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https://www.readbyqxmd.com/read/28107520/pgrmc1-is-a-novel-potential-tumor-biomarker-of-human-renal-cell-carcinoma-based-on-quantitative-proteomic-and-integrative-biological-assessments
#1
Dan Zhang, Xiangying Xia, Xixi Wang, Peng Zhang, Weiliang Lu, Yamei Yu, Shi Deng, Hanshuo Yang, Hongxia Zhu, Ningzhi Xu, Shufang Liang
Progesterone receptor membrane component 1 (PGRMC1) is widely observed with an elevated level in multiple human cancers. However, the roles of PGRMC1 in renal cancer are not clear and merit further study. In this report, we made a systematic, integrative biological assessment for PGRMC1 in renal cell carcinoma (RCC) by a quantitative proteomic identification, immunohistochemical detection, and its clinic pathologic significance analysis. We found that PGRMC1 abundance is increased by 3.91-fold in RCC tissues compared with its autologous para-cancerous tissues by a quantitative proteome identification...
2017: PloS One
https://www.readbyqxmd.com/read/28105916/gpcrs-from-fusarium-graminearum-detection-modeling-and-virtual-screening-the-search-for-new-routes-to-control-head-blight-disease
#2
Emmanuel Bresso, Roberto Togawa, Kim Hammond-Kosack, Martin Urban, Bernard Maigret, Natalia Florencio Martins
BACKGOUND: Fusarium graminearum (FG) is one of the major cereal infecting pathogens causing high economic losses worldwide and resulting in adverse effects on human and animal health. Therefore, the development of new fungicides against FG is an important issue to reduce cereal infection and economic impact. In the strategy for developing new fungicides, a critical step is the identification of new targets against which innovative chemicals weapons can be designed. As several G-protein coupled receptors (GPCRs) are implicated in signaling pathways critical for the fungi development and survival, such proteins could be valuable efficient targets to reduce Fusarium growth and therefore to prevent food contamination...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28104704/perspective-the-promise-of-proteomics-in-the-study-of-oncogenic-viruses
#3
Alison Anne McBride
Oncogenic viruses are responsible for about 15% human cancers. This article explores the promise and challenges of viral proteomics in the study of the oncogenic human DNA viruses, HPV, McPyV, EBV and KSHV. These viruses have coevolved with their hosts and cause persistent infections. Each virus encodes oncoproteins that manipulate key cellular pathways to promote viral replication and evade the host immune response. Viral proteomics can identify cellular pathways perturbed by viral infection, identify cellular proteins that are crucial for viral persistence and oncogenesis, and identify important diagnostic and therapeutic targets...
January 19, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28103802/proteomics-informed-by-transcriptomics-for-characterising-active-transposable-elements-and-genome-annotation-in-aedes-aegypti
#4
Kevin Maringer, Amjad Yousuf, Kate J Heesom, Jun Fan, David Lee, Ana Fernandez-Sesma, Conrad Bessant, David A Matthews, Andrew D Davidson
BACKGROUND: Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs...
January 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28103535/down-regulation-of-histone-deacetylase-4-5-and-6-as-a-mechanism-of-synergistic-enhancement-of-apoptosis-in-human-lung-cancer-cells-treated-with-the-combination-of-a-synthetic-retinoid-am80-and-green-tea-catechin
#5
Yukiko Oya, Anupom Mondal, Anchalee Rawangkan, Sonthaya Umsumarng, Keisuke Iida, Tatsuro Watanabe, Miki Kanno, Kaori Suzuki, Zhenghao Li, Hiroyuki Kagechika, Koichi Shudo, Hirota Fujiki, Masami Suganuma
(-)-Epigallocatechin gallate (EGCG), a green tea catechin, acts as a synergist with various anticancer drugs, including retinoids. Am80 is a synthetic retinoid with a different structure from all-trans-retinoic acid: Am80 is now clinically utilized as a new drug for relapsed and intractable acute promyelocytic leukemia patients. Our experiments showed that the combination of EGCG and Am80 synergistically induced both apoptosis in human lung cancer cell line PC-9 and up-regulated expressions of growth arrest and DNA damage-inducible gene 153 (GADD153), death receptor 5, and p21(waf1) genes in the cells...
January 8, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28103160/yersinia-pestis-acetyltransferase-mediated-dual-acetylation-at-the-serine-and-lysine-residues-enhances-the-auto-ubiquitination-of-ubiquitin-ligase-march8-in-human-cells
#6
Cuiling Li, Daoguang Wang, Xin Lv, Ruirui Jing, Baibin Bi, Xinjun Chen, Jisheng Guo, Fengqin Wang, Shengnan Sun, Kazem M Azadzoi, Jing-Hua Yang
Lysine acetylation is known as a post translational modification (PTM) by histone acetyltransferases (HAT) that modifies histones and non-histone proteins to regulate gene expression. Serine acetylation, however, is reported in mammalian hosts by serine acetyltransferase of Yersinia pestis (YopJ) during infection. The protein target and cellular function of bacterial YopJ in mammalian systems are not fully addressed. Here we report dual acetylation at the serine and lysine residues by transiently expressed serine acetyltransferase YopJ mimicking Y...
