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Proteomics

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https://www.readbyqxmd.com/read/28727291/proteomic-analysis-and-bioluminescent-reporter-gene-assays-to-investigate-effects-of-simulated-microgravity-on-caco-2-cells
#1
Giorgia La Barbera, Anna Laura Capriotti, Elisa Michelini, Susy Piovesana, Maria Maddalena Calabretta, Riccardo Zenezini Chiozzi, Aldo Roda, Aldo Laganà
Microgravity is one of the most important features in spaceflight. Previous evidence from in-vitro studies has shown that significant changes occur under simulated microgravity. For this reason, human colon adenocarcinoma Caco-2 cells were selected as cell model of intestinal epithelial barrier and their response to altered gravity conditions was investigated, especially on the protein level. In this study, we combined label-free shotgun proteomics and bioluminescent reporter gene assays to identify key proteins and pathways involved in the response of Caco-2 cells under reference and microgravity conditions...
July 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28722797/highly-selective-enrichment-of-phosphopeptides-by-on-chip-indium-oxide-functionalized-magnetic-nanoparticles-coupled-with-maldi-tof-ms
#2
Dandan Jiang, Naizhong Song, Xiqian Li, Jiutong Ma, Qiong Jia
Selective and efficient preconcentration is indispensable for low concentration of phosphopeptides in phosphorylated protein-related samples prior to MS-based analysis. Herein, an on-chip system coupled magnetic SPE with MALDI-TOF MS was designed. A metal oxide affinity chromatography (MOAC) material, indium oxide, was coated on the surface of Fe3 O4 magnetic nanoparticles (MNPs) to prepare the adsorbent, spatially confined with an applied magnetic field. The adsorbent exhibited high selectivity for phosphopeptides in tryptic digests of the mixture of β-casein and BSA (1:1000) and the mixture of β-casein, BSA, and ovalbumin (1:100:100)...
July 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28722786/oncogenic-transformation-of-lung-cells-results-in-distinct-exosome-protein-profile-similar-to-the-cell-of-origin
#3
Richard J Lobb, Marcus L Hastie, Emma L Norris, Rosa van Amerongen, Jeffrey J Gorman, Andreas Möller
Lung cancer is responsible for the highest rate of cancer mortality worldwide. Lung cancer patients are often ineligible for tumour biopsies due to co-morbidities. As a result, patients may not have the most effective treatment regimens administered. Patients with mutations in the epidermal growth factor receptor (EGFR) have improved survival in response to EGFR tyrosine kinase inhibitors (TKIs). A non-invasive method of determining EGFR mutations in patients would have promising clinical applications. Exosomes have the potential to be non-invasive novel diagnostic markers in cancer...
July 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28722341/proteomic-analysis-of-neuroblastoma-derived-exosomes-new-insights-into-a-metastatic-signature
#4
Marta Colletti, Andrea Petretto, Angela Galardi, Virginia Di Paolo, Luigi Tomao, Chiara Lavarello, Elvira Inglese, Maurizio Bruschi, Ana Amor Lopez, Luisa Pascucci, Birgit Geoerger, Hector Peinado, Locatelli Franco, Di Giannatale Angela
Neuroblastoma (NB) is the most common extracranial pediatric solid tumor. Around 70% of patients with metastatic disease at diagnosis present bone-marrow infiltration, which is considered a marker of poor outcome; however, the mechanism underlying this specific tropism has to be elucidated. Tumor-derived exosomes may support metastatic progression in several tumors by interacting with the microenvironment, and may serve as tumor biomarkers. The main objective of this study was to identify an exosomal signature associated with NB metastatic bone-marrow dissemination...
July 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28719092/what-is-targeted-proteomics-a-concise-revision-of-targeted-acquisition-and-targeted-data-analysis-in-mass-spectrometry
#5
Eva Borràs, Eduard Sabidó
No abstract text is available yet for this article.
July 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28714192/secreted-tumor-antigens-immune-biomarkers-for-diagnosis-and-therapy
#6
REVIEW
Els N Meeusen, Elgene Lim, Suresh Mathivanan
With the advent of immunotherapies for cancer, there is growing interest in the identification of tumor antigens. Tumor antigens are self-molecules altered through genetic mutations (neoantigens), protein truncation, protein misfolding or abnormal post translational modifications. To induce an immune response, tumor antigens need to be secreted into the tumor environment and presented to the immune system in the draining lymph nodes, resulting in the generation of tumor-specific effector cells and antibodies...
July 17, 2017: Proteomics
https://www.readbyqxmd.com/read/28686798/multiplierz-v2-0-a-python-based-ecosystem-for-shared-access-and-analysis-of-native-mass-spectrometry-data
#7
William M Alexander, Scott B Ficarro, Guillaume Adelmant, Jarrod A Marto
The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data...
July 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28665052/discovery-of-breast-putative-cancer-antigens-using-an-integrative-platform-of-genomics-driven-immunoproteomics
#8
Veneta Qendro, Deborah H Lundgren, Samuel Palczewski, Poornima Hegde, Christina Stevenson, Laurie Perpetua, Ardian Latifi, Jesse Merriman, Grace Bugos, David K Han
Recent advances in cancer immuno-therapeutics such as checkpoint inhibitors, chimeric antigen-receptor T cells, and tumor infiltrating T cells (TIL) are now significantly impacting cancer patients in a positive manner. Although very promising, reports indicate no more than 25% of cases result in complete remission. One of the limitations of these treatments is the identity of putative cancer antigens in each patient as it is technically challenging to identify of cancer antigens in a rapid fashion. Thus, identification of cancer antigens followed by targeted treatment will increase the efficacy of cancer immunotherapies...
