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MS and proteomics

Nanthini Jayabalan, Andrew Lai, Valeska Ormazabal, Stefanie Adam, Dominic Guanzon, Carlos Palma, Katherin Scholz-Romero, Ratana Lim, Thomas Jansson, Harold David McIntyre, Martha Lappas, Carlos Salomon
Context: Molecules produced by adipose tissue (AT) function as an endocrine link between maternal AT and fetal growth by regulating placental function in normal and gestational diabetes mellitus (GDM). Objective: We hypothesised that AT-derived exosomes from women with GDM carry a specific set of proteins that influences glucose metabolism in placenta. Design: Exosomes were isolated from omental AT-conditioned media from pregnant women with normal glucose tolerance (exo-NGT, n=65) and women with GDM (exo-GDM, n=82)...
December 3, 2018: Journal of Clinical Endocrinology and Metabolism
Tz-Wen Yang, Divya Sahu, Yi-Wen Chang, Chia-Lang Hsu, Chiao-Hui Hsieh, Hsuan-Cheng Huang, Hsueh-Fen Juan
The interaction of long noncoding RNAs (lncRNAs) with one or more RNA-binding proteins (RBPs) are important to a plethora of cellular and physiological processes. The lncRNA SNHG1 was reported to be aberrantly expressed and associated with poor patient prognosis in several cancers, including neuroblastoma. However, the interacting RBPs and biological functions associated with SNHG1 in neuroblastoma remains unknown. In this study, we identified 283, 31, and 164 SNHG1-interacting proteins in SK-N-BE(2)C, SK-N-DZ and SK-N-AS neuroblastoma cells, respectively, using a RNA-protein pull-down assay coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
December 5, 2018: Journal of Proteome Research
Sachin Khurana, Michael J Coffey, Alan John, Alessandro D Uboldi, My-Hang Huynh, Rebecca J Stewart, Vern Carruthers, Christopher J Tonkin, Ethan D Goddard-Borger, Nichollas E Scott
Toxoplasma gondii is a ubiquitous, obligate intracellular eukaryotic parasite that causes congenital birth defects, disease in immunocompromised individuals, and blindness. Protein glycosylation plays an important role in the infectivity and evasion of immune responses of many eukaryotic parasites and is also of great relevance to vaccine design. Here, we demonstrate that micronemal protein 2 (MIC2), a motility-associated adhesin of T. gondii, has highly glycosylated thrombospondin repeat (TSR) domains. Using affinity-purified MIC2 and MS/MS analysis along with enzymatic digestion assays, we observed that at least seven C-linked and three O-linked glycosylation sites exist within MIC2, with > 95% occupancy at these O-glycosylation sites...
December 4, 2018: Journal of Biological Chemistry
Elisa Caiola, Francesca Falcetta, Silvia Giordano, Mirko Marabese, Marina C Garassino, Massimo Broggini, Roberta Pastorelli, Laura Brunelli
BACKGROUND: Non-small-cell lung cancer (NSCLC) is a heterogeneous disease, with multiple different oncogenic mutations. Approximately 25-30% of NSCLC patients present KRAS mutations, which confer poor prognosis and high risk of tumor recurrence. About half of NSCLCs with activating KRAS lesions also have deletions or inactivating mutations in the serine/threonine kinase 11 (LKB1) gene. Loss of LKB1 on a KRAS-mutant background may represent a significant source of heterogeneity contributing to poor response to therapy...
December 4, 2018: Journal of Experimental & Clinical Cancer Research: CR
Carsten Schmelter, Sebastian Funke, Jana Treml, Anja Beschnitt, Natarajan Perumal, Caroline Manicam, Norbert Pfeiffer, Franz H Grus
Proper sample preparation protocols represent a critical step for liquid chromatography-mass spectrometry (LC-MS)-based proteomic study designs and influence the speed, performance and automation of high-throughput data acquisition. The main objective of this study was to compare two commercial solid-phase extraction (SPE)-based sample preparation protocols (comprising SOLAµTM HRP SPE spin plates from Thermo Fisher Scientific and ZIPTIP® C18 pipette tips from Merck Millipore) for analytical performance, reproducibility, and analysis speed...
December 3, 2018: International Journal of Molecular Sciences
Jian Jing, Zhenhuan Du, Songyang Ji, Keqiang Han
The hypercoagulable state occurs in a group of prothrombotic disorders associated with an increased risk for thromboembolic events, but it is difficult to diagnose due to the lack of available biomarkers. This study aimed to investigate systematic changes of urinary proteome in acute hypercoagulable state induced by certain antifibrinolytics. To reduce the effects of both genetic and environmental factors on the urinary proteome, we used a rat model of acute hypercoagulable state induced by an antifibrinolytic agent ε-aminocaproic acid, resembling human hypercoagulable state...
