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proteomics and visualization

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https://www.readbyqxmd.com/read/28199731/proteomic-profiling-analysis-reveals-a-link-between-experimental-autoimmune-uveitis-and-complement-activation-in-rats
#1
Dadong Guo, Bing Hu, Hongying Tang, Yuanyuan Sun, Bin Liu, Qingmei Tian, Hongsheng Bi
Uveitis is an autoimmune disease that usually damages the vision function, leading to poor visual quality in patients. As an autoimmune ocular inflammatory disease, the pathogenesis of uveitis is associated with abnormal expression of some proteins and aberrant regulation of multiple signaling pathways. Nevertheless, the detailed mechanism remains unclear. In this study, we induced an experimental autoimmune uveitis (EAU) model in rats. We determined the levels of C3a and membrane attack complex C5b-9 (soluble C5b-9, sC5b-9) in both plasma and aqueous humor, identified the differentially expressed proteins in plasma by liquid chromatography-tandem mass spectrometry, and employed bioinformatics algorithms to analyze differentially expressed proteins in EAU rat plasma...
February 15, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28188539/statistical-assessment-of-qc-metrics-on-raw-lc-ms-ms-data
#2
Xia Wang
Data quality assessment is important for reproducibility of proteomics experiments and reusability of proteomics data. We describe a set of statistical tools to routinely visualize and examine the quality control (QC) metrics obtained for raw LC-MS/MS data on different instrument types and mass spectrometers. The QC metrics used here are the identification free QuaMeter metrics. Statistical assessments introduced include (a) principal component analysis, (b) dissimilarity measures, (c) T (2)-chart for quality control, and (d) change point analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28188532/pathway-informed-discovery-and-targeted-proteomic-workflows-using-mass-spectrometry
#3
Caroline S Chu, Christine A Miller, Andy Gieschen, Steve M Fischer
Recent advancements in mass spectrometry (MS) and data analysis software have enabled new strategies for biological discovery using proteomics. Proteomics has evolved from routine discovery and identification of proteins to integrated multi-omics projects relating specific proteins to their genes and metabolites. Using additional information, such as that contained in biological pathways, has enabled the use of targeted protein quantitation for monitoring fold changes in expression as well as biomarker discovery...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28187409/pgminer-reloaded-fully-automated-proteogenomic-annotation-tool-linking-genomes-to-proteomes
#4
Canan Has, Sergey A Lashin, Alexey V Kochetov, Jens Allmer
Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28186866/toward-postgenomics-ophthalmology-a-proteomic-map-of-the-human-choroid-retinal-pigment-epithelium-tissue
#5
Manjunath Dammalli, Krishna R Murthy, Sneha M Pinto, Kalpana Babu Murthy, Raja Sekhar Nirujogi, Anil K Madugundu, Gourav Dey, Bipin Nair, Harsha Gowda, Thottethodi Subrahmanya Keshava Prasad
Ophthalmology and visual health research have received relatively limited attention from the personalized medicine community, but this trend is rapidly changing. Postgenomics technologies such as proteomics are being utilized to establish a baseline biological variation map of the human eye and related tissues. In this context, the choroid is the vascular layer situated between the outer sclera and the inner retina. The choroidal circulation serves the photoreceptors and retinal pigment epithelium (RPE). The RPE is a layer of cuboidal epithelial cells adjacent to the neurosensory retina and maintains the outer limit of the blood-retina barrier...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186774/quantitative-map-of-%C3%AE-lactone-induced-virulence-regulation
#6
Joanna Krysiak, Matthias Stahl, Jan Vomacka, Christian Fetzer, Markus Lakemeyer, Anja Fux, Stephan A Sieber
β-Lactones have recently been introduced as the first selective ClpP inhibitors that attenuate virulence of both sensitive Staphylococcus aureus and multiresistant strains (MRSA). Although previous knockout studies showed that ClpP is essential for S. aureus alpha-toxin production, a link between β-lactone inhibition and molecular virulence mechanisms has been lacking so far. We here perform a chemical-proteomic approach to elucidate antivirulence pathways. First, we demonstrate by gel-free activity-based protein profiling that ClpP is the predominant target of β-lactones...
