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proteomics and visualization

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https://www.readbyqxmd.com/read/28726848/patch-clamp-technique-to-characterize-ion-channels-in-enlarged-individual-endolysosomes
#1
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
#2
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
#3
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
#4
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
#5
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...
July 3, 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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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...
June 4, 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
#13
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
https://www.readbyqxmd.com/read/28578394/integrated-proteomic-and-metabolomic-analysis-reveals-that-rhodomyrtone-reduces-the-capsule-in-streptococcus-pneumoniae
#14
Watcharapong Mitsuwan, Alfonso Olaya-Abril, Mónica Calderón-Santiago, Irene Jiménez-Munguía, José Antonio González-Reyes, Feliciano Priego-Capote, Supayang P Voravuthikunchai, Manuel J Rodríguez-Ortega
The emergence of antibiotic-resistant pathogenic bacteria is a healthcare problem worldwide. We evaluated the antimicrobial activity of rhodomyrtone, an acylphloroglucinol present in Rhodomyrtus tomentosa leaves, against the human Gram-positive pathogen Streptococcus pneumoniae. The compound exhibited pronounced anti-pneumococcal activity against a broad collection of clinical isolates. We studied the effects at the molecular level by integrated proteomic and metabolomic analysis. The results revealed alterations in enzymes and metabolites involved in several metabolic pathways including amino acid biosynthesis, nucleic acid biosynthesis, glucid, and lipid metabolism...
June 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28553947/structural-basis-for-high-affinity-fluorophore-binding-and-activation-by-rna-mango
#15
Robert J Trachman, Natalia A Demeshkina, Matthew W L Lau, Shanker Shyam S Panchapakesan, Sunny C Y Jeng, Peter J Unrau, Adrian R Ferré-D'Amaré
Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (Kd ∼3 nM), and, in complex with related ligands, it is one of the most redshifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1...
July 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28549691/27-hydroxycholesterol-upregulates-the-production-of-heat-shock-protein-60-of-monocytic-cells
#16
Bo-Young Kim, Yonghae Son, Jeongyoon Choi, Seong-Kug Eo, Young Chul Park, Koanhoi Kim
Investigating differentially expressed proteins in a milieu rich in cholesterol oxidation products, we found via mass spectrometry-based proteomics that surface levels of heat shock protein 60 (HSP60) were upregulated on monocytic cells in the presence of 27-hydroxycholesterol (27OHChol). The elevated levels of cytoplasmic membrane HSP60 were verified via Western blot analysis and visualized by confocal microscopy. Treatment with 27OHChol also resulted in increased levels of cellular HSP60 without altering its transcription...
May 23, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28536537/-gestaltomics-systems-biology-schemes-for-the-study-of-neuropsychiatric-diseases
#17
REVIEW
Nora A Gutierrez Najera, Osbaldo Resendis-Antonio, Humberto Nicolini
The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the "psychiatric phenotype" is to provide an improved vision of the shape of the phenotype as it is visualized by "Gestalt" psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28529698/seven-perspectives-on-gpcr-h-d-exchange-proteomics-methods
#18
Xi Zhang
Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor...
2017: F1000Research
https://www.readbyqxmd.com/read/28520987/proteosign-an-end-user-online-differential-proteomics-statistical-analysis-platform
#19
Georgios Efstathiou, Andreas N Antonakis, Georgios A Pavlopoulos, Theodosios Theodosiou, Peter Divanach, David C Trudgian, Benjamin Thomas, Nikolas Papanikolaou, Michalis Aivaliotis, Oreste Acuto, Ioannis Iliopoulos
Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28501997/using-laser-capture-microdissection-to-isolate-cortical-laminae-in-nonhuman-primate-brain
#20
Brian A Corgiat, Claudius Mueller
Laser capture microdissection (LCM) is a technique that allows procurement of an enriched cell population from a heterogeneous tissue sample under direct microscopic visualization. Fundamentally, laser capture microdissection consists of three main steps: (1) visualizing the desired cell population by microscopy, (2) melting a thermolabile polymer onto the desired cell populations using infrared laser energy to form a polymer-cell composite (capture method) or photovolatizing a region of tissue using ultraviolet laser energy (cutting method), and (3) removing the desired cell population from the heterogeneous tissue...
2017: Methods in Molecular Biology
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