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proteomics and visualization

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https://www.readbyqxmd.com/read/28755236/date-fruit-proteomics-during-development-and-ripening-stages
#1
Claudius Marondedze
Gel-based comparative proteomics approach is a valuable technique for studying the changes in abundance of proteins in any given system. The combination of this technique with mass spectrometry has provided immense insight into protein dynamics during fruit development and ripening. This chapter describes, informatively, the procedures for carrying out comparative proteomics analysis of date palm (Phoenix dactylifera L.) fruits at different developmental stages using a combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometry...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28754825/fluorescent-imaging-of-protein-myristoylation-during-cellular-differentiation-and-development
#2
Andrew J Witten, Karin F K Ejendal, Lindsey M Gengelbach, Meghan A Traore, Xu Wang, David M Umulis, Sarah Calve, Tamara L Kinzer-Ursem
Protein post-translational modifications (PTMs) serve to give proteins new cellular functions and can influence spatial localization and enzymatic activity; greatly enriching the complexity of the proteome. Lipidation is a PTM that regulates protein stability, function and subcellular localization. To complement advances in proteomic identification of lipidated proteins, we have developed methods to image the spatial distribution of proteins that have been co- and post-translationally modified via the addition of myristic acid to the N-terminus...
July 28, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28747503/identification-of-vaccinia-virus-replisome-and-transcriptome-proteins-by-ipond-coupled-with-mass-spectrometry
#3
Tatiana G Senkevich, George Katsafanas, Andrea Weisberg, Lisa R Olano, Bernard Moss
Poxviruses replicate within the cytoplasm and encode proteins for DNA and mRNA synthesis. To investigate poxvirus replication and transcription from a new perspective, we incorporated 5-ethynyl-2' -deoxyuridine (EdU) into nascent DNA in cells infected with vaccinia virus (VACV). The EdU-labeled DNA was conjugated to fluor- or biotin-azide and visualized by confocal, super resolution and transmission electron microscopy. Nuclear labeling decreased dramatically after infection, accompanied by intense labeling of cytoplasmic foci...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28735397/global-proteomic-profiling-and-identification-of-stress-responsive-proteins-using-two-dimensional-gel-electrophoresis
#4
Pragya Barua, Dipak Gayen, Nilesh Vikram Lande, Subhra Chakraborty, Niranjan Chakraborty
Global proteome profiling is a direct representation of the protein set in an organism, organ, tissues, or an organelle. One of the main objectives of proteomic analysis is the comparison and relative quantitation of proteins under a defined set of conditions. Two-dimensional gel electrophoresis (2-DE) has gained prominence over the last 4 decades for successfully aiding differential proteomics, providing visual confirmation of changes in protein abundance, which otherwise cannot be predicted from genome analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#5
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28729539/comparative-proteomic-analysis-of-human-embryonic-stem-cell-derived-and-primary-human-retinal-pigment-epithelium
#6
Heidi Hongisto, Antti Jylhä, Janika Nättinen, Jochen Rieck, Tanja Ilmarinen, Zoltán Veréb, Ulla Aapola, Roger Beuerman, Goran Petrovski, Hannu Uusitalo, Heli Skottman
Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) provide an unlimited cell source for retinal cell replacement therapies. Clinical trials using hESC-RPE to treat diseases such as age-related macular degeneration (AMD) are currently underway. Human ESC-RPE cells have been thoroughly characterized at the gene level but their protein expression profile has not been studied at larger scale. In this study, proteomic analysis was used to compare hESC-RPE cells differentiated from two independent hESC lines, to primary human RPE (hRPE) using Isobaric tags for relative quantitation (iTRAQ)...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728879/identification-of-universal-diagnostic-peptide-candidates-for-neglected-tropical-diseases-caused-by-cestodes-through-the-integration-of-multi-genome-wide-analyses-and-immunoinformatic-predictions
#7
Sebastián Miles, Marco Navatta, Sylvia Dematteis, Gustavo Mourglia-Ettlin
Neglected tropical diseases caused by helminth infections currently affect millions of people worldwide. Among them, there are three tapeworm species of outstanding importance: Echinococcus granulosus, E. multilocularis, and Taenia solium, which are responsible for cystic echinococcosis, alveolar echinococcosis, and cysticercosis, respectively. Despite several attempts, there is still a need for an effective and low-cost serological diagnostic test that can be used in endemic countries. In the present work, we described an innovative bioinformatic workflow for a rational prediction of putative peptide candidates for one-step serological diagnosis of any of these infections...
