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proteomics pathway ontology

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https://www.readbyqxmd.com/read/27896924/detailed-tail-proteomic-analysis-of-axolotl-ambystoma-mexicanum-using-an-mrna-seq-reference-database
#1
Turan Demircan, Ilknur Keskin, Seda Nilgun Dumlu, Nilufer Ayturk, Mahmut Erhan Avsaroglu, Emel Akgun, Gurkan Ozturk, Ahmet Tarik Baykal
Salamander Axolotl has been emerging as an important model for stem cell research due to its powerful regenerative capacity. Several advantages, such as the high capability of advanced tissue, organ and appendages regeneration, promote Axolotl as an ideal model system to extend our current understanding on the mechanisms of regeneration. Acknowledging the common molecular pathways between amphibians and mammals, there is a great potential to translate the messages from Axolotl research to mammalian studies...
November 29, 2016: Proteomics
https://www.readbyqxmd.com/read/27878450/mass-spectrometry-based-proteomics-profiling-of-human-monocytes
#2
Yong Zeng, Fei-Yan Deng, Wei Zhu, Lan Zhang, Hao He, Chao Xu, Qing Tian, Ji-Gang Zhang, Li-Shu Zhang, Hong-Gang Hu, Hong-Wen Deng
Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged...
November 22, 2016: Protein & Cell
https://www.readbyqxmd.com/read/27862958/nicotine-induced-protein-expression-profiling-reveals-mutually-altered-proteins-across-four-human-cell-lines
#3
Joao A Paulo, Steven P Gygi
Mass spectrometry-based proteomic strategies can profile the expression level of proteins in response to external stimuli. Nicotine affects diverse cellular pathways, however, the nicotine-induced alterations on the global proteome across human cell lines have not been fully elucidated. We measured perturbations in protein levels resulting from nicotine treatment in four cell lines - HEK, HeLa, PaSC, and SH-SY5Y- in a single experiment using tandem mass tags (TMT10-plex) and high-resolution mass spectrometry...
November 12, 2016: Proteomics
https://www.readbyqxmd.com/read/27836980/proteome-profiling-outperforms-transcriptome-profiling-for-co-expression-based-gene-function-prediction
#4
Jing Wang, Zihao Ma, Steven A Carr, Philipp Mertins, Hui Zhang, Zhen Zhang, Daniel W Chan, Matthew J C Ellis, R Reid Townsend, Richard D Smith, Jason E McDermott, Xian Chen, Amanda G Paulovich, Emily S Boja, Mehdi Mesri, Christopher R Kinsinger, Henry Rodriguez, Karin D Rodland, Daniel C Liebler, Bing Zhang
Co-expression of mRNAs under multiple conditions is commonly used to infer co-functionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for co-expression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein co-expression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC)...
November 11, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27809461/differentially-expressed-serum-proteins-associated-with-calcium-regulation-and-hypocalcemia-in-dairy-cows
#5
Shi Shu, Yunlong Bai, Gang Wang, Xinhuan Xiao, Ziling Fan, Jiang Zhang, Chang Zhao, Yang Zhao, Cheng Xia, Hongyou Zhang
Hypocalcemia is an important metabolic disease of dairy cows during the transition period, although the effect of hypocalcemia on biological function in dairy cows remains unknown. In this study, proteomic, mass spectrum, bioinformatics and western blotting were employed to identify differentially expressed proteins related to serum Ca concentration. Serum samples from dairy cows were collected at three time points: 3rd days before calving (day -3), the day of calving (day 0), and 3rd days after calving (day +3)...
November 3, 2016: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/27791462/deregulation-of-focal-adhesion-formation-and-cytoskeletal-tension-due-to-loss-of-a-type-lamins
#6
Tobias D J Corne, Tom Sieprath, Jonathan Vandenbussche, Danahe Mohammed, Mariska Te Lindert, Kris Gevaert, Sylvain Gabriele, Katarina Wolf, Winnok H De Vos
The nuclear lamina mechanically integrates the nucleus with the cytoskeleton and extracellular environment and regulates gene expression. These functions are exerted through direct and indirect interactions with the lamina's major constituent proteins, the A-type lamins, which are encoded by the LMNA gene. Using quantitative stable isotope labeling-based shotgun proteomics we have analyzed the proteome of human dermal fibroblasts in which we have depleted A-type lamins by means of a sustained siRNA-mediated LMNA knockdown...
