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Proteomics

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https://www.readbyqxmd.com/read/29793202/itraq-based-quantitative-proteomic-analysis-of-the-earthworm-eisenia-fetida-response-to-escherichia-coli-o157-h7
#1
Xing Wang, Xiaoqin Li, Zhenjun Sun
Soil environment contaminated by Escherichia coli O157:H7 which come from the waste of infected animals. Earthworms can live in the pathogens-polluted soil by their innate immunity. How the proteins of earthworms E. fetida will response to E. coli O157:H7-contaminated-soil still unclear? To identify the defense proteins under E. coli O157:H7 stress, we performed a proteomic analysis of earthworm under E. coli O157:H7 exposure through an iTRAQ technology. In total, we found 283 non-redundant proteins, including fibrinolytic protease 1, lombricine kinase, lysozyme, gelsolin, coelomic cytolytic factor-1, antimicrobial peptide lumbricin-l, lysenin, and et al...
May 21, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29792946/investigation-of-nonalcoholic-fatty-liver-disease-induced-drug-metabolism-by-comparative-global-toxicoproteomics
#2
Ann-Yae Na, Jung Jae Jo, Ok Kwang Kwon, Riya Shrestha, Piljoung Cho, Kyu Min Kim, Sung Hwan Ki, Tae Hee Lee, Tae Won Jeon, Tae Cheon Jeong, Sangkyu Lee
Non-alcoholic fatty liver disease (NAFLD) includes conditions such as steatosis, non-alcoholic steatohepatitis, and ultimately hepatocellular carcinoma. Although the pathology of NAFLD is well-established, NAFLD-induced drug metabolism mediated by cytochrome P450 (CYP) in the liver has remained largely unexplored. Therefore, we investigated NAFLD-induced drug metabolism mediated by CYP by quantitative toxicoproteomics analysis. After administration of a methionine-choline deficient (MCD) diet to induce development of NAFLD, tandem mass tags-based liquid chromatography-tandem mass spectrometry analysis was conducted to investigate the dynamics of hepatic proteins...
May 21, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29792918/translational-omics-future-potential-and-current-challenges-in-precision-medicine
#3
Arsalan Wafi, Reza Mirnezami
Rapid advances in computational science and biotechnology are paving the way for precision medicine - a vision in next-generation healthcare that promises to provide a care package uniquely tailored to each individual's molecular make-up. Until relatively recently, the focus has been firmly centred around the genome; however, over the past two decades there has been a surge in the study of molecular activity within other biological domains (proteome/transcriptome/metabolome) involved in health and pathogenesis...
May 21, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29792880/molecular-alterations-during-larval-development-of-haemonchus-contortus-in-vitro-are-under-tight-post-transcriptional-control
#4
Guangxu Ma, Tao Wang, Pasi K Korhonen, Ching-Seng Ang, Nicholas A Williamson, Neil D Young, Andreas J Stroehlein, Ross S Hall, Anson V Koehler, Andreas Hofmann, Robin B Gasser
In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (×L3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations (r = 0...
May 22, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29792824/a-host-proteome-atlas-of-streptococcus-pyogenes-infection
#5
Amelia T Soderholm, Mark J Walker
Multiplex quantitative proteomics analysis of mice infected with Group A Streptococcus reveals organ-specific biomarkers of infection.
May 23, 2018: Cell Systems
https://www.readbyqxmd.com/read/29792801/developing-a-novel-sulfoxide-containing-ms-cleavable-homobifunctional-cysteine-reactive-cross-linker-for-studying-protein-protein-interactions
#6
Craig B Gutierrez, Sarah A Block, Clinton Yu, Stephanie M Soohoo, Alexander S Huszagh, Scott D Rychnovsky, Lan Huang
Cross-linking mass spectrometry (XL-MS) has become an emerging technology for defining protein-protein interactions (PPIs) and elucidating architectures of large protein complexes. Up to now, the mostly widely used cross-linking reagents are targeting lysines. While such reagents have been successfully applied to map PPIs at the proteome-wide scale, comprehensive PPI profiling would require additional cross-linking chemistries. Cysteine is one of the most reactive amino acids and an attractive target for cross-linking owing to its unique role in protein structures...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792708/nonalcoholic-fatty-liver-disease-and-diabetes-is-associated-with-decreased-cyp3a4-protein-expression-and-activity-in-human-liver
#7
Rohitash Jamwal, Suzanne M de la Monte, Ken Ogasawara, Sravani Adusumalli, Benjamin B Barlock, Fatemeh Akhlaghi
Nonalcoholic fatty liver disease (NAFLD) is a major cause of chronic liver disease in Western population. We investigated the effect of nonalcoholic fatty liver disease (NAFLD) and diabetes mellitus on CYP3A4 activity in human liver tissue from brain dead donors (N=74). Histopathologically graded livers were grouped into normal (n=24), nonalcoholic fatty liver (NAFL, n=26) and nonalcoholic steatohepatitis (NASH, n=24) categories. The rate of conversion of midazolam to its 1-hydroxy metabolite was used to assess in vitro CYP3A4 activity in human liver microsomes (HLM)...
