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https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#1
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899614/suba4-the-interactive-data-analysis-centre-for-arabidopsis-subcellular-protein-locations
#2
Cornelia M Hooper, Ian R Castleden, Sandra K Tanz, Nader Aryamanesh, A Harvey Millar
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27890865/csf-pr-2-0-an-interactive-literature-guide-to-quantitative-cerebrospinal-fluid-mass-spectrometry-data-from-neurodegenerative-disorders
#3
Astrid Guldbrandsen, Yehia Farag, Ann C Kroksveen, Eystein Oveland, Ragnhild R Lereim, Jill A Opsahl, Kjell-Morten Myhr, Frode S Berven, Harald Barsnes
The rapidly growing number of biomedical studies supported by mass spectrometry based quantitative proteomics data has made it increasingly difficult to obtain an overview of the current status of the research field. A better way of organizing the biomedical proteomics information from these studies and making it available to the research community is therefore called for. In the presented work, we have investigated scientific publications describing the analysis of the cerebrospinal fluid proteome in relation to multiple sclerosis, Parkinsons disease and Alzheimers disease...
November 27, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27877091/conserved-chemosensory-proteins-in-the-proboscis-and-eyes-of-lepidoptera
#4
Jiao Zhu, Immacolata Iovinella, Francesca Romana Dani, Yu-Ling Liu, Ling-Qiao Huang, Yang Liu, Chen-Zhu Wang, Paolo Pelosi, Guirong Wang
Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are endowed with several different functions besides being carriers for pheromones and odorants. Based on a previous report of a CSP acting as surfactant in the proboscis of the moth Helicoverpa armigera, we revealed the presence of orthologue proteins in two other moths Plutella xylostella and Chilo suppressalis, as well as two butterflies Papilio machaon and Pieris rapae, using immunodetection and proteomic analysis. The unusual conservation of these proteins across large phylogenetic distances indicated a common specific function for these CSPs...
2016: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/27864160/blotting-free-and-lossless-cryo-electron-microscopy-grid-preparation-from-nanoliter-sized-protein-samples-and-single-cell-extracts
#5
Stefan A Arnold, Stefan Albiez, Andrej Bieri, Anastasia Syntychaki, Ricardo Adaixo, Robb A McLeod, Kenneth N Goldie, Henning Stahlberg, Thomas Braun
We present a sample preparation method for cryo-electron microscopy (cryo-EM) that requires only 3 to 20 nanoliters of sample to prepare a cryo-EM grid, depending on the protocol used. The sample is applied and spread on the grid by a microcapillary. The procedure does not involve any blotting steps, and real-time monitoring allows the water film thickness to be assessed and decreased to an optimum value prior to vitrification. We demonstrate that the method is suitable for high-resolution cryo-EM and will enable alternative electron microscopy approaches, such as single-cell visual proteomics...
November 15, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27851981/panget-pan-genomics-tool
#6
Iyyappan Yuvaraj, Jayavel Sridhar, Daliah Michael, Kanagaraj Sekar
A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to understand their physiology and gain insights into the mechanism of genome evolution. Subsequently, this will aid in identifying diagnostic targets and in developing and selecting vaccines...
November 13, 2016: Gene
https://www.readbyqxmd.com/read/27830853/integration-of-fluorescence-imaging-with-proteomics-enables-visualization-and-identification-of-metallo-proteomes-in-living-cells
#7
Yau-Tsz Lai, Ya Yang, Ligang Hu, Tianfan Cheng, Yuen-Yan Chang, Mohamad Koohi-Moghadam, Yuchuan Wang, Jiang Xia, Junwen Wang, Hongyan Li, Hongzhe Sun
Metalloproteins account for nearly one-third of proteins in proteomes. To date, the identification of metalloproteins relies mainly on protein purification and the subsequent characterization of bound metals, which often leads to losses of metal ions bound weakly and transiently. Herein, we developed a strategy to visualize and subsequently identify endogenous metalloproteins and metal-binding proteins in living cells via integration of fluorescence imaging with proteomics. We synthesized a "metal-tunable" fluorescent probe (denoted as M(n+)-TRACER) that rapidly enters cells to target proteins with 4-40 fold fluorescence enhancements...