January 19, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28102851/cellular-prion-protein-mediates-early-apoptotic-proteome-alternation-and-phospho-modification-in-human-neuroblastoma-cells
#7
Saima Zafar, Christina Behrens, Hassan Dihazi, Matthias Schmitz, Inga Zerr, Walter J Schulz-Schaeffer, Sanja Ramljak, Abdul R Asif
Anti-apoptotic properties of physiological and elevated levels of the cellular prion protein (PrP(c)) under stress conditions are well documented. Yet, detrimental effects of elevated PrP(c) levels under stress conditions, such as exposure to staurosporine (STS) have also been described. In the present study, we focused on discerning early apoptotic STS-induced proteome and phospho-proteome changes in SH-SY5Y human neuroblastoma cells stably transfected either with an empty or PRNP-containing vector, expressing physiological or supraphysiological levels of PrP(c), respectively...
January 19, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28102850/japanese-encephalitis-virus-induces-human-neural-stem-progenitor-cell-death-by-elevating-grp78-phb-and-hnrnpc-through-er-stress
#8
Sriparna Mukherjee, Noopur Singh, Nabonita Sengupta, Mahar Fatima, Pankaj Seth, Anita Mahadevan, Susarla Krishna Shankar, Arindam Bhattacharyya, Anirban Basu
Japanese encephalitis virus (JEV), which is a causative agent of sporadic encephalitis, harbours itself inside the neural stem/progenitor cells. It is a well-known fact that JEV infects neural stem/progenitor cells and decreases their proliferation capacity. With mass spectrometry-based quantitative proteomic study, it is possible to reveal the impact of virus on the stem cells at protein level. Our aim was to perceive the stem cell proteomic response upon viral challenge. We performed a two-dimensional gel electrophoresis-based proteomic study of the human neural stem cells (hNS1 cell line) post JEV infection and found that 13 proteins were differentially expressed...
January 19, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28102076/kinobead-and-single-shot-lc-ms-profiling-identifies-selective-pkd-inhibitors
#9
Martin Golkowski, Rama Subba Rao Vidadala, Chloe K Lombard, Hyong Won Suh, Dustin J Maly, Shao-En Ong
ATP-competitive protein kinase inhibitors are important research tools and therapeutic agents. Because there are >500 human kinases that contain highly conserved active sites, the development of selective inhibitors is extremely challenging. Methods to rapidly and efficiently profile kinase inhibitor targets in cell lysates are urgently needed to discover selective compounds and to elucidate the mechanisms of action for polypharmacological inhibitors. Here, we describe a protocol for microgram-scale chemoproteomic profiling of ATP-competitive kinase inhibitors using kinobeads...
January 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28099817/applying-proteomics-to-tick-vaccine-development-where-are-we
#10
Margarita Villar, Anabel Marina, José de la Fuente
Ticks are second to mosquitoes as a vector of human diseases and are the first vector of animal diseases with a great impact on livestock farming. Tick vaccines represent a sustainable and effective alternative to chemical acaricides for the control of tick infestations and transmitted pathogens. The application of proteomics to tick vaccine development is a fairly recent area, which has resulted in the characterization of some tick-host-pathogen interactions and the identification of candidate protective antigens...
January 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28098518/a-4-nitroquinoleneoxide-induced-pleurotus-eryngii-mutant-variety-increases-pin1-expression-in-rat-brain
#11
Yoonhwa Jeong, Mina Jung, Myeung Ju Kim, Cheol Ho Hwang
To develop Pleurotus eryngii varieties with improved medicinal qualities, protoplasts of P. eryngii were mutagenized using 4-nitroquinoleneoxide. The effects of the resulting variant mushrooms on a human cell were evaluated by applying their aqueous extracts to the human hepatoma cell line, HepG2, in vitro and examining any alteration in the proteomes of the treated HepG2. The P. eryngii mutant, NQ2A-12, was selected for its effects on increasing the expression level of Pin1 in HepG2. Pin1 is one of the peptidyl-prolyl cis-trans isomerases known to play an important role in repressing Alzheimer's disease pathogenesis...