May 24, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29792683/top-down-deep-sequencing-of-ubiquitin-using-two-dimensional-mass-spectrometry
#8
Federico Floris, Lionel Chiron, Alice Lynch, Mark P Barrow, Marc-André Delsuc, Peter B O'Connor
Two-dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (2D FT-ICR MS or 2D MS) allows data independent fragmentation of all ions in a sample, and correlation of fragment ions to their precursors without isolation prior to fragmentation. Developments in computer capabilities and implementations in FTMS over of the last decade have allowed the technique to become a useful analytical tool for bottom-up proteomics (BUP), and more recently in top-down protein analysis (TDP). In this work, a new method of TDP is developed using two-dimensional mass spectrometry, called MS/2D FT-ICR MS or MS/2DMS...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792268/toward-individual-glomerular-phenotyping-advent-of-precision-medicine-in-kidney-biopsies
#9
Kumar Sharma, Ljiljana Paša-Tolić
The road to precision medicine for nephrology is approaching quickly. In the present volume, the glomerular proteome has now been characterized at a single glomerulus level in mouse and human kidneys. Using the Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) approach the authors demonstrated that LAMP1 is a key lysosomal protein that is increased in glomerular diseases and may play a pathogenic role.
June 2018: Kidney International
https://www.readbyqxmd.com/read/29792171/embryonic-transcriptome-and-proteome-analyses-on-hepatic-lipid-metabolism-in-chickens-divergently-selected-for-abdominal-fat-content
#10
Wei Na, Yuan-Yuan Wu, Peng-Fei Gong, Chun-Yan Wu, Bo-Han Cheng, Yu-Xiang Wang, Ning Wang, Zhi-Qiang Du, Hui Li
BACKGROUND: In avian species, liver is the main site of de novo lipogenesis, and hepatic lipid metabolism relates closely to adipose fat deposition. Using our fat and lean chicken lines of striking differences in abdominal fat content, post-hatch lipid metabolism in both liver and adipose tissues has been studied extensively. However, whether molecular discrepancy for hepatic lipid metabolism exists in chicken embryos remains obscure. RESULTS: We performed transcriptome and proteome profiling on chicken livers at five embryonic stages (E7, E12, E14, E17 and E21) between the fat and lean chicken lines...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792109/computational-functional-genomics-based-approaches-in-analgesic-drug-discovery-and-repurposing
#11
Catharina Lippmann, Dario Kringel, Alfred Ultsch, Jörn Lötsch
Persistent pain is a major healthcare problem affecting a fifth of adults worldwide with still limited treatment options. The search for new analgesics increasingly includes the novel research area of functional genomics, which combines data derived from various processes related to DNA sequence, gene expression or protein function and uses advanced methods of data mining and knowledge discovery with the goal of understanding the relationship between the genome and the phenotype. Its use in drug discovery and repurposing for analgesic indications has so far been performed using knowledge discovery in gene function and drug target-related databases; next-generation sequencing; and functional proteomics-based approaches...
May 24, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29792094/regulatory-context-and-validation-of-assays-for-clinical-mass-spectrometry-proteomics-cmsp-methods
#12
Christophe Hirtz, Pauline Bros, Cato Brede, Pierre Lescuyer, Aleksandra M Maceski, Jerome Vialaret, Vincent Delatour, Sylvain Lehmann
Clinical mass spectrometry proteomics (cMSP) assays are being increasingly used in clinical laboratories for analyzing peptides and proteins. It has therefore become urgent to characterize and validate the methods available for liquid chromatography-tandem mass spectrometry (LC/MS-MS) targeted quantification of peptide and protein biomarkers in biological fluids in the context of in vitro diagnostics. LC-MS/MS for the detection of peptides and proteins is currently the main approach used in the field of cMSP...
