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proteomics pathway analysis

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https://www.readbyqxmd.com/read/28938583/ppa1-regulates-tumor-malignant-potential-and-clinical-outcome-of-colon-adenocarcinoma-through-jnk-pathways
#1
Ping Wang, Yi Zhou, Qi Mei, Jing Zhao, Liu Huang, Qiang Fu
Colorectal cancer (CRC) represents one of the most prevalent malignancies and the third leading cause of cancer death worldwide. Inorganic pyrophosphatase (PPA1) is an enzyme that catalyzes the hydrolysis of pyrophosphate to inorganic phosphate, therefore participates in the energy metabolism. Proteomic studies have demonstrated the up-regulated expression of PPA1 in various tumors, however, its expression pattern in CRC hasn't been reported. In the current study, we used RT-qCR, Western Blot and immunohistochemical (IHC) staining to explore the expression of PPA1 in 113 paired colon cancer tissues and adjacent normal tissues, which revealed that PPA1 was correlated with lymph node metastasis...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28936799/proteomic-features-of-colorectal-cancer-identify-tumor-subtypes-independent-of-oncogenic-mutations-and-independently-predict-relapse-free-survival
#2
Callisia N Clarke, Michael S Lee, Wei Wei, Ganiraju Manyam, Zhi-Qin Jiang, Yiling Lu, Jeffrey Morris, Bradley Broom, David Menter, Eduardo Vilar-Sanchez, Kanwal Raghav, Cathy Eng, George J Chang, Iris Simon, Rene Bernards, Michael Overman, Gordon B Mills, Dipen Maru, Scott Kopetz
BACKGROUND: The directed study of the functional proteome in colorectal cancer (CRC) has identified critical protein markers and signaling pathways; however, the prognostic relevance of many of these proteins remains unclear. METHODS: We determined the prognostic implications of the functional proteome in 263 CRC tumor samples from patients treated at MD Anderson Cancer Center (MDACC) and 462 patients from The Cancer Genome Atlas (TCGA) to identify patterns of protein expression that drive tumorigenesis...
September 21, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/28935859/a-non-transcriptional-role-for-the-glucocorticoid-receptor-in-mediating-the-cell-stress-response
#3
Marina Ptushkina, Toryn Poolman, Mudassar Iqbal, Mark Ashe, Janni Petersen, Joanna Woodburn, Magnus Rattray, Anthony Whetton, David Ray
The glucocorticoid receptor (GR) is essential for the stress response in mammals. We investigated potential non-transcriptional roles of GR in cellular stress response using fission yeast as a model.We surprisingly discovered marked heat stress resistance in yeast ectopically expressing human GR, which required expression of both the N-terminal transactivation domain, and the C-terminal ligand binding domain, but not the DNA-binding domain of the GR. This effect was not affected by GR ligand exposure, and occurred without significant GR nuclear accumulation...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28934723/neural-mechanisms-underlying-the-disruption-of-male-courtship-behavior-by-adult-exposure-to-di-2-ethylhexyl-phthalate-in-mice
#4
Carlos Dombret, Daphné Capela, Kevin Poissenot, Caroline Parmentier, Emma Bergsten, Cédric Pionneau, Solenne Chardonnet, Hélène Hardin-Pouzet, Valérie Grange-Messent, Matthieu Keller, Isabelle Franceschini, Sakina Mhaouty-Kodja
BACKGROUND: Courtship behavior plays a critical role in attracting females and reproduction success. However, the effects of exposure to a ubiquitous contaminant di(2-ethylhexyl) phthalate (DEHP) on these behaviors and, in particular, on courtship vocalizations have not been examined. OBJECTIVE: The effects of adult exposure to DEHP on courtship and mating behaviors and gonadotropic axis and neural mechanisms involved in DEHP-induced effects were analyzed in male mice...
September 1, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28933205/mass-spectrometry-methods-to-study-protein-metabolite-interactions
#5
Hongbo Guo, Hui Peng, Andrew Emili
To ​​​​understand and manipulate biochemical processes and signaling pathways, the knowledge of endogenous protein-metabolite interactions would be extremely helpful. Recent developments in precision mass spectrometry, high-throughput proteomics and sensitive metabolomic profiling are beginning to converge on a possible solution, heralding a new era of global metabolome-proteome 'interactome' studies that promise to change biomedical research and drug discovery. Areas covered: Here, we review innovative mass spectrometry-based methods and recent pioneering studies aimed at elucidating the physical associations of small molecule ligands with cellular proteins...
