keyword
MENU ▼
Read by QxMD icon Read
search

proteomics and visualization

keyword
https://www.readbyqxmd.com/read/28440506/association-between-high-mobility-group-box%C3%A2-1-protein-expression-and-cell-death-in-acute-pancreatitis
#1
Enjun Gao, Yanfeng Jiang, Zhituo Li, Dongbo Xue, Weihui Zhang
The present study used caerulein stimulation of AR42J rat pancreatic cells as an in vitro acute pancreatitis (AP) model to investigate proteins differentially expressed in apoptosis and necrosis. AR42J cells were stimulated with 10‑8mol/l caerulein and incubated for 24 h. Apoptosis and necrosis were detected using flow cytometry. The sorted Annexin V‑positive cells (apoptotic) and the Annexin V/propidium iodide double‑positive cells (necrotic) were analysed using proteomics. Results showed that numerous proteins were differentially expressed in these 2 groups...
April 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28438675/integrating-cell-biology-and-proteomic-approaches-in-plants
#2
Tomáš Takáč, Olga Šamajová, Jozef Šamaj
Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science...
April 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28391044/experimental-design-and-data-analysis-in-label-free-quantitative-lc-ms-proteomics-a-tutorial-with-msqrob
#3
Ludger J E Goeminne, Kris Gevaert, Lieven Clement
Label-free shotgun proteomics is routinely used to assess proteomes. However, extracting relevant information from the massive amounts of generated data remains difficult. This tutorial provides a strong foundation on analysis of quantitative proteomics data. We provide key statistical concepts that help researchers to design proteomics experiments and we showcase how to analyze quantitative proteomics data using our recent free and open-source R package MSqRob, which was developed to implement the peptide-level robust ridge regression method for relative protein quantification described by Goeminne et al...
April 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28386060/single-molecule-translation-imaging-visualizes-the-dynamics-of-local-%C3%AE-actin-synthesis-in-retinal-axons
#4
Florian Ströhl, Julie Qiaojin Lin, Romain F Laine, Hovy Ho-Wai Wong, Vasja Urbančič, Roberta Cagnetta, Christine E Holt, Clemens F Kaminski
Local mRNA translation occurs in growing axons enabling precise control of the proteome in response to signals. To measure quantitatively the spatiotemporal dynamics of protein synthesis in growth cones, we further developed a technique for single molecule translation imaging (SMTI). We report that Netrin-1 triggers a burst of β-actin synthesis at multiple non-repetitive sites, particularly in the periphery. The response is remarkably rapid starting within 20 seconds of cue application.
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28379287/viptree-the-viral-proteomic-tree-server
#5
Yosuke Nishimura, Takashi Yoshida, Megumi Kuronishi, Hideya Uehara, Hiroyuki Ogata, Susumu Goto
Summary: ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. ViPTree also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes...
March 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28374590/binding-site-characterization-of-am1336-a-novel-covalent-inverse-agonist-at-human-cannabinoid-2-receptor-using-mass-spectrometric-analysis
#6
Srikrishnan Mallipeddi, Simion Kreimer, Nikolai Zvonok, V Kiran Vemuri, Barry L Karger, Alexander R Ivanov, Alexandros Makriyannis
Cannabinoid 2 receptor (CB2R), a Class A G-protein coupled receptor (GPCR), is a promising drug target in a wide array of pathological conditions. Rational drug design has been hindered due to our poor understanding of the structural features involved in ligand binding. Binding of a high-affinity biarylpyrazole inverse agonist AM1336 to a library of the human CB2 receptor (hCB2R) cysteine-substituted mutants provided indirect evidence that two cysteines in transmembrane helix-7 (H7) were critical for the covalent attachment...
April 4, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28370546/cancer-associated-stimuli-driven-turn-on-theranostics-for-multimodality-imaging-and-therapy
#7
REVIEW
Xingshu Li, Jihoon Kim, Juyoung Yoon, Xiaoyuan Chen
Advances in bioinformatics, genomics, proteomics, and metabolomics have facilitated the development of novel anticancer agents that have decreased side effects and increased safety. Theranostics, systems that have combined therapeutic effects and diagnostic capabilities, have garnered increasing attention recently because of their potential use in personalized medicine, including cancer-targeting treatments for patients. One interesting approach to achieving this potential involves the development of cancer-associated, stimuli-driven, turn on theranostics...
