mengxi Yu, Ke Wang, Shasha Luo, Wenjun Zou, Ying Zhou, Biao Yan, Qin Jiang
Rhegmatogenous retinal detachment associated with choroidal detachment (RRDCD) is a complicated and serious type of rhegmatogenous retinal detachment (RRD). In this study, we identified differentially expressed proteins in the vitreous humors of RRDCD and RRD using isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano-liquid chromatography-electrospray ion trap-mass spectrometry-mass spectrometry (nano-LC-ESI-MS/MS) and bioinformatic analysis. Our result shows that 103 differentially expressed proteins, including 54 up-regulated and 49 down-regulated proteins were identified in RRDCD...
December 7, 2016: International Journal of Molecular Sciences
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