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proteomics and visualization

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https://www.readbyqxmd.com/read/29140531/an-update-on-sorfs-org-a-repository-of-small-orfs-identified-by-ribosome-profiling
#1
Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136207/linkedomics-analyzing-multi-omics-data-within-and-across-32-cancer-types
#2
Suhas V Vasaikar, Peter Straub, Jing Wang, Bing Zhang
The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29118029/giapronto-a-one-click-graph-visualization-software-for-proteomics-datasets
#3
Amber Kathryn Weiner, Simone Sidoli, Sharon J Diskin, Ben Garcia
Here we present a free interactive web tool to process and visualize proteomics datasets with a single click. GiaPronto can process all proteomics quantification methods, i.e. label-free, SILAC and isobaric labeling, and analyze post-translational modifications (PTMs). The software performs normalization and statistics, assists determination of regulated proteins, biomarkers and Gene Ontology (GO) enrichment, and provides high resolution images and tables for further data analysis. We foresee that GiaPronto will become the most rapid and simple tool for assessing data quality and determining most relevant features of proteomic datasets...
November 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29117645/proteomic-profiling-of-tgfbi-null-mouse-corneas-reveals-only-minor-changes-in-matrix-composition-supportive-of-tgfbi-knockdown-as-therapy-against-tgfbi-linked-corneal-dystrophies
#4
Ebbe Toftgaard Poulsen, Kasper Runager, Nadia Sukusu Nielsen, Marie V Lukassen, Karen Thomsen, Paige Snider, Olga Simmons, Henrik Vorum, Simon J Conway, Jan J Enghild
TGFBIp is a constituent of the extracellular matrix in many human tissues including the cornea, where it is one of the most abundant proteins expressed. TGFBIp interacts with Type I, II, IV, VI and XII collagens as well as several members of the integrin family, suggesting it plays an important role in maintaining structural integrity and possibly corneal transparency as well. Significantly, more than 60 point mutations within the TGFBI gene have been reported to result in aberrant TGFBIp folding and aggregation in the cornea, resulting in severe visual impairment and blindness...
November 8, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29117316/vitreous-fibronectin-and-fibrinogen-expression-increased-in-eyes-with-proliferative-diabetic-retinopathy-after-intravitreal-anti-vegf-therapy
#5
Qiaoling Wei, Ting Zhang, Rui Jiang, Qing Chang, Yanqiong Zhang, Xin Huang, Xing Gao, Hong Jin, Gezhi Xu
Purpose: To evaluate vitreous humor (VH) protein expression profiles in patients with proliferative diabetic retinopathy (PDR), with and without intravitreal injection (IVI) of anti-vascular endothelial growth factor (anti-VEGF) before vitrectomy. Methods: We enrolled consecutive PDR patients who needed pars plana vitrectomy (PPV) with or without IVI or pan-retinal photocoagulation (PRP). Visual acuity, duration, and treatment of diabetes mellitus, ocular treatment history, and fundus examinations were recorded...
November 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29115129/time-gated-luminescence-imaging-of-immunolabeled-human-tissues
#6
Ting Chen, Rui Hong, Darren Magda, Christopher Bieniarz, Larry Morrison, Lawrence W Miller
Multiplexed immunofluorescence imaging of formalin-fixed, paraffin-embedded tissues is a powerful tool for investigating proteomic profiles and diagnosing disease. However, conventional immunofluorescence with organic dyes is limited in the number of colors that can be simultaneously visualized, is made less sensitive by tissue autofluorescence background, and is usually incompatible with commonly used hematoxylin and eosin staining. Herein, we demonstrate the comparative advantages of using time-gated luminescence microscopy in combination with an emissive Tb(III) complex, Lumi4-Tb, for tissue imaging in terms of sensitivity, multiplexing potential, and compatibility with common immunohistochemistry protocols...