March 29, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28368001/genetic-and-proteomic-characterization-of-bile-salt-export-pump-bsep-in-snake-liver
#8
Xinle Tan, Fei Gao, Hexiu Su, Yajun Gong, Jie Zhang, Mitchell A Sullivan, Jiachun Chen
Snake gallbladder, a traditional Chinese medicine, has been believed in various Asian countries to improve visual acuity and alleviate rheumatism. Bile acids, a major component of the gallbladder, are toxic to the liver and kidney in humans and animals due to its detergent effects, while also exhibiting therapeutic effects due to an increase in the gallbladder contractions of muscle strips in patients with cholesterol gallstones. Secretion of bile acids in human and mammals depends on the bile salt export pump (BSEP), a liver-specific adenosine triphosphate (ATP)-binding cassette transporter encoded by ABCB11...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28366874/impaired-vitreous-composition-and-retinal-pigment-epithelium-function-in-the-foxg1-lrp2-myopic-mice
#9
Olivier Cases, Antoine Obry, Sirine Ben-Yacoub, Sébastien Augustin, Antoine Joseph, Géraldine Toutirais, Manuel Simonutti, Annabel Christ, Pascal Cosette, Renata Kozyraki
High myopia (HM) is one of the main causes of visual impairment and blindness all over the world and an unsolved medical problem. Persons with HM are predisposed to other eye pathologies such as retinal detachment, myopic retinopathy or glaucomatous optic neuropathy, complications that may at least partly result from the extensive liquefaction of the myopic vitreous gel. To identify the involvement of the liquid vitreous in the pathogenesis of HM we here analyzed the vitreous of the recently described highly myopic low density lipoprotein receptor-related protein 2 (Lrp2)-deficient eyes...
March 30, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28358118/combiroc-an-interactive-web-tool-for-selecting-accurate-marker-combinations-of-omics-data
#10
Saveria Mazzara, Riccardo L Rossi, Renata Grifantini, Simone Donizetti, Sergio Abrignani, Mauro Bombaci
Diagnostic accuracy can be improved considerably by combining multiple markers, whose performance in identifying diseased subjects is usually assessed via receiver operating characteristic (ROC) curves. The selection of multimarker signatures is a complicated process that requires integration of data signatures with sophisticated statistical methods. We developed a user-friendly tool, called CombiROC, to help researchers accurately determine optimal markers combinations from diverse omics methods. With CombiROC data from different domains, such as proteomics and transcriptomics, can be analyzed using sensitivity/specificity filters: the number of candidate marker panels rising from combinatorial analysis is easily optimized bypassing limitations imposed by the nature of different experimental approaches...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28349699/limiting-the-hydrolysis-and-oxidation-of-maleimide-peptide-adducts-improves-detection-of-protein-thiol-oxidation
#11
Amber E Boyatzis, Scott D Bringans, Matthew J Piggott, Marisa N Duong, Richard J Lipscombe, Peter G Arthur
Oxidative stress, caused by reactive oxygen and nitrogen species (RONS), is important in the pathophysiology of many diseases. A key target of RONS is the thiol group of protein cysteine residues. As thiol oxidation can affect protein function, mechanistic information about how oxidative stress affects tissue function can be ascertained by identifying oxidized proteins. The probes used must be specific and sensitive, such as maleimides for the alkylation of reduced cysteine thiols. However, we find that maleimide-alkylated peptides (MAPs) are oxidized and hydrolysed under sample preparation conditions common for proteomic studies...
March 28, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28343001/comprehensive-functional-analysis-of-large-lists-of-genes-and-proteins
#12
Bernhard Mlecnik, Jérôme Galon, Gabriela Bindea
The interpretation of high dimensional datasets resulting from genomic and proteomic experiments in a timely and efficient manner is challenging. ClueGO software is a Cytoscape App that extracts representative functional biological information for large lists of genes or proteins. The functional enrichment analysis is based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO. Predefined settings for the selection of the terms are provided to facilitate the analysis...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28334231/protvista-visualization-of-protein-sequence-annotations
#13
Xavier Watkins, Leyla J Garcia, Sangya Pundir, Maria J Martin, The UniProt Consortium
Summary: ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations...