July 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28726848/patch-clamp-technique-to-characterize-ion-channels-in-enlarged-individual-endolysosomes
#8
Cheng-Chang Chen, Chunlei Cang, Stefanie Fenske, Elisabeth Butz, Yu-Kai Chao, Martin Biel, Dejian Ren, Christian Wahl-Schott, Christian Grimm
According to proteomics analyses, more than 70 different ion channels and transporters are harbored in membranes of intracellular compartments such as endosomes and lysosomes. Malfunctioning of these channels has been implicated in human diseases such as lysosomal storage disorders, neurodegenerative diseases and metabolic pathologies, as well as in the progression of certain infectious diseases. As a consequence, these channels have engendered very high interest as future drug targets. Detailed electrophysiological characterization of intracellular ion channels is lacking, mainly because standard methods to analyze plasma membrane ion channels, such as the patch-clamp technique, are not readily applicable to intracellular organelles...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28726736/protozoadb-2-0-a-trypanosoma-brucei-case-study
#9
Rodrigo Jardim, Diogo Tschoeke, Alberto M R Da Vila
Over the last decade new species of Protozoa have been sequenced and deposited in GenBank. Analyzing large amounts of genomic data, especially using Next Generation Sequencing (NGS), is not a trivial task, considering that researchers used to deal or focus their studies on few genes or gene families or even small genomes. To facilitate the information extraction process from genomic data, we developed a database system called ProtozoaDB that included five genomes of Protozoa in its first version. In the present study, we present a new version of ProtozoaDB called ProtozoaDB 2...
July 20, 2017: Pathogens
https://www.readbyqxmd.com/read/28710380/biological-analysis-of-cancer-specific-micrornas-on-function-modeling-in-osteosarcoma
#10
Hao Wang, Min Tang, Liping Ou, Mengyi Hou, Tianyu Feng, Yu-E Huang, Yaqian Jin, Heng Zhang, Guowei Zuo
Osteosarcoma (OS) is the most common bone tumor characterized with a high risk of amputation and malignant morbidity among teenagers and adolescents. However, relevant pathogenic/biological mechanisms underlying OS-genesis remains to be ambiguous. The aim of this study was to elucidate functional relationship about microRNAs-mRNAs networks and to identify potential molecular markers via a computational method. Gene expression profile (GSE70415) was recruited from Gene Expression Omnibus. 3856 differentially expressed genes and 250 significantly expressed microRNAs were identified by using GCBI...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28672066/a-low-molecular-weight-color-pi-markers-to-monitor-on-line-the-peptide-focusing-process-in-offgel-fractionation
#11
Sylvie Michelland, Sandrine Bourgoin-Voillard, Valérie Cunin, Axel Tollance, Pascal Bertolino, Karel Slais, Michel Seve
High-throughput mass spectrometry-based proteomic analysis requires peptide fractionation to simplify complex biological samples and increase proteome coverage. OFFGEL fractionation technology became a common method to separate peptides or proteins using isoelectric focusing in an immobilized pH gradient. However, the OFFGEL focusing process may be further optimized and controlled in terms of separation time and pI resolution. Here, we evaluated OFFGEL technology to separate peptides from different samples in the presence of low-molecular-weight (LMW) color pI markers to visualize the focusing process...
July 3, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28669375/morphogenesis-related-gene-expression-profile-in-porcine-oocytes-before-and-after-in-vitro-maturation
#12
Joanna Budna, Adrian Chachuła, Dominika Kaźmierczak, Marta Rybska, Sylwia Ciesiółka, Artur Bryja, Wiesława Kranc, Sylwia Borys, Agnieszka Żok, Dorota Bukowska, Paweł Antosik, Małgorzata Bruska, Klaus P Brüssow, Michał Nowicki, Maciej Zabel, Bartosz Kempisty
Mammalian oocyte maturation is achieved when oocytes reach metaphase II (MII) stage, and accumulate mRNA and proteins in the cytoplasm following fertilization. It has been shown that oocytes investigated before and after in vitro maturation (IVM) differ significantly in transcriptomic and proteomic profiles. Additionally, folliculogenesis and oogenesis is accompanied by morphogenetic changes, which significantly influence further zygote formation and embryo growth. This study aimed to determine new transcriptomic markers of porcine oocyte morphogenesis that are associated with cell maturation competence...
June 2017: Zygote: the Biology of Gametes and Early Embryos
https://www.readbyqxmd.com/read/28665768/identification-of-a-sensitive-urinary-biomarker-selenium-binding-protein-1-for-early-detection-of-acute-kidney-injury
#13
Kyeong Seok Kim, Hun Yong Yang, Hosup Song, Ye Rim Kang, JiHoon Kwon, JiHye An, Ji Yeon Son, Seung Jun Kwack, Young-Mi Kim, Ok-Nam Bae, Mee-Young Ahn, Jaewon Lee, Sungpil Yoon, Byung Mu Lee, Hyung Sik Kim
Acute kidney injury (AKI) is associated with increased mortality rate in patients but clinically available biomarkers for disease detection are currently not available. Recently, a new biomarker, selenium-binding protein 1 (SBP1), was identified for detection of nephrotoxicity using proteomic analysis. The aim of this study was to assess the sensitivity of urinary SBP1 levels as an early detection of AKI using animal models such as cisplatin or ischemia/reperfusion (I/R). Sprague-Dawley rats were injected with cisplatin (6 mg/kg, once i...