September 21, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28932706/global-proteomics-revealed-klebsiella-pneumoniae-induced-autophagy-and-oxidative-stress-in-caenorhabditis-elegans-by-inhibiting-pi3k-akt-mtor-pathway-during-infection
#6
Arumugam Kamaladevi, Krishnaswamy Balamurugan
The enterobacterium, Klebsiella pneumoniae invades the intestinal epithelium of humans by interfering with multiple host cell response. To uncover a system-level overview of host response during infection, we analyzed the global dynamics of protein profiling in Caenorhabditis elegans using quantitative proteomics approach. Comparison of protein samples of nematodes exposed to K. pneumoniae for 12, 24, and 36 h by 2DE revealed several changes in host proteome. A total of 266 host-encoded proteins were identified by 2DE MALDI-MS/MS and LC-MS/MS and the interacting partners of the identified proteins were predicted by STRING 10...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28930563/mass-spectrometry-based-proteomic-analysis-of-the-dna-damage-response
#7
Matthew P Stokes, Yiying Zhu, Charles L Farnsworth
In response to DNA damage, cells have evolved mechanisms to halt cell cycle progression, activate repair, or initiate apoptosis. These DNA damage response (DDR) pathways are critical for cellular survival in response to genomic insult, and play important roles in growth, development, and disease. Historically, mediators of DNA damage response signaling have been studied one or a few proteins at a time. Advances in mass spectrometry instrumentation and enrichment methods now allow for more global analysis of the DDR in cells and tissues...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28929768/protein-corona-analysis-of-silver-nanoparticles-links-to-their-cellular-effects
#8
Sabine Juling, Alicia Niedzwiecka, Linda Böhmert, Dajana Lichtenstein, Soeren Selve, Albert Braeuning, Andreas F Thünemann, Eberhard Krause, Alfonso Lampen
The breadth of applications of nanoparticles and the access to food-associated consumer products containing nano-sized materials lead to oral human exposure to such particles. In biological fluids nanoparticles dynamically interact with biomolecules and form a protein corona. Knowledge about the protein corona is of great interest for understanding the molecular effects of particles as well as their fate inside the human body. We used a mass spectrometry-based toxicoproteomics approach to elucidate mechanisms of toxicity of silver nanoparticles and to comprehensively characterize the protein corona formed around silver nanoparticles in Caco-2 human intestinal epithelial cells...
September 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28927270/proteomic-analysis-of-peripheral-blood-mononuclear-cells-pbmc-after-a-high-fat-high-carbohydrate-meal-with-orange-juice
#9
Daniela F Seixas Chaves, Paulo C Carvalho, Elisa Brasili, Marcelo Macedo Rogero, Neuza Mariko Aymoto Hassimotto, Jolene K Diedrich, James J Moresco, John R Yates, Franco Maria Lajolo
Oxidative stress and inflammation play a role in the physiopathology of insulin resistance, diabetes and cardiovascular disease. A single high-fat, high-carbohydrate (HFHC) meal induces an increase in inflammatory and oxidative stress markers in peripheral blood mononuclear cells (PBMC). Previous studies have shown that orange juice is able to prevent this response by inhibiting toll like receptors (TLR) expression and endotoxemia. Our goal was to study the proteome response in PBMC after the consumption of a HFHC meal consumed with water, orange juice or an isocaloric beverage (water with glucose)...
September 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28927258/a-proteomics-based-approach-reveals-differential-regulation-of-visceral-adipose-tissue-proteins-between-metabolically-healthy-and-unhealthy-obese-patients
#10
Assim A Alfadda, Afshan Masood, Mohammed Y Al-Naami, Pierre Chaurand, Hicham Benabdelkamel
Obesity and the metabolic disorders that constitute metabolic syndrome are a primary cause of morbidity and mortality in the world. Nonetheless, the changes in the proteins and the underlying molecular pathways involved in the relevant pathogenesis are poorly understood.In this study a proteomic analysis of the visceral adipose tissue isolated from metabolically healthy and unhealthy obese patients was used to identify presence of altered pathway(s) leading to metabolic dysfunction. Samples were obtained from 18 obese patients undergoing bariatric surgery and were subdivided into two groups based on the presence or absence of comorbidities as defined by the International Diabetes Federation...