December 1, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Kiran Rawat, Amit Shard, Manali Jadhav, Mayuri Gandhi, Prince Anand, Rituraj Purohit, Yogendra Padwad, Arun K Sinha
Gliomas are lethal and aggressive form of brain tumors with resistance to conventional radiation and cytotoxic chemotherapies; inviting continuous efforts for drug discovery and drug delivery. Interestingly, small molecule hybrids are one such pharmacophore that continues to capture interest owing to their pluripotent medicinal effects. Accordingly, we earlier reported synthesis of potent Styryl-cinnamate hybrids (analogues of Salvianolic acid F) along with its plausible mode of action (MOA). We explored iTRAQ-LC/MS-MS technique to deduce differentially expressed landscape of native & phospho-proteins in treated glioma cells...
December 1, 2018: Experimental Cell Research
Lei Wang, Sujun Li, Haixu Tang
Large-scale proteomics projects often generate massive and highly redundant tandem mass spectra(MS/MS). Spectral clustering algorithms can reduce the redundancy in these datasets, and thus speed up database searching for peptide identification, a major bottleneck for proteomic data analysis. The key challenge of spectral clustering is to reduce the redundancy in the MS/MS spectra data, while retaining sufficient sensitivity to identify peptides from the clustered spectra. In this paper, we present the software msCRUSH, which implements a novel spectral clustering algorithm based on the locality sensitive hashing (LSH) technique...
December 4, 2018: Journal of Proteome Research
Gayatree Mohapatra, Preksha Gaur, M Prabhakar, Mukesh Singh, Sarika Rana, Shivendra Singh, Navneet Kaur, Smriti Verma, V Krishna, Nirpendra Singh, C V Srikanth
Salmonella Typhimurium (ST) is an intracellular pathogen that causes gastroenteritis in humans. Aided by a battery of effector proteins, ST resides intracellularly in a specialized vesicle, called Salmonella -containing vacuole (SCV) that utilizes the host endocytic vesicular-transport pathway (VTP). Here we probed the possible role of SUMOylation, a post-translation modification pathway, in SCV biology. Proteome analysis by complex mass-spectrometry (MS/MS) revealed a dramatically altered SUMO-proteome (SUMOylome) in ST infected cells...
December 3, 2018: Journal of Cell Science
Sneha P Couvillion, Ying Zhu, Gabe Nagy, Joshua N Adkins, Charles Ansong, Ryan S Renslow, Paul D Piehowski, Yehia M Ibrahim, Ryan T Kelly, Thomas O Metz
Mass-spectrometry based omics technologies - namely proteomics, metabolomics and lipidomics - have enabled the molecular level systems biology investigation of organisms in unprecedented detail. There has been increasing interest for gaining a thorough, functional understanding of the biological consequences associated with cellular heterogeneity in a wide variety of research areas such as developmental biology, precision medicine, cancer research and microbiome science. Recent advances in mass spectrometry (MS) instrumentation and sample handling strategies are quickly making comprehensive omics analyses of single cells feasible, but key breakthroughs are still required to push through remaining bottlenecks...
December 3, 2018: Analyst
Sze Wan Shan, Dennis Yan-Yin Tse, Bing Zuo, Chi Ho To, Quan Liu, Sally A McFadden, Rachel Ka-Man Chun, Jingfang Bian, King Kit Li, Thomas Chuen Lam
Myopia is generally regarded as a failure of normal emmetropization process, however, its underlying molecular mechanisms are unclear. Retinal protein profile changes using integrated SWATH and MRM-HR MS were studied in guinea pigs at 3- and 21-days of age, where the axial elongation was significantly detected. Differential proteins expressions were identified, and related to pathways which are important in postnatal development in retina, proliferation, breakdown of glycogen-energy and visual phototransduction...
December 2018: Data in Brief
Andreas Monoyios, Karin Hummel, Katharina Nöbauer, Martina Patzl, Sarah Schlosser, Michael Hess, Ivana Bilic
The unicellular protozoan Histomonas meleagridis is notorious for being the causative agent of histomonosis, which can cause high mortality in turkeys and substantial production losses in chickens. The complete absence of commercially available curative strategies against the disease renders the devising of novel approaches a necessity. A fundamental step toward this objective is to understand the flagellate's virulence and attenuation mechanisms. For this purpose we have previously conducted a comparative proteomic analysis of an in vitro cultivated virulent and attenuated histomonad parasite using two-dimensional electrophoresis and MALDI-TOF/TOF...
2018: Frontiers in Cellular and Infection Microbiology
Prem Prakash Das, Qingsong Lin, Sek-Man Wong
Tobacco mosaic virus (TMV) is a positive single-stranded RNA virus. Its 5' end ORF codes for the replicase proteins, namely 126 kDa and 183 kDa, respectively. These proteins interact with many host proteins to form a virus replication complex (VRC). This study aims to dissect the proteome profile of TMV-infected Nicotiana tabacum in host cellular and molecular pathways. We used the isobaric tags for relative and absolute quantification (iTRAQ) technique to analyse the differential global proteomic profile of TMV infected and mock infected plants...