January 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28098164/uncovering-the-sumoylation-and-ubiquitylation-crosstalk-in-human-cells-using-sequential-peptide-immunopurification
#12
Frédéric Lamoliatte, Francis P McManus, Ghizlane Maarifi, Mounira K Chelbi-Alix, Pierre Thibault
Crosstalk between the SUMO and ubiquitin pathways has recently been reported. However, no approach currently exists to determine the interrelationship between these modifications. Here, we report an optimized immunoaffinity method that permits the study of both protein ubiquitylation and SUMOylation from a single sample. This method enables the unprecedented identification of 10,388 SUMO sites in HEK293 cells. The sequential use of SUMO and ubiquitin remnant immunoaffinity purification facilitates the dynamic profiling of SUMOylated and ubiquitylated proteins in HEK293 cells treated with the proteasome inhibitor MG132...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28096900/ms_histonedb-a-manually-curated-resource-for-proteomic-analysis-of-human-and-mouse-histones
#13
Sara El Kennani, Annie Adrait, Alexey K Shaytan, Saadi Khochbin, Christophe Bruley, Anna R Panchenko, David Landsman, Delphine Pflieger, Jérôme Govin
BACKGROUND: Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28095645/what-we-can-learn-from-a-tadpole-about-ciliopathies-and-airway-diseases-using-systems-biology-in-xenopus-to-study-cilia-and-mucociliary-epithelia
#14
REVIEW
Peter Walentek, Ian K Quigley
Over the past years, the Xenopus embryo has emerged as an incredibly useful model organism for studying the formation and function of cilia and ciliated epithelia in vivo. This has led to a variety of findings elucidating the molecular mechanisms of ciliated cell specification, basal body biogenesis, cilia assembly and ciliary motility. These findings also revealed the deep functional conservation of signaling, transcriptional, post-transcriptional and protein networks employed in the formation and function of vertebrate ciliated cells...
January 17, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28095616/using-xenopus-to-understand-human-disease-and-developmental-disorders
#15
REVIEW
Amy Sater, Sally A Moody
Model animals are crucial to biomedical research. Among the commonly used model animals, the amphibian, Xenopus, has had tremendous impact because of its unique experimental advantages, cost effectiveness, and close evolutionary relationship with mammals as a tetrapod. Over the past 50 years the use of Xenopus has made possible many fundamental contributions to biomedicine, and it is a cornerstone of research in cell biology, developmental biology, evolutionary biology, immunology, molecular biology, neurobiology, and physiology...
January 17, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28095327/proteomic-and-peptidomic-analysis-of-human-sweat-with-emphasis-on-proteolysis
#16
Yijing Yu, Ioannis Prassas, Carla M J Muytjens, Eleftherios P Diamandis
: Sweat is produced by eccrine and apocrine glands and represents a biological fluid with established roles in thermo-regulation and host infection defense. The composition of sweat is highly dynamic and alters significantly in various skin and other disorders. Therefore, in-depth profiling of sweat protein composition is expected to augment our understanding of the pathobiology of several skin diseases and may lead to the identification of useful sweat-based disease biomarkers. We here reported an in-depth analysis of the human sweat proteome and peptidome...
January 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28093123/synthesis-of-stable-isotopically-labeled-peptides-with-filter-assisted-enzymatic-labeling-for-the-diagnosis-of-hepatitis-b-virus-infection-utilizing-mass-spectrometry-based-proteomics-strategy
#17
Hsing-Fen Tsai, He-Hsuan Hsiao
A facile method for the preparation of stable isotopically labeled peptides was developed by means of filter-assisted tryptic (16)O/(18)O water labeling, which could be directly applied to the determination of hepatitis B virus infection from human serum with tandem mass spectrometry. Tryptic peptides of hepatitis B surface antigen or hepatitis B e antigen from different subtypes of hepatitis B virus were synthesized with traditional solid-phase peptide synthesis as potential biomarkers. Trypsin catalyzed oxygen-18 exchange at their amidated c-terminus of arginine or lysine residue...
March 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28092031/expression-and-production-of-sh2-domain-proteins
#18
Bernard A Liu, Mari Ogiue-Ikeda, Kazuya Machida
The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092029/an-efficient-semi-supervised-learning-approach-to-predict-sh2-domain-mediated-interactions
#19
Kousik Kundu, Rolf Backofen
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091625/mplex-a-method-for-simultaneous-pathogen-inactivation-and-extraction-of-samples-for-multi-omics-profiling
#20
Kristin E Burnum-Johnson, Jennifer E Kyle, Amie J Eisfeld, Cameron P Casey, Kelly G Stratton, Juan F Gonzalez, Fabien Habyarimana, Nicholas M Negretti, Amy C Sims, Sadhana Chauhan, Larissa B Thackray, Peter J Halfmann, Kevin B Walters, Young-Mo Kim, Erika M Zink, Carrie D Nicora, Karl K Weitz, Bobbie-Jo M Webb-Robertson, Ernesto S Nakayasu, Brian Ahmer, Michael E Konkel, Vladimir Motin, Ralph S Baric, Michael S Diamond, Yoshihiro Kawaoka, Katrina M Waters, Richard D Smith, Thomas O Metz
The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements...
January 16, 2017: Analyst
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