February 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28174738/microgeographic-proteomic-networks-of-the-human-colonic-mucosa-and-their-association-with-inflammatory-bowel-disease
#7
Xiaoxiao Li, James LeBlanc, David Elashoff, Ian McHardy, Maomeng Tong, Bennett Roth, Andrew Ippoliti, Gildardo Barron, Dermot McGovern, Keely McDonald, Rodney Newberry, Thomas Graeber, Steve Horvath, Lee Goodglick, Jonathan Braun
BACKGROUND & AIMS: Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal-luminal interface to study the disease-related biology of the human colonic mucosa. METHODS: We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28174513/cervical-mucus-proteome-in-endometriosis
#8
Giuseppe Grande, Federica Vincenzoni, Domenico Milardi, Giuseppina Pompa, Domenico Ricciardi, Erika Fruscella, Francesca Mancini, Alfredo Pontecorvi, Massimo Castagnola, Riccardo Marana
BACKGROUND: Endometriosis is a chronic gynecological inflammatory disease characterized by the presence of functional endometrial glands and stroma outside of the uterine cavity. It affects 7-10% of women of reproductive age and up to 50% of women with infertility. The current gold standard for the diagnosis combines laparoscopic evaluation and biopsy of the visualized lesions. However, laparoscopy requires general anesthesia and developed surgical skills and it has a high procedural cost...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28154130/trifunctional-lipid-probes-for-comprehensive-studies-of-single-lipid-species-in-living-cells
#9
Doris Höglinger, André Nadler, Per Haberkant, Joanna Kirkpatrick, Martina Schifferer, Frank Stein, Sebastian Hauke, Forbes D Porter, Carsten Schultz
Lipid-mediated signaling events regulate many cellular processes. Investigations of the complex underlying mechanisms are difficult because several different methods need to be used under varying conditions. Here we introduce multifunctional lipid derivatives to study lipid metabolism, lipid-protein interactions, and intracellular lipid localization with a single tool per target lipid. The probes are equipped with two photoreactive groups to allow photoliberation (uncaging) and photo-cross-linking in a sequential manner, as well as a click-handle for subsequent functionalization...
February 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28152603/large-scale-and-targeted-quantitative-cross-linking-ms-using-isotope-labeled-protein-interaction-reporter-pir-cross-linkers
#10
Xuefei Zhong, Arti T Navare, Juan D Chavez, Jimmy K Eng, Devin K Schweppe, James E Bruce
Quantitative measurement of chemically cross-linked proteins is crucial to reveal dynamic information about protein structures and protein-protein interactions and how these are differentially regulated during stress, aging, drug treatment, and most perturbations. Previously, we demonstrated how quantitative in vivo cross-linking (CL) with stable isotope labeling of amino acids in cell culture (SILAC) enables both heritable and dynamic changes in cells to be visualized. In this work, we demonstrate the technical feasibility of proteome-scale quantitative in vivo CL-MS using isotope-labeled protein interaction reporter (PIR) cross-linkers and E...
February 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28150236/bioinformatics-analysis-of-protein-phosphorylation-in-plant-systems-biology-using-p3db
#11
Qiuming Yao, Dong Xu
Protein phosphorylation is one of the most pervasive protein post-translational modification events in plant cells. It is involved in many plant biological processes, such as plant growth, organ development, and plant immunology, by regulating or switching signaling and metabolic pathways. High-throughput experimental methods like mass spectrometry can easily characterize hundreds to thousands of phosphorylation events in a single experiment. With the increasing volume of the data sets, Plant Protein Phosphorylation DataBase (P3DB, http://p3db...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28139890/pharmacogenomics-of-17-alpha-hydroxyprogesterone-caproate-for-recurrent-preterm-birth-a-case-control-study
#12
T A Manuck, W S Watkins, M S Esplin, J Biggio, R Bukowski, S Parry, H Zhan, H Huang, W Andrews, G Saade, Y Sadovsky, U M Reddy, J Ilekis, M Yandell, M W Varner, L B Jorde
OBJECTIVE: To compare maternal genotypes between women with and without significant prolongation of pregnancy in the setting of 17-alpha hydroxyprogesterone caproate (17-P) administration for the prevention of recurrent preterm birth (PTB). DESIGN: Case-control. SETTING: Three tertiary-care centres across the USA. POPULATION: Women (n = 99) with ≥ 1 prior singleton spontaneous PTB, receiving 17-P. METHODS: Women were classified as having successful prolongation of pregnancy during the 17-P treated pregnancy, in two ways: (1) Definition A: success/non-success based on difference in gestational age at delivery between 17-P-treated and untreated pregnancies (success: delivered ≥ 3 weeks later with 17-P) and (2) Definition B: success/non-success based on reaching term (success: delivered at term with 17-P)...
January 31, 2017: BJOG: An International Journal of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28128880/single-cell-proteomics-in-biomedicine-high-dimensional-data-acquisition-visualization-and-analysis
#13
Yapeng Su, Qihui Shi, Wei Wei
New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data...