June 30, 2017: Proteomics
https://www.readbyqxmd.com/read/28665046/features-of-lineage-specific-haematopoietic-metabolism-revealed-by-mitochondrial-proteomics
#9
Claudia Billing, Michael Walker, Nicole Noack, Christian Böhme, Uta Ceglarek, Dietger Niederwieser, Anthony Whetton, Michael Cross
Hematopoietic bone marrow is a regenerative tissue of high clinical relevance, yet relatively little is known about the metabolism of the stem and progenitor populations concerned. We have used a multipotent murine cell line to generate sufficient numbers of cells undergoing self-renewal, erythroid or myeloid differentiation to allow a proteomics analysis of enriched mitochondria. Stringent analysis identified 37 mitochondria-associated proteins changing on differentiation in this system. Those induced during differentiation were commonly associated with mature cell functions, while those inactivated upon differentiation indicate widespread changes in mitochondrial transport, fatty acid catabolism and oxidative phosphorylation...
June 30, 2017: Proteomics
https://www.readbyqxmd.com/read/28665021/proteomes-and-phosphoproteomes-of-anther-and-pollen-availability-and-progress
#10
REVIEW
Zaibao Zhang, Menghui Hu, Xiaobing Feng, Andong Gong, Lin Cheng, Hongyu Yuan
In flowering plants, anther development plays crucial role in sexual reproduction. Within the anther, microspore mother cells meiosis produces microspores, which further develop into pollen grains that play decisive role in plant reproduction. Previous studies on anther biology mainly focused on single gene functions relying on genetic and molecular methods. Recently, anther development has been expanded from multiple OMICS approaches like transcriptomics, proteomics/phosphoproteomics, and metabolomics. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins which can characterize proteomes and their modulation during normal development, biotic and abiotic stresses in anther development...
June 30, 2017: Proteomics
https://www.readbyqxmd.com/read/28665015/autotransporter-adhesins-in-escherichia-coli-pathogenesis
#11
REVIEW
Julieanne L Vo, Gabriela Constanza Martínez Ortiz, Pramod Subedi, Shivakumar Keerthikumar, Suresh Mathivanan, Jason J Paxman, Begoña Heras
Most bacteria produce adhesion molecules to facilitate the interaction with host cells and establish successful infections. An important group of bacterial adhesins belong to the autotransporter (AT) superfamily, the largest group of secreted and outer membrane proteins in Gram-negative bacteria. AT adhesins possess diverse functions that facilitate bacterial colonisation, survival and persistence, and as such are often associated with increased bacterial fitness and pathogenic potential. In this review, we will describe AIDA-I type AT adhesins, which comprise the biggest and most diverse group in the AT family...
June 30, 2017: Proteomics
https://www.readbyqxmd.com/read/28664610/targeted-functional-investigations-guided-by-integrative-proteome-network-analysis-revealed-significant-perturbations-of-renal-tubular-cell-functions-induced-by-high-glucose
#12
Siripat Aluksanasuwan, Supapron Khamchun, Visith Thongboonkerd
Recently, several studies employed various proteomic approaches to define diabetes-induced changes in renal proteins. However, functional significance of those datasets in diabetic nephropathy (DN) remained unclear. We thus performed integrative proteome network analysis of such datasets followed by various targeted functional studies in distal renal tubular cells treated with high-glucose (HG) (25 mM) compared to normal-glucose (NG) (5.5 mM) and NG+mannitol (M) (5.5+19.5 mM). The data showed that at 96-h when cell proliferation/death, tight junction protein and β-/F-actin expression and organization, and transepithelial resistance remained unchanged, only HG caused increased levels of HSP90, HSP70 and HSP60, and increased accumulation of intracellular protein aggregates...
June 30, 2017: Proteomics
https://www.readbyqxmd.com/read/28664598/comparison-of-fractionation-proteomics-for-local-swath-library-building
#13
Elisabeth Govaert, Katleen Van Steendam, Sander Willems, Liesbeth Vossaert, Maarten Dhaenens, Dieter Deforce
For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation...
June 30, 2017: Proteomics
https://www.readbyqxmd.com/read/28643940/proteomic-profiling-of-extracellular-vesicles-secreted-from-toxoplasma-gondii
#14
Pryscilla Fanini Wowk, Maria Luisa Zardo, Halisson Tesseroli Miot, Samuel Goldenberg, Paulo Costa Carvalho, Patricia Alves Mörking
Toxoplasma gondii infects a wide range of hosts worldwide, including humans and domesticated animals causing toxoplasmosis disease. Recently, exosomes, small extracellular vesicles (EV) that contain nucleic acids, proteins, and lipids derived from their original cells were linked with disease protection. The effect of EVs derived from T. gondii on the immune response and its relevance in a physiological context is unknown. Here we disclose the first proteomic profiling of T. gondii EVs compared to EVs isolated from a human foreskin fibroblast infected cell line cultured in a vesicle- free medium...
June 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28643936/phenotypic-analysis-of-organoids-by-proteomics
#15
REVIEW
Alexis Gonneaud, Claude Asselin, François Boudreau, François-Michel Boisvert
The development of 3D cell cultures into self-organizing organ-like structures named organoids provides a model that better