September 20, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28926933/itraq-based-quantitative-proteomic-analysis-reveals-cold-responsive-proteins-involved-in-leaf-senescence-in-upland-cotton-gossypium-hirsutum-l
#11
Xuewei Zheng, Shuli Fan, Hengling Wei, Chengcheng Tao, Qiang Ma, Qifeng Ma, Siping Zhang, Hongbin Li, Chaoyou Pang, Shuxun Yu
Premature leaf senescence occurs in the ultimate phase of the plant, and it occurs through a complex series of actions regulated by stress, hormones and genes. In this study, a proteomic analysis was performed to analyze the factors that could induce premature leaf senescence in two cotton cultivars. We successfully identified 443 differential abundant proteins (DAPs) from 7388 high-confidence proteins at four stages between non-premature senescence (NS) and premature senescence (PS), among which 158 proteins were over-accumulated, 238 proteins were down-accumulated at four stages, and 47 proteins displayed overlapped accumulation...
September 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28925539/expression-and-functional-proteomic-analyses-of-osteocytes-from-xenopus-laevis-tested-under-mechanical-stress-conditions-preliminary-observations-on-an-appropriate-new-animal-model
#12
Jessika Bertacchini, Marta Benincasa, Marta Checchi, Francesco Cavani, Alberto Smargiassi, Marzia Ferretti, Carla Palumbo
Hitherto, the role of the osteocyte as transducer of mechanical stimuli into biological signals is far from settled. In this study, we used an appropriate model represented by the cortex of Xenopus laevis long bone diaphysis lacking (unlike the mammalian one) of vascular structures and containing only osteocytes inside the bone matrix. These structural features allow any change of protein profile that might be observed upon different experimental conditions, such as bone adaptation to stress/mechanical loading, to be ascribed specifically to osteocytes...
September 19, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/28925163/-proteomics-research-of-intervention-effect-of-qi-enriching-herbs-on-qi-deficiency-rats-based-on-technology-of-nanolc-ltq-orbitrap
#13
Yin-Fang Chen, Ying-Jun Fu, Chao Liu, Min Hou, Guo-Liang Xu, Ri-Yue Yu, Hong-Ning Liu, Li-Ping Huang
Proteomics method, based on NanoLC-LTQ-Orbitrap technology, was applied to explore the biological basis of intervention effect of "Qi enriching" herbs on "Qi deficiency" rats. The "Qi deficiency" rat model was established with caloric restriction combined with excessive swimming. Muscle proteins of vastus lateralis from the blank group, the model group and the ginseng group were detected by NanoLC-LTQ-Orbitrap system. The data were imported into Protein Discovery software to identify the proteins and all the raw datum were analyzed by SIEVE software...
October 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28923896/experimental-and-theoretical-approaches-to-investigate-the-immunogenicity-of-taenia-solium-derived-ke7-antigen
#14
Raúl J Bobes, José Navarrete-Perea, Adrián Ochoa-Leyva, Víctor Hugo Anaya, Marisela Hernández, Jacquelynne Cervantes-Torres, Karel Estrada, Filiberto Sánchez-Lopez, Xavier Soberón, Gabriela Rosas, Cáris Maroni Nunes, Martín García-Varela, Rogerio Rafael Sotelo-Mundo, Alonso Alexis López-Zavala, Goar Gevorkian, Gonzalo Acero, Juan P Laclette, Gladis Fragoso, Edda Sciutto
Taenia solium cysticercosis, a parasitic disease that affects human health in various regions of the world, is preventable by vaccination. Both the 97-amino-acid-long KETc7 peptide and its carboxyl-terminal, 18-amino-acid-long sequence (GK-1) are found in Taenia crassiceps Both peptides, with proven protective capacity against cysticercosis, are part of the highly conserved, cestode-native, 264-amino-acid long protein KE7. KE7 belongs to a ubiquitously distributed family of proteins associated to membrane processes and may participate in several vital cell pathways...
September 18, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28918527/alterations-in-epididymal-proteomics-and-antioxidant-activity-of-mice-exposed-to-fluoride
#15
Zilong Sun, Sujuan Li, Yuxiang Yu, Hongyu Chen, Mohammad Mehdi Ommati, Ram Kumar Manthari, Ruiyan Niu, Jundong Wang
It is well known that high fluoride results in low fertility. Epididymis is the important place for spermatozoa maturation, which is essential for successful fertilization. In the previous studies, fluoride was reported to damage the epididymal structure of mouse and rabbit. However, the mechanism underlying sodium fluoride (NaF)-induced epididymal toxicity has not yet been well elucidated. The aim of this study is to explore the global protein alterations in epididymis of mice exposed to NaF using the iTRAQ technique...