January 27, 2017: Proteomics
https://www.readbyqxmd.com/read/28122643/identification-of-potential-saliva-and-tear-biomarkers-in-primary-sj%C3%A3-gren-s-syndrome-utilising-the-extraction-of-extracellular-vesicles-and-proteomics-analysis
#14
Lara A Aqrawi, Hilde Kanli Galtung, Beate Vestad, Reidun Øvstebø, Bernd Thiede, Shermin Rusthen, Alix Young, Eduarda M Guerreiro, Tor Paaske Utheim, Xiangjun Chen, Øygunn Aass Utheim, Øyvind Palm, Janicke Liaaen Jensen
BACKGROUND: There is a long-lasting need for non-invasive, more accurate diagnostic techniques when evaluating primary Sjögren's syndrome (pSS) patients. Incorporation of additional diagnostics involving screening for disease-specific biomarkers in biological fluid is a promising concept that requires further investigation. In the current study we aimed to explore novel disease biomarkers in saliva and tears from pSS patients. METHODS: Liquid chromatography-mass spectrometry (LC-MS) was performed on stimulated whole saliva and tears from 27 pSS patients and 32 healthy controls, and salivary and tear proteomic biomarker profiles were generated...
January 25, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28117783/a-rapid-scalable-method-for-the-isolation-functional-study-and-analysis-of-cell-derived-extracellular-matrix
#15
Andrew L Hellewell, Silvia Rosini, Josephine C Adams
The extracellular matrix (ECM) is recognized as a diverse, dynamic, and complex environment that is involved in multiple cell-physiological and pathological processes. However, the isolation of ECM, from tissues or cell culture, is complicated by the insoluble and cross-linked nature of the assembled ECM and by the potential contamination of ECM extracts with cell surface and intracellular proteins. Here, we describe a method for use with cultured cells that is rapid and reliably removes cells to isolate a cell-derived ECM for downstream experimentation...
January 4, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28112434/label-free-deep-shotgun-proteomics-reveals-protein-dynamics-during-tomato-fruit-tissues-development
#16
Jedrzej Szymanski, Yishai Levin, Alon Savidor, Dario Breitel, Louise Chappell-Maor, Uwe Heinig, Nadine Töpfer, Asaph Aharoni
Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large-scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages. The depth of our assay enabled identification of 61 differentially expressed transcription factors including renowned ripening-related regulators and elements of ethylene signaling...
January 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28106223/next-generation-of-network-medicine-interdisciplinary-signaling-approaches
#17
REVIEW
Tamas Korcsmaros, Maria Victoria Schneider, Giulio Superti-Furga
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more...
January 20, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28104718/boncat-enables-time-resolved-analysis-of-protein-synthesis-in-native-plant-tissue
#18
Weslee Glenn, Shannon E Stone, Samuel H Ho, Michael J Sweredoski, Annie Moradian, Sonja Hess, Julia Bailey-Serres, David A Tirrell
Proteomic plasticity undergirds stress responses in plants, and understanding such responses requires accurate measurement of the extent to which proteins levels are adjusted to counter external stimuli. Here, we adapt bioorthogonal non-canonical amino acid tagging (BONCAT) to interrogate protein synthesis in vegetative Arabidopsis thaliana seedlings. BONCAT relies on the translational incorporation of a non-canonical amino acid (ncAA) probe into cellular proteins. In this study, the probe is the methionine surrogate azidohomoalanine (Aha), which carries a reactive azide moiety in its amino acid side chain...
January 19, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28092651/long-lasting-antinociceptive-effects-of-green-light-in-acute-and-chronic-pain-in-rats
#19
Mohab M Ibrahim, Amol Patwardhan, Kerry B Gilbraith, Aubin Moutal, Xiaofang Yang, Lindsey A Chew, Tally Largent-Milnes, T Philip Malan, Todd W Vanderah, Frank Porreca, Rajesh Khanna
Treatments for chronic pain are inadequate, and new options are needed. Nonpharmaceutical approaches are especially attractive with many potential advantages including safety. Light therapy has been suggested to be beneficial in certain medical conditions such as depression, but this approach remains to be explored for modulation of pain. We investigated the effects of light-emitting diodes (LEDs), in the visible spectrum, on acute sensory thresholds in naive rats as well as in experimental neuropathic pain...
February 2017: Pain
https://www.readbyqxmd.com/read/28092030/proteomic-clustering-analysis-of-sh2-domain-datasets
#20
Karl Jablonowski
Proteomic clustering analysis provides a means of identifying relationships and visualizing those relationships in an extremely complex field of study with many interacting parts. With recent high-throughput studies of Src Homology 2 (SH2) domains, many and varied datasets are being amassed. A strategy for analyzing patterns between these large datasets is required to transform the information into knowledge. The methods for creating neighbor-joining phylogenetic trees, pairs scatter plots, and two-dimensional hierarchical clustering heatmaps are just a few of the diverse methods available to a proteomic researcher...
2017: Methods in Molecular Biology
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