November 29, 2018: Journal of Proteomics
Vladimir Lopez, Elisabeth van der Heijden, Margarita Villar, Anita Michel, Pilar Alberdi, Christian Gortázar, Victor Rutten, José de la Fuente
There is an imperative need for effective control of bovine tuberculosis (BTB) on a global scale and vaccination of cattle may prove to be pivotal in achieving this. The oral and parenteral use of a heat-inactivated Mycobacterium bovis (M. bovis) vaccine has previously been found to confer partial protection against BTB in several species. A role for complement factor C3 has been suggested in wild boar, but the exact mechanism by which this vaccine provides protection remains unclear. In the present study, a quantitative proteomics approach was used to analyze the white blood cell proteome of vaccinated cattle in comparison to unvaccinated controls, prior (T0) and in response to vaccination, skin test and challenge (T9 and T12)...
December 2018: Veterinary Immunology and Immunopathology
Eliška Syslová, Přemysl Landa, Lucie Raisová Stuchlíková, Petra Matoušková, Lenka Skálová, Barbora Szotáková, Martina Navrátilová, Tomáš Vaněk, Radka Podlipná
Fenbendazole, a broad spectrum anthelmintic used especially in veterinary medicine, may impact non-target organisms in the environment. Nevertheless, information about the effects of fenbendazole in plants is limited. We investigated the biotransformation of fenbendazole and the effect of fenbendazole and its metabolites on gene expression in the model plant Arabidopsis thaliana. High-sensitive UHPLC coupled with tandem mass spectrometry, RNA-microarray analysis together with qPCR verification and nanoLC-MS proteome analysis were used in this study...
November 24, 2018: Chemosphere
Tao Liu, Jing Zhou, Hanjin Cui, Pengfei Li, Jiekun Luo, Yang Wang, Tao Tang
ETHNOPHARMACOLOGICAL RELEVANCE: Rhubarb is a traditional Chinese medicine(TCM), that possesses neuroprotective, anti-inflammatory, antibacterial, antioxidative, purgative and anticancer properties, and has been used to treat intracerebral hemorrhage (ICH) and many other diseases. AIMS OF THE STUDY: This study aimed to investigate the changes of brain protein in ICH rats treated with rhubarb and to explore the multi-target mechanism of rhubarb in the treatment of ICH via bioinformatics analysis of differentially expressed proteins (DEPs)...
November 28, 2018: Journal of Ethnopharmacology
Ting Yang, Pengfei Xu, Lize Gu, Zhiyuan Xu, Weihong Ge, Qing Li, Feifei Xu
BACKGROUND: Heat shock protein 27 (HSP27) may take part in the epithelial ovarian cancer (EOC) malignant process because it is elevated in the serum of EOC patients, suggesting that HSP27 may serve as an EOC biomarker to complement the standard serum carbohydrate antigen 125 (CA125) test. Thus, accurate quantification of serum HSP27 would assist the diagnosis of EOC. METHODS: Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics coupled with an immunoaffinity enrichment assay was developed and validated to monitor HSP27 concentrations in serum...
November 28, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Nengguo Tao, Yue Chen, Yalan Wu, Xiao Wang, Lu Li, Andan Zhu
Herein, the dosage effect of limonene on the P. digitatum spore germination and its regulatory mechanisms were investigated. Results showed that limonene only at low concentrations displayed a stimulatory role, with the optimal concentration being 0.25 μL/mL. GC-MS and GC analysis revealed that limonene contents remained relative stable and no evidence of transformation was observed at stimulatory concentrations. Metabolomics analysis showed that 61 metabolites including organic acids, amino acids, sugars, nucleosides, fatty acids, and their derivatives, were significantly changed (P < 0...
March 30, 2019: Food Chemistry
Xin-He Mao, Ying-Xi Xu, Hai-Yan Xing, Zheng Tian, Ke-Jing Tang, Lu Liu, Qing Rao, Min Wang, Jian-Xiang Wang
OBJECTIVE: To screen the differentially expressed proteins at the early stage of K562 cells treated with meisoindigo by using tandem mass tags (TMT)-based proteomics technology, and to explore the mechanism for meisoindigo-inducing apoptosis. METHODS: The half inhibitory concentration (IC50 ) of mesoindigo on K562 cells was determined by CCK8. The flow cytometry was used to assay the apoptosis of K562 cells treated by meisoindigo or DMSO. Total proteins were extracted from the cells treated with 0...
December 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
Martin C H Gruhlke, Haike Antelmann, Jörg Bernhardt, Veronika Kloubert, Lothar Rink, Alan J Slusarenko
A single clove of edible garlic (Allium sativum L.) of about 10g produces up to 5mg of allicin (diallylthiosulfinate), a thiol-reactive sulfur-containing defence substance that gives injured garlic tissue its characteristic smell. Allicin induces apoptosis or necrosis in a dose-dependent manner but biocompatible doses influence cellular metabolism and signalling cascades. Oxidation of protein thiols and depletion of the glutathione pool are thought to be responsible for allicin's physiological effects. Here, we studied the effect of allicin on post-translational thiol-modification in human Jurkat T-cells using shotgun LC-MS/MS analyses...
November 27, 2018: Free Radical Biology & Medicine
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