November 10, 2016: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/27805363/nitrilase-activatable-noncanonical-amino-acid-precursors-for-cell-selective-metabolic-labeling-of-proteomes
#8
Zefan Li, Yuntao Zhu, Yuting Sun, Ke Qin, Weibing Liu, Wen Zhou, Xing Chen
Cell-selective protein metabolic labeling is of great interest for studying cell-cell communications and tissue homeostasis. We herein describe a nitrilase-activatable noncanonical amino acid tagging (NANCAT) strategy that exploits an exogenous nitrilase to enzymatically convert the nitrile-substituted precursors to their corresponding noncanonical amino acids (ncAAs), l-azidohomoalanine (Aha) or homopropargylglycine (Hpg), in living cells. Only cells expressing the nitrilase can generate Aha or Hpg in cellulo and metabolically incorporate them into the nascent proteins...
November 2, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/27784647/annexin-a2-and-alpha-actinin-4-expression-correlates-with-metastatic-potential-of-primary-endometrial-cancer
#9
Parul Mittal, Manuela Klingler-Hoffmann, Georgia Arentz, Lyron Winderbaum, Gurjeet Kaur, Lyndal Anderson, James Scurry, Yee Leung, Colin Jr Stewart, Jonathan Carter, Peter Hoffmann, Martin K Oehler
The prediction of lymph node metastasis using clinic-pathological data and molecular information from endometrial cancers lacks accuracy and is therefore currently not routinely used in patient management. Consequently, although only a small percentage of patients with endometrial cancers suffer from metastasis, the majority undergo radical surgery including removal of pelvic lymph nodes. Upon analysis of publically available data and published research, we compiled a list of 60 proteins having the potential to display differential abundance between primary endometrial cancers with versus those without lymph node metastasis...
October 23, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27778282/activity-based-lipid-esterase-profiling-of-m-bovis-bcg-at-different-metabolic-states-using-tetrahydrolipstatin-thl-as-bait
#10
Madhu Sudhan Ravindran, Markus R Wenk
This chapter provides a step-by-step protocol using activity-based protein profiling (ABPP) as a chemical-proteomic tool to survey the antibiotic properties of a small molecule. Here, we investigate the molecular mechanism behind the bactericidal activity of tetrahydrolipstatin (THL). ABPP relies on small molecule probes that target the active site of specific enzymes in complex proteomes. These probes in turn are equipped with a reporter tag that allows capturing, visualization, enrichment, identification, and quantification of its targets either in vitro or in situ...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27771868/proteome-rebalancing-in-transgenic-camelina-occurs-within-the-enlarged-proteome-induced-by-%C3%AE-carotene-accumulation-and-storage-protein-suppression
#11
Monica A Schmidt, Ken Pendarvis
Oilseed crops are global commodities for their oil and protein seed content. We have engineered the oilseed Camelina sativa to exhibit increased protein content with a slight decrease in oil content. The introduction of a phytoene synthase gene with an RNAi cassette directed to suppress the storage protein 2S albumin resulted in seeds with an 11-24 % elevation in overall protein. The phytoene synthase cassette alone produced enhanced β-carotene content of an average 275 ± 6.10 μg/g dry seed and an overall altered seed composition of 11 % less protein and comparable nontransgenic amounts of both oil and carbohydrates...
October 22, 2016: Transgenic Research
https://www.readbyqxmd.com/read/27755872/in-situ-characterization-of-tissue-resident-immune-cells-by-maldi-mass-spectrometry-imaging
#12
Matthias Holzlechner, Katharina Strasser, Elitsa Zareva, Luise Steinhaeuser, Hanna Birnleitner, Andrea Beer, Michael Bergmann, Rudolf Oehler, Martina Marchetti-Deschmann
Tissue-resident immune cells differ from the corresponding blood cells in many functional aspects. Although the proteome of blood immune cells is well investigated there are almost no data on tissue-resident immune cells. Here we explored the potential of MALDI-TOF-MS imaging (MSI) to investigate these cells in colon tissue, which exhibits a strong immune infiltration. MSI identified several proteinaceous markers that colocalized with specific structures of the colon such as mucosa or muscularis mucosae in six patients...
October 18, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27755556/muscadine-grape-skin-extract-induces-an-unfolded-protein-response-mediated-autophagy-in-prostate-cancer-cells-a-tmt-based-quantitative-proteomic-analysis
#13
Liza J Burton, Mariela Rivera, Ohuod Hawsawi, Jin Zou, Tamaro Hudson, Guangdi Wang, Qiang Zhang, Luis Cubano, Nawal Boukli, Valerie Odero-Marah
Muscadine grape skin extract (MSKE) is derived from muscadine grape (Vitis rotundifolia), a common red grape used to produce red wine. Endoplasmic reticulum (ER) stress activates the unfolded protein response (UPR) that serves as a survival mechanism to relieve ER stress and restore ER homeostasis. However, when persistent, ER stress can alter the cytoprotective functions of the UPR to promote autophagy and cell death. Although MSKE has been documented to induce apoptosis, it has not been linked to ER stress/UPR/autophagy...