March 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28320317/navigo-interactive-tool-for-visualization-and-functional-similarity-and-coherence-analysis-with-gene-ontology
#14
Qing Wei, Ishita K Khan, Ziyun Ding, Satwica Yerneni, Daisuke Kihara
BACKGROUND: The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28306714/reconstruction-and-signal-propagation-analysis-of-the-syk-signaling-network-in-breast-cancer-cells
#15
Aurélien Naldi, Romain M Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J Coopman, Ovidiu Radulescu
The ability to build in-depth cell signaling networks from vast experimental data is a key objective of computational biology. The spleen tyrosine kinase (Syk) protein, a well-characterized key player in immune cell signaling, was surprisingly first shown by our group to exhibit an onco-suppressive function in mammary epithelial cells and corroborated by many other studies, but the molecular mechanisms of this function remain largely unsolved. Based on existing proteomic data, we report here the generation of an interaction-based network of signaling pathways controlled by Syk in breast cancer cells...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28286470/screening-the-molecular-framework-underlying-local-dendritic-mrna-translation
#16
REVIEW
Sanjeev V Namjoshi, Kimberly F Raab-Graham
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28273538/differential-effects-of-bisphenol-a-toxicity-on-oyster-crassostrea-angulata-gonads-as-revealed-by-label-free-quantitative-proteomics
#17
Lianzhong Luo, Qinghong Zhang, Xue Kong, Heqing Huang, Caihuan Ke
Bisphenol A (BPA) is widely used in industry, and is released in large amounts into the environment. BPA is a teratogen and an estrogen receptor agonist and negatively affects reproduction, particularly in aquatic animals, which is of concern for the aquaculture industry. Although there is a large body of literature on the mechanisms that underlie BPA disruption and the effects of different toxicities on invertebrate reproduction, many of the mechanisms involved in invertebrate responses to BPA remain unknown...
February 28, 2017: Chemosphere
https://www.readbyqxmd.com/read/28263889/proteomic-analysis-of-chondromodulin-i-induced-differentiation-of-mesenchymal-stem-cells-into-chondrocytes
#18
Shuang-Chun Xing, Lian-Xin Du, Wei Zhou, Yu-Qiang Hu, Ya Feng, Hong-Feng Liang, Lin Sang, Min Qi, Li-Jie Zhai, Zhi-Qiang Wang
To identify novel proteins that might help clarify the molecular mechanisms underlying chondromodulin-I (ChM-I) induction of mesenchymal stem cells (MSCs) differentiate into chondrocytes. MSCs are triggered to differentiate into chondrocytes, which are recognized as important factors in cartilage tissue engineering. ChM-I is a glycoprotein that stimulates the growth of chondrocytes and inhibits angiogenesis in vitro. In this study, the proteomic approach was used to evaluate protein changes between undifferentiated MSCs and ChM-I-transfected MSCs...
March 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28248244/arabidopsis-regenerating-protoplast-a-powerful-model-system-for-combining-the-proteomics-of-cell-wall-proteins-and-the-visualization-of-cell-wall-dynamics
#19
REVIEW
Ryusuke Yokoyama, Hiroaki Kuki, Takeshi Kuroha, Kazuhiko Nishitani
The development of a range of sub-proteomic approaches to the plant cell wall has identified many of the cell wall proteins. However, it remains difficult to elucidate the precise biological role of each protein and the cell wall dynamics driven by their actions. The plant protoplast provides an excellent means not only for characterizing cell wall proteins, but also for visualizing the dynamics of cell wall regeneration, during which cell wall proteins are secreted. It therefore offers a unique opportunity to investigate the de novo construction process of the cell wall...
November 17, 2016: Proteomes
https://www.readbyqxmd.com/read/28248242/a-proof-of-concept-to-bridge-the-gap-between-mass-spectrometry-imaging-protein-identification-and-relative-quantitation-msi-lc-ms-ms-lf
#20
Laëtitia Théron, Delphine Centeno, Cécile Coudy-Gandilhon, Estelle Pujos-Guillot, Thierry Astruc, Didier Rémond, Jean-Claude Barthelemy, Frédéric Roche, Léonard Feasson, Michel Hébraud, Daniel Béchet, Christophe Chambon
Mass spectrometry imaging (MSI) is a powerful tool to visualize the spatial distribution of molecules on a tissue section. The main limitation of MALDI-MSI of proteins is the lack of direct identification. Therefore, this study focuses on a MSI~LC-MS/MS-LF workflow to link the results from MALDI-MSI with potential peak identification and label-free quantitation, using only one tissue section. At first, we studied the impact of matrix deposition and laser ablation on protein extraction from the tissue section...
October 26, 2016: Proteomes
keyword
keyword
72072
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"