May 23, 2018: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29791858/a-multi-layered-quantitative-in-vivo-expression-atlas-of-the-podocyte-unravels-kidney-disease-candidate-genes
#13
Markus M Rinschen, Markus Gödel, Florian Grahammer, Stefan Zschiedrich, Martin Helmstädter, Oliver Kretz, Mostafa Zarei, Daniela A Braun, Sebastian Dittrich, Caroline Pahmeyer, Patricia Schroder, Carolin Teetzen, HeonYung Gee, Ghaleb Daouk, Martin Pohl, Elisa Kuhn, Bernhard Schermer, Victoria Küttner, Melanie Boerries, Hauke Busch, Mario Schiffer, Carsten Bergmann, Marcus Krüger, Friedhelm Hildebrandt, Joern Dengjel, Thomas Benzing, Tobias B Huber
Damage to and loss of glomerular podocytes has been identified as the culprit lesion in progressive kidney diseases. Here, we combine mass spectrometry-based proteomics with mRNA sequencing, bioinformatics, and hypothesis-driven studies to provide a comprehensive and quantitative map of mammalian podocytes that identifies unanticipated signaling pathways. Comparison of the in vivo datasets with proteomics data from podocyte cell cultures showed a limited value of available cell culture models. Moreover, in vivo stable isotope labeling by amino acids uncovered surprisingly rapid synthesis of mitochondrial proteins under steady-state conditions that was perturbed under autophagy-deficient, disease-susceptible conditions...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791839/ubiquitylation-dynamics-of-the-clock-cell-proteome-and-timeless-during-a-circadian-cycle
#14
Áron Szabó, Christian Papin, David Cornu, Elisabeth Chélot, Zoltán Lipinszki, Andor Udvardy, Virginie Redeker, Ugo Mayor, François Rouyer
Circadian clocks have evolved as time-measuring molecular devices to help organisms adapt their physiology to daily changes in light and temperature. Transcriptional oscillations account for a large fraction of rhythmic protein abundance. However, cycling of various posttranslational modifications, such as ubiquitylation, also contributes to shape the rhythmic protein landscape. In this study, we used an in vivo ubiquitin labeling assay to investigate the circadian ubiquitylated proteome of Drosophila melanogaster...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791771/minimal-information-about-an-immuno-peptidomics-experiment-miaipe
#15
Jennie R Lill, Peter A van Veelen, Stefan Tenzer, Arie Admon, Etienne Caron, Josh Elias, Albert J R Heck, Miguel Marcilla, Fabio Marino, Markus Müller, Bjoern Peters, Anthony Purcell, Alessandro Sette, Theo Sturm, Nicola Ternette, Juan Antonio Vizcaíno, Michal Bassani-Sternberg
Minimal Information about an Immuno-Peptidomics Experiment (MIAIPE) is an initiative of the members of the Human Immuno-Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement and associated mass spectrometry (MS)-related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (Minimal Information About a Proteomics Experiment) guidelines...
May 23, 2018: Proteomics
https://www.readbyqxmd.com/read/29791506/shmt2-and-the-brcc36-brisc-deubiquitinase-regulate-hiv-1-tat-k63-ubiquitylation-and-destruction-by-autophagy
#16
Muyu Xu, James J Moresco, Max Chang, Amey Mukim, Davey Smith, Jolene K Diedrich, John R Yates, Katherine A Jones
HIV-1 Tat is a key regulator of viral transcription, however little is known about the mechanisms that control its turnover in T cells. Here we use a novel proteomics technique, called DiffPOP, to identify the molecular target of JIB-04, a small molecule compound that potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines. Mass-spectrometry analysis of whole-cell extracts from 2D10 Jurkat T cells revealed that JIB-04 targets Serine Hydroxymethyltransferase 2 (SHMT2), a regulator of glycine biosynthesis and an adaptor for the BRCC36 K63Ub-specific deubiquitinase in the BRISC complex...
May 23, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29791134/identification-of-yth-domain-containing-proteins-as-the-readers-for-n1-methyladenosine-in-rna
#17
Xiaoxia Dai, Tianlu Wang, Gwendolyn Gonzalez, Yinsheng Wang
N1-methyladenosine (m1 A) is an important post-transcriptional modification in RNA; however, the exact biological role of m1 A remains to be determined. By employing a quantitative proteomics method, we identified multiple putative protein readers of m1 A in RNA, including several YTH domain family proteins. We showed that YTHDF1-3 and YTHDC1, but not YTHDC2, could bind directly to m1 A in RNA. We also found that Trp432 in YTHDF2, a conserved residue in the hydrophobic pocket of the YTH domain that is necessary for its binding to N6 -methyladenosine (m6 A), is required for its recognition of m1 A...
May 25, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29790989/the-galaxy-platform-for-accessible-reproducible-and-collaborative-biomedical-analyses-2018-update
#18
Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel Blankenberg
Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790911/panda-view-an-easy-to-use-tool-for-statistical-analysis-and-visualization-of-quantitative-proteomics-data
#19
Cheng Chang, Kaikun Xu, Chaoping Guo, Jinxia Wang, Qi Yan, Jian Zhang, Fuchu He, Yunping Zhu
Summary: Compared with the numerous software tools developed for identification and quantification of -omics data, there remains a lack of suitable tools for both downstream analysis and data visualization. To help researchers better understand the biological meanings in their -omics data, we present an easy-to-use tool, named PANDA-view, for both statistical analysis and visualization of quantitative proteomics data and other -omics data. PANDA-view contains various kinds of analysis methods such as normalization, missing value imputation, statistical tests, clustering and principal component analysis, as well as the most commonly-used data visualization methods including an interactive volcano plot...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790754/epiprofile-2-0-a-computational-platform-for-processing-epi-proteomics-mass-spectrometry-data
#20
Zuo-Fei Yuan, Simone Sidoli, Dylan M Marchione, Johayra Simithy, Kevin A Janssen, Mary R Szurgot, Benjamin A Garcia
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here, we present EpiProfile 2.0, an extended version of our 2015 software (v1.0) for accurate quantification of histone peptides based on liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis...
May 23, 2018: Journal of Proteome Research
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