September 16, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28918157/differential-proteomic-profiling-of-endometrium-and-plasma-indicate-the-importance-of-hydrolysis-in-bovine-endometritis
#16
Shi-Dong Zhang, Shu-Wei Dong, Dong-Sheng Wang, Chike F Oguejiofor, Ali A Fouladi-Nashta, Zhi-Qiang Yang, Zuo-Ting Yan
Endometritis is an important disease of dairy cows that leads to significant economic losses in the dairy cattle industry. To investigate the alteration of proteins associated with endometritis in the dairy cow, the isobaric tags for relative and absolute quantification (iTRAQ) technique was applied to quantitatively identify differentially expressed proteins (DEP) in the endometrium and peripheral plasma of Chinese Holstein cows with endometritis. Compared with the normal (control) group, 159 DEP in the endometrium and 137 DEP in the plasma were identified in cows with endometritis...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28916756/identification-of-the-s100-fused-type-protein-hornerin-as-a-regulator-of-tumor-vascularity
#17
Michael F Gutknecht, Marc E Seaman, Bo Ning, Daniel Auger Cornejo, Emily Mugler, Patrick F Antkowiak, Christopher A Moskaluk, Song Hu, Frederick H Epstein, Kimberly A Kelly
Sustained angiogenesis is essential for the development of solid tumors and metastatic disease. Disruption of signaling pathways that govern tumor vascularity provide a potential avenue to thwart cancer progression. Through phage display-based functional proteomics, immunohistochemical analysis of human pancreatic ductal carcinoma (PDAC) specimens, and in vitro validation, we reveal that hornerin, an S100 fused-type protein, is highly expressed on pancreatic tumor endothelium in a vascular endothelial growth factor (VEGF)-independent manner...
September 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28916745/cadmium-effects-on-dna-and-protein-metabolism-in-oyster-crassostrea-gigas-revealed-by-proteomic-analyses
#18
Jie Meng, Wenxiong Wang, Li Li, Qi Yin, Guofan Zhang
Marine molluscs, including oysters, can concentrate high levels of cadmium (Cd) in their soft tissues, but the molecular mechanisms of Cd toxicity remain speculative. In this study, Pacific oysters (Crassostrea gigas) were exposed to Cd for 9 days and their gills were subjected to proteomic analysis, which were further confirmed with transcriptomic analysis. A total of 4,964 proteins was quantified and 515 differentially expressed proteins were identified in response to Cd exposure. Gene Ontology enrichment analysis revealed that excess Cd affected the DNA and protein metabolism...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28915803/tartrate-resistant-acid-phosphatase-trap-acp5-promotes-metastasis-related-properties-via-tgf%C3%AE-2-t%C3%AE-r-and-cd44-in-mda-mb-231-breast-cancer-cells
#19
Anja Reithmeier, Elena Panizza, Michael Krumpel, Lukas M Orre, Rui M M Branca, Janne Lehtiö, Barbro Ek-Rylander, Göran Andersson
BACKGROUND: Tartrate-resistant acid phosphatase (TRAP/ACP5), a metalloenzyme that is characteristic for its expression in activated osteoclasts and in macrophages, has recently gained considerable focus as a driver of metastasis and was associated with clinically relevant parameters of cancer progression and cancer aggressiveness. METHODS: MDA-MB-231 breast cancer cells with different TRAP expression levels (overexpression and knockdown) were generated and characterized for protein expression and activity levels...
September 15, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28914500/comprehensive-proteomics-analysis-of-exosomes-derived-from-human-seminal-plasma
#20
C Yang, W-B Guo, W-S Zhang, J Bian, J-K Yang, Q-Z Zhou, M-K Chen, W Peng, T Qi, C-Y Wang, C-D Liu
Exosomes are membranous nanovesicles of endocytic origin that carry and transfer regulatory bioactive molecules and mediate intercellular communication between cells and tissues. Although seminal exosomes have been identified in human seminal plasma, their exact composition and possible physiologic function remain unknown. The objective of this study was to perform a comprehensive proteomics analysis of exosomes derived from human seminal plasma. Seminal exosomes were isolated and purified from 12 healthy donors using a 30% sucrose cushion-based exosome-isolation protocol, followed by characterization by western blot, transmission electron microscopy, and nanoparticle tracking analysis before performing extensive liquid chromatography tandem mass spectrometry proteomics analysis...
September 2017: Andrology
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