2016: PloS One
https://www.readbyqxmd.com/read/27742821/hieranoidb-a-database-of-orthologs-inferred-by-hieranoid
#14
Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L L Sonnhammer
HieranoiDB (http://hieranoiDB.sbc.su.se) is a freely available on-line database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. It infers orthologs at each node in a species guide tree with the InParanoid algorithm as it progresses from the leaves to the root. Here we present a database HieranoiDB with a web interface that makes it easy to search and visualize the output of Hieranoid, and to download it in various formats. Searching can be performed using protein description, identifier or sequence...
October 13, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27733501/the-human-induced-pluripotent-stem-cell-initiative-data-resources-for-cellular-genetics
#15
Ian Streeter, Peter W Harrison, Adam Faulconbridge, Paul Flicek, Helen Parkinson, Laura Clarke
The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases...
October 12, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27725197/in%C3%A2-vitro-secretomics-study-of-pterygium-derived-fibroblasts-by-itraq-based-quantitative-proteomics-strategy
#16
Aihua Hou, Kai Pong Law, Min Qi Tin, Yoon Pin Lim, Louis Tong
Pterygium is a triangular shaped ocular fibrous surface lesion growing from conjunctiva towards central cornea, causing ocular irritation, astigmatism, and visual disturbance. The condition is characterized by epithelial proliferation, fibrovascular growth, chronic inflammation, and prominent extracellular matrix remodeling. Studies have suggested that aberrant extracellular proteins secreted by fibroblasts lead to abnormal matrix production and tissue invasion contributing to the development of the disease...
October 8, 2016: Experimental Eye Research
https://www.readbyqxmd.com/read/27716029/simulating-cryo-electron-tomograms-of-crowded-cell-cytoplasm-for-assessment-of-automated-particle-picking
#17
Long Pei, Min Xu, Zachary Frazier, Frank Alber
BACKGROUND: Cryo-electron tomography is an important tool to study structures of macromolecular complexes in close to native states. A whole cell cryo electron tomogram contains structural information of all its macromolecular complexes. However, extracting this information remains challenging, and relies on sophisticated image processing, in particular for template-free particle extraction, classification and averaging. To develop these methods it is crucial to realistically simulate tomograms of crowded cellular environments, which can then serve as ground truth models for assessing and optimizing methods for detection of complexes in cell tomograms...
October 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27704949/visualizing-the-architectures-and-interactions-of-nuclear-receptors
#18
Sepideh Khorasanizadeh, Fraydoon Rastinejad
Nuclear receptors (NRs) are master regulators of broad genetic programs in metazoans. These programs are regulated in part by the small-molecule ligands that bind NRs and modulate their interactions with transcriptional coregulatory factors. X-ray crystallography is now delivering more complete pictures of how the multi-domain architectures of NR homo- and heterodimers are physically arranged on their DNA elements, and how ligands and coactivator peptides act through these complexes. Complementary studies are also pointing to a variety of novel mechanisms by which NRs access their DNA response elements within chromatin...
October 5, 2016: Endocrinology
https://www.readbyqxmd.com/read/27700092/an-automated-pipeline-to-monitor-system-performance-in-liquid-chromatography-tandem-mass-spectrometry-proteomic-experiments
#19
Michael S Bereman, Joshua Beri, Vagisha Sharma, Cory Nathe, Josh Eckels, Brendan MacLean, Michael J MacCoss
We report the development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments. LC-MS/MS runs are automatically imported into Skyline and multiple identification-free metrics are extracted from targeted peptides. These data are then uploaded to the Panorama Skyline document repository where metrics can be viewed in a web-based interface using powerful process control techniques, including Levey-Jennings and Pareto plots. The interface is versatile and takes user input, which allows the user significant control over the visualization of the data...
October 4, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27680298/apostl-an-interactive-galaxy-pipeline-for-reproducible-analysis-of-affinity-proteomics-data
#20
Brent M Kuenzi, Adam L Borne, Jiannong Li, Eric B Haura, Steven A Eschrich, John M Koomen, Uwe Rix, Paul A Stewart
With continuously increasing scale and depth of coverage in affinity proteomics (AP-MS) data, the analysis and visualization is becoming more challenging. A number of tools have been developed to identify high-confidence interactions; however, a cohesive and intuitive pipeline for analysis and visualization is still needed. Here we present Automated Processing of SAINT Templated Layouts (APOSTL), a freely available Galaxy-integrated software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data...
October 21, 2016: Journal of Proteome Research
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