October 28, 2016: Cell Adhesion & Migration
https://www.readbyqxmd.com/read/27770818/progranulin-promotes-peripheral-nerve-regeneration-and-reinnervation-role-of-notch-signaling
#7
Christine Altmann, Verica Vasic, Stefanie Hardt, Juliana Heidler, Annett Häussler, Ilka Wittig, Mirko H H Schmidt, Irmgard Tegeder
BACKGROUND: Peripheral nerve injury is a frequent cause of lasting motor deficits and chronic pain. Although peripheral nerves are capable of regrowth they often fail to re-innervate target tissues. RESULTS: Using newly generated transgenic mice with inducible neuronal progranulin overexpression we show that progranulin accelerates axonal regrowth, restoration of neuromuscular synapses and recovery of sensory and motor functions after injury of the sciatic nerve...
October 22, 2016: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/27748441/identification-of-cofilin-1-induces-g0-g1-arrest-and-autophagy-in-angiotensin-1-7-treated-human-aortic-endothelial-cells-from-itraq-quantitative-proteomics
#8
Huang-Joe Wang, Sung-Fang Chen, Wan-Yu Lo
The angiotensin-converting enzyme 2/angiotensin-(1-7)/Mas axis is a pathway that acts against the detrimental effects of the renin-angiotensin system. However, the effects of angiotensin-(1-7) on endothelial protein expression and the related phenotypes are unclear. We performed a duplicate of iTRAQ quantitative proteomic analysis on human aortic endothelial cells (HAECs) treated with angiotensin-(1-7) for 6 hours. Cofilin-1 was identified as a highly abundant candidate with consistent >30% coverage and >1...
October 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27745870/discovery-of-novel-plasma-proteins-as-biomarkers-for-the-development-of-incisional-hernias-after-midline-incision-in-patients-with-colorectal-cancer-the-colocare-study
#9
Jürgen Böhm, Frank Pianka, Nina Stüttgen, Junghyun Rho, Biljana Gigic, Yuzheng Zhang, Nina Habermann, Petra Schrotz-King, Clare Abbenhardt-Martin, Lin Zielske, Paul D Lampe, Alexis Ulrich, Markus K Diener, Cornelia M Ulrich
BACKGROUND: Ventral incisional hernia is the most common long-term complication after an abdominal operation. Among newly diagnosed colorectal cancer patients, we screened the preoperative plasma proteome to explore predictive markers for the development of an incisional hernia. METHODS: We utilized preoperative plasma samples of 72 newly diagnosed colorectal cancer patients who underwent midline incision for tumor resection between 2010 and 2013. A total of 21 patients with incisional hernia occurrence were matched with 51 patients with at least 18 months follow-up without an incisional hernia by sex, age, and body mass index...
October 13, 2016: Surgery
https://www.readbyqxmd.com/read/27742266/proteomic-analysis-of-muccopolysaccharidosis-i-mouse-brain-with-two-dimensional-polyacrylamide-gel-electrophoresis
#10
Li Ou, Michael J Przybilla, Chester B Whitley
Mucopolysaccharidosis type I (MPS I) is due to deficiency of α-l-iduronidase (IDUA) and subsequent storage of undegraded glycosaminoglycans (GAG). The severe form of the disease, known as Hurler syndrome, is characterized by mental retardation and neurodegeneration of unknown etiology. To identify potential biomarkers and unveil the neuropathology mechanism of MPS I disease, two-dimensional polyacrylamide gel electrophoresis (PAGE) and nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) were applied to compare proteome profiling of brains from MPS I and control mice (5-month old)...