November 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29106664/proteomicsdb
#7
Tobias Schmidt, Patroklos Samaras, Martin Frejno, Siegfried Gessulat, Maximilian Barnert, Harald Kienegger, Helmut Krcmar, Judith Schlegl, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Kuster, Mathias Wilhelm
ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29094729/chinese-herbal-formula-fuzheng-huayu-alleviates-ccl4-induced-liver-fibrosis-in-rats-a-transcriptomic-and-proteomic-analysis
#8
Shu Dong, Fei-Fei Cai, Qi-Long Chen, Ya-Nan Song, Yang Sun, Bin Wei, Xiao-Yan Li, Yi-Yang Hu, Ping Liu, Shi-Bing Su
Liver fibrosis is a consequence of chronic liver disease that can progress to liver cirrhosis or even hepatocarcinoma. Fuzheng Huayu (FZHY), a Chinese herbal formula, has been shown to exert anti-fibrotic effects. To better understand the molecular mechanisms underlying the anti-fibrotic effects of FZHY, we analyzed transcriptomic and proteomic combination profiles in CCl4-induced liver fibrosis in rats, which were treated with extracted FZHY powder (0.35 g/kg/d, ig) for 3 weeks. We showed that FZHY administration significantly improved liver function, alleviated hepatic inflammatory and fibrotic changes, and decreased the hydroxyproline content in the livers of CCl4-treated rats...
November 2, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/29092939/explore-visualize-and-analyze-functional-cancer-proteomic-data-using-the-cancer-proteome-atlas
#9
Jun Li, Rehan Akbani, Wei Zhao, Yiling Lu, John N Weinstein, Gordon B Mills, Han Liang
Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications. The first one focuses on RPPA data of patient tumors, which contains >8,000 samples of 32 cancer types from The Cancer Genome Atlas and other independent patient cohorts...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29092938/p-martcancer-interactive-online-software-to-enable-analysis-of-shotgun-cancer-proteomic-datasets
#10
Bobbie-Jo M Webb-Robertson, Lisa M Bramer, Jeffrey L Jensen, Markus A Kobold, Kelly G Stratton, Amanda M White, Karin D Rodland
P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry-based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium at the peptide, gene, and protein levels...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29091996/visualization-portal-for-genetic-variation-vizgvar-a-tool-for-interactive-visualization-of-snps-and-somatic-mutations-in-exons-genes-and-protein-domains
#11
Antonio Solano Román, Verónica Alfaro, Carlos Cruz, Allan Orozco Solano
Motivation: VizGVar was designed to meet the growing need of the research community for improved genomic and proteomic data viewers that benefit from better information visualization. Results: We implemented a new information architecture and applied user centered design principles to provide a new improved way of visualizing genetic information and protein data related to human disease. VizGVar connects the entire database of Ensembl protein motifs, domains, genes and exons with annotated SNPs and somatic variations from PharmGKB and COSMIC...
October 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29056560/membrane-biology-visualized-in-nanometer-sized-discs-formed-by-styrene-maleic-acid-polymers
#12
REVIEW
Mansoore Esmaili, Michael Overduin
Discovering how membrane proteins recognize signals and passage molecules remains challenging. Life depends on compartmentalizing these processes into dynamic lipid bilayers that are technically difficult to work with. Several polymers have proven adept at separating the responsible machines intact for detailed analysis of their structures and interactions. Styrene maleic acid (SMA) co-polymers efficiently solubilize membranes into native nanodiscs and, unlike amphipols and membrane scaffold proteins, require no potentially destabilizing detergents...
October 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29036683/cr2cancer-a-database-for-chromatin-regulators-in-human-cancer
#13
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29029129/a-visual-review-of-the-human-pathogen-streptococcus-pneumoniae
#14
Ditte Høyer Engholm, Mogens Kilian, David S Goodsell, Ebbe Sloth Andersen, Rikke Schmidt Kjærgaard
Being the principal causative agent of bacterial pneumonia, otitis media, meningitis and septicemia, the bacterium Streptococcus pneumoniae is a major global health problem. To highlight the molecular basis of this problem, we have portrayed essential biological processes of the pneumococcal life cycle in eight watercolor paintings. The paintings are done to a consistent nanometer scale based on currently available data from structural biology and proteomics. In this review article, the paintings are used to provide a visual review of protein synthesis, carbohydrate metabolism, cell wall synthesis, cell division, teichoic acid synthesis, virulence, transformation and pilus synthesis based on the available scientific literature within the field of pneumococcal biology...
