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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
#1
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...
January 1, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28039103/itraq-based-proteome-analysis-of-fluoroquinolone-resistant-staphylococcus-aureus
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/27927957/the-proteome-of-bloc-1-genetic-defects-identifies-the-arp2-3-actin-polymerization-complex-to-function-downstream-of-the-schizophrenia-susceptibility-factor-dysbindin-at-the-synapse
#6
Avanti Gokhale, Cortnie Hartwig, Amanda H Freeman, Ravi Das, Stephanie A Zlatic, Rachel Vistein, Amelia Burch, Guillemette Carrot, Arielle F Lewis, Sheldon Nelms, Dion K Dickman, Manojkumar A Puthenveedu, Daniel N Cox, Victor Faundez
: Proteome modifications downstream of monogenic or polygenic disorders have the potential to uncover novel molecular mechanisms participating in pathogenesis and/or extragenic modification of phenotypic expression. We tested this idea by determining the proteome sensitive to genetic defects in a locus encoding dysbindin, a protein required for synapse biology and implicated in schizophrenia risk. We applied quantitative mass spectrometry to identify proteins expressed in neuronal cells the abundance of which was altered after downregulation of the schizophrenia susceptibility factor dysbindin (Bloc1s8) or two other dysbindin-interacting polypeptides, which assemble into the octameric biogenesis of lysosome-related organelles complex 1 (BLOC-1)...
December 7, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27896924/detailed-tail-proteomic-analysis-of-axolotl-ambystoma-mexicanum-using-an-mrna-seq-reference-database
#7
Turan Demircan, Ilknur Keskin, Seda Nilgün Dumlu, Nilüfer Aytürk, Mahmut Erhan Avşaroğlu, Emel Akgün, Gürkan Öztürk, Ahmet Tarık 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...
January 2017: Proteomics
https://www.readbyqxmd.com/read/27878450/mass-spectrometry-based-proteomics-profiling-of-human-monocytes
#8
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
#9
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. We quantified 8590 proteins across all cell lines...
January 2017: Proteomics
https://www.readbyqxmd.com/read/27836980/proteome-profiling-outperforms-transcriptome-profiling-for-coexpression-based-gene-function-prediction
#10
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
Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality 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 coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression 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)...
January 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27809461/differentially-expressed-serum-proteins-associated-with-calcium-regulation-and-hypocalcemia-in-dairy-cows
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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