October 11, 2016: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/27717806/convergent-transcriptomics-and-proteomics-of-environmental-enrichment-and-cocaine-identifies-novel-therapeutic-strategies-for-addiction
#11
Yafang Zhang, Elizabeth J Crofton, Xiuzhen Fan, Dingge Li, Fanping Kong, Mala Sinha, Bruce A Luxon, Heidi M Spratt, Cheryl F Lichti, Thomas A Green
Transcriptomic and proteomic approaches have separately proven effective at identifying novel mechanisms affecting addiction-related behavior; however, it is difficult to prioritize the many promising leads from each approach. A convergent secondary analysis of proteomic and transcriptomic results can glean additional information to help prioritize promising leads. The current study is a secondary analysis of the convergence of recently published separate transcriptomic and proteomic analyses of nucleus accumbens (NAc) tissue from rats subjected to environmental enrichment vs...
December 17, 2016: Neuroscience
https://www.readbyqxmd.com/read/27711237/proteomic-analysis-implicates-dominant-alterations-of-rna-metabolism-and-the-proteasome-pathway-in-the-cellular-response-to-carbon-ion-irradiation
#12
Yu Wang, Hua Guan, Da-Fei Xie, Yi Xie, Xiao-Dan Liu, Qi Wang, Li Sui, Man Song, Hong Zhang, Jianhua Zhou, Ping-Kun Zhou
Radiotherapy with heavy ions is considered advantageous compared to irradiation with photons due to the characteristics of the Braggs peak and the high linear energy transfer (LET) value. To understand the mechanisms of cellular responses to different LET values and dosages of heavy ion radiation, we analyzed the proteomic profiles of mouse embryo fibroblast MEF cells exposed to two doses from different LET values of heavy ion 12C. Total proteins were extracted from these cells and examined by Q Exactive with Liquid Chromatography (LC)-Electrospray Ionization (ESI) Tandem MS (MS/MS)...
2016: PloS One
https://www.readbyqxmd.com/read/27711126/integrated-left-ventricular-global-transcriptome-and-proteome-profiling-in-human-end-stage-dilated-cardiomyopathy
#13
Dilek Colak, Ayodele A Alaiya, Namik Kaya, Nzioka P Muiya, Olfat AlHarazi, Zakia Shinwari, Editha Andres, Nduna Dzimiri
AIMS: The disease pathways leading to idiopathic dilated cardiomyopathy (DCM) are still elusive. The present study investigated integrated global transcriptional and translational changes in human DCM for disease biomarker discovery. METHODS: We used identical myocardial tissues from five DCM hearts compared to five non-failing (NF) donor hearts for both transcriptome profiling using the ABI high-density oligonucleotide microarrays and proteome expression with One-Dimensional Nano Acquity liquid chromatography coupled with tandem mass spectrometry on the Synapt G2 system...
2016: PloS One
https://www.readbyqxmd.com/read/27704275/dynamic-quantitative-proteomics-characterization-of-tnf-%C3%AE-induced-necroptosis
#14
Yang Wang, Zhi-Hao Huang, Yang-Jia Li, Gui-Wei He, Ru-Yuan Yu, Jie Yang, Wan-Ting Liu, Bin Li, Qing-Yu He
Emerging evidence suggested that necroptosis has essential functions in many human inflammatory diseases, but the molecular mechanisms of necroptosis remain unclear. Here, we employed SILAC quantitatively dynamic proteomics to compare the protein changes during TNF-α-induced necroptosis at different time points in murine fibrosarcoma L929 cells with caspase-8 deficiency, and then performed the systematical analysis on the signaling networks involved in the progress using bioinformatics methods. Our results showed that a total of 329, 421 and 378 differentially expressed proteins were detected at three stages of necroptosis, respectively...
October 4, 2016: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/27696853/quantitative-proteomic-and-phosphoproteomic-comparison-of-2d-and-3d-colon-cancer-cell-culture-models
#15
Xiaoshan Yue, Jessica K Lukowski, Eric M Weaver, Susan B Skube, Amanda B Hummon
Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined and notable differences in both the proteome and the phosphoproteome were determined by nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) to assess how growth configuration affects molecular expression...