November 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29027734/high-resolution-visualization-and-exo-proteomics-reveal-the-physiological-role-of-xlnr-and-arar-in-plant-biomass-colonization-and-degradation-by-aspergillus-niger
#15
Joanna E Kowalczyk, Claire Khosravi, Samuel Purvine, Alice Dohnalkova, William B Chrisler, Galya Orr, Errol Robinson, Erika Zink, Ad Wiebenga, Mao Peng, Evy Battaglia, Scott Baker, Ronald P de Vries
In A. niger, two transcription factors, AraR and XlnR, regulate the production of enzymes involved in degradation of arabinoxylan and catabolism of the released L-arabinose and D-xylose. Deletion of both araR and xlnR in leads to reduced production of (hemi)cellulolytic enzymes and reduced growth on arabinan, arabinogalactan and xylan. In this study we investigated the colonization and degradation of wheat bran by the A. niger reference strain CBS 137562 and araR/xlnR regulatory mutants using high-resolution microscopy and exo-proteomics...
October 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29024724/paxgene-fixation-enables-comprehensive-metabolomic-and-proteomic-analyses-of-tissue-specimens-by-maldi-msi
#16
Christian Urban, Achim Buck, Jens T Siveke, Florian Lordick, Birgit Luber, Axel Walch, Michaela Aichler
An alcohol-based non-crosslinking tissue fixative, PAXgene Tissue System, has been proposed as alternative fixation method to formalin, providing superior and morphological preservation. To date, metabolites have not been assessed in PAXgene-fixed tissues. The study focuses on a comparison between PAXgene and standard formalin fixation for metabolomic analysis by MALDI mass spectrometry imaging. Therefore, fifty-six samples from seven mice organs were fixed with PAXgene (PFPE) or formalin (FFPE), embedded in paraffin, and processed to a tissue microarray...
January 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29019142/immunofluorescence-microscopy-for-dige-based-proteomics
#17
Rustam R Mundegar, Margit Zweyer, Dieter Swandulla
Alterations in the proteome of a tissue in different settings, as assessed by difference gel electrophoresis, can be verified for single proteins using immunohistochemistry. In fluorescence immunohistochemistry, an antibody to a particular antigen is applied to tissue sections, and fluorophores conjugated to a secondary antibody allow for the detection of target antigen with fluorescent microscopy. Visual comparison is sufficient for the detection of significant alterations in the abundance of a certain protein in different settings...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29019141/immunoblot-analysis-of-dige-based-proteomics
#18
Martin Landsberger, Heinrich Brinkmeier
Proteins can be separated according to their size by gel electrophoresis and further analyzed by Western blotting. The proteins can be transferred to a membrane made of nitrocellulose or polyvinylidene fluoride (PVDF), which results in a replica of the proteins' separation patterns. The proteins on the membrane can be detected by specific antibodies followed by visualization either on the membrane itself, on film or by CCD cameras. Western blotting is a sensitive technique to verify data obtained from difference gel electrophoresis (DIGE)-based proteomics...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29019132/rapid-2d-dige-proteomic-analysis-of-mouse-liver
#19
Shotaro Kamata, Isao Ishii
Several years have passed since LC-MS(/MS) became the mainstream for proteomic analysis; however, conventional 2D DIGE (two-dimensional difference gel electrophoresis) continues to be an important technology that enables rapid and direct visualization of hundreds to thousands of proteins and their quantitative analyses. We can get global proteomic views using 2D DIGE within 3 days, and then identify proteins with differential expression levels using MALDI-TOF/MS and MASCOT search engine within a week. Here, we describe our routine 2D DIGE proteomic analysis of the liver isolated from mice in pathological conditions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29019125/comparative-two-dimensional-fluorescence-gel-electrophoresis
#20
Doreen Ackermann, Simone König
Two-dimensional comparative fluorescence gel electrophoresis (CoFGE) uses an internal standard to increase the reproducibility of coordinate assignment for protein spots visualized on 2D polyacrylamide gels. This is particularly important for samples, which need to be compared without the availability of replicates and thus cannot be studied using differential gel electrophoresis (DIGE). CoFGE corrects for gel-to-gel variability by co-running with the sample proteome a standardized marker grid of 80-100 nodes, which is formed by a set of purified proteins...
2018: Methods in Molecular Biology
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