June 30, 2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/28661499/prohits-viz-a-suite-of-web-tools-for-visualizing-interaction-proteomics-data
#14
James D R Knight, Hyungwon Choi, Gagan D Gupta, Laurence Pelletier, Brian Raught, Alexey I Nesvizhskii, Anne-Claude Gingras
No abstract text is available yet for this article.
June 29, 2017: Nature Methods
https://www.readbyqxmd.com/read/28632769/combining-omics-and-microscopy-to-visualize-interactions-between-the-asian-citrus-psyllid-vector-and-the-huanglongbing-pathogen-candidatus-liberibacter-asiaticus-in-the-insect-gut
#15
Angela Kruse, Somayeh Fattah-Hosseini, Surya Saha, Richard Johnson, EricaRose Warwick, Kasie Sturgeon, Lukas Mueller, Michael J MacCoss, Robert G Shatters, Michelle Cilia Heck
Huanglongbing, or citrus greening disease, is an economically devastating bacterial disease of citrus. It is associated with infection by the gram-negative bacterium Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). For insect transmission to occur, CLas must be ingested during feeding on infected phloem sap and cross the gut barrier to gain entry into the insect vector. To investigate the effects of CLas exposure at the gut-pathogen interface, we performed RNAseq and mass spectrometry-based proteomics to analyze the transcriptome and proteome, respectively, of ACP gut tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28632260/visualization-of-the-protein-corona-towards-a-biomolecular-understanding-of-nanoparticle-cell-interactions
#16
Maria Kokkinopoulou, Johanna Simon, Katharina Landfester, Volker Mailänder, Ingo Lieberwirth
The use of nanocarriers in biology and medicine is complicated by the current need to understand how nanoparticles interact in complex biological surroundings. When nanocarriers come into contact with serum, proteins immediately adsorb onto their surface, forming a protein corona which defines their biological identity. Although the composition of the protein corona has been widely determined by proteomics, its morphology still remains unclear. In this study we show for the first time the morphology of the protein corona using transmission electron microscopy...
June 29, 2017: Nanoscale
https://www.readbyqxmd.com/read/28618240/omics-for-precious-rare-biosamples-characterization-of-ancient-human-hair-by-a-proteomic-approach
#17
Margaux Fresnais, Pascale Richardin, Marcela Sepúlveda, Emmanuelle Leize-Wagner, Armelle Charrié-Duhaut
Omics technologies have far-reaching applications beyond clinical medicine. A case in point is the analysis of ancient hair samples. Indeed, hair is an important biological indicator that has become a material of choice in archeometry to study the ancient civilizations and their environment. Current characterization of ancient hair is based on elemental and structural analyses, but only few studies have focused on the molecular aspects of ancient hair proteins-keratins-and their conservation state. In such cases, applied extraction protocols require large amounts of raw hair, from 30 to 100 mg...
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28608218/transfer-zymography
#18
Daniel Pan, Karl A Wilson, Anna Tan-Wilson
The technique described here, transfer zymography, was developed to overcome two limitations of conventional zymography. When proteolytic enzymes are resolved by nonreducing SDS-PAGE into a polyacrylamide gel with copolymerized protein substrate, the presence of the protein substrate can result in anomalous, often slower, migration of the protease and an estimated mass higher than its actual mass. A further drawback is that the presence of a high background of substrate protein interferes with proteomic analysis of the protease band by excision, tryptic digestion, and LC-MS/MS analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28591626/multi-omics-analysis-provides-insight-to-the-ignicoccus-hospitalis-nanoarchaeum-equitans-association
#19
Rachel A Rawle, Timothy Hamerly, Brian P Tripet, Richard J Giannone, Louie Wurch, Robert L Hettich, Mircea Podar, Valerie Copié, Brian Bothner
BACKGROUND: Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted 'omics' analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea...
September 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28582591/a-tool-for-integrating-genetic-and-mass-spectrometry-based-peptide-data-proteogenomics-viewer-pv-a-genome-browser-like-tool-which-includes-ms-data-visualization-and-peptide-identification-parameters
#20
REVIEW
José Eduardo Kroll, Vandeclécio Lira da Silva, Sandro José de Souza, Gustavo Antonio de Souza
In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts...
June 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
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