October 3, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27696471/global-proteomic-analysis-of-lysine-acetylation-in-zebrafish-danio-rerio-embryos
#16
Oh Kwang Kwon, Sunjoo Kim, Sangkyu Lee
Lysine acetylation is an important post-translational modification (PTM). Since the development of MS-based proteomics technology, important roles of lysine acetylation beyond histones have focused on chromatin remodeling during the cell cycle and regulation of nuclear transport, metabolism, and translation. Zebrafish (Danio rerio) is a widely used vertebrate model in genetics and biologic studies. Although studies in several mammalian species have been performed, the mechanism of lysine acetylation in D. rerio embryos is incompletely understood...
October 2, 2016: Electrophoresis
https://www.readbyqxmd.com/read/27696427/proteomic-analysis-of-peel-browning-of-nanguo-pears-after-low-temperature-storage
#17
Jun-Wei Wang, Xin Zhou, Qian Zhou, Zhi-Yong Liu, Lei Sheng, Long Wang, Shun-Chang Cheng, Shu-Juan Ji
BACKGROUND: Postharvest ripening of the 'Nanguo' pear (Pyrus ussuriensis Maxim.) can be impeded by low-temperature storage. However, pears after long-term refrigeration are prone to peel browning when returned to room temperature conditions. This study investigated the browning mechanism of 'Nanguo' pear stored at a low temperature by analysing the differentially expressed proteins between healthy fruit and fruit with peel browning. RESULTS: The results showed that 181 proteins underwent statistically significant changes...
October 3, 2016: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/27678076/a-drug-target-slim-using-gene-ontology-and-gene-ontology-annotations-to-navigate-protein-ligand-target-space-in-chembl
#18
Prudence Mutowo, A Patrícia Bento, Nathan Dedman, Anna Gaulton, Anne Hersey, Jane Lomax, John P Overington
BACKGROUND: The process of discovering new drugs is a lengthy, time-consuming and expensive process. Modern day drug discovery relies heavily on the rapid identification of novel 'targets', usually proteins that can be modulated by small molecule drugs to cure or minimise the effects of a disease. Of the 20,000 proteins currently reported as comprising the human proteome, just under a quarter of these can potentially be modulated by known small molecules Storing information in curated, actively maintained drug discovery databases can help researchers access current drug discovery information quickly...
September 27, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27667388/quantitative-proteomics-reveals-ecological-fitness-cost-of-multi-herbicide-resistant-barnyardgrass-echinochloa-crus-galli-l
#19
Xia Yang, Zichang Zhang, Tao Gu, Mingchao Dong, Qiong Peng, Lianyang Bai, Yongfeng Li
: Barnyardgrass (Echinochloa crus-galli) is one of the top 15 herbicide-resistant weeds around the world that interferes with rice growth, resulting in major losses of rice yield. Thus, multi-herbicide resistance in barnyardgrass presents a major threat, with the underlying mechanisms that contribute to resistance requiring elucidation. In an attempt to characterize this multi-herbicide resistance at the proteomic level, comparative analysis of resistant and susceptible barnyardgrasses was performed using iTRAQ, both with and without quinclorac, bispyribac-sodium and penoxsulam herbicidal treatment...
September 23, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27663888/proteomic-study-of-hepatocellular-carcinoma-using-a-novel-modified-aptamer-based-array-somascan%C3%A2-platform
#20
Zhiwei Qiao, Xiaoqing Pan, Cuneyd Parlayan, Hidenori Ojima, Tadashi Kondo
Vascular invasion is a pathological hallmark of hepatocellular carcinoma (HCC), associated with poor prognosis; it is strongly related to the early recurrence and poor survival after curative resection. In order to determine the proteomic backgrounds of HCC carcinogenesis and vascular invasion, we employed a novel modified aptamer-based array (SOMAscan) platform. SOMAscan is based on the Slow Off-rate Modified Aptamers (SOMAmers), which rely on the natural 3D folding of single-stranded DNA-based protein affinity reagents...
September 20, 2016: Biochimica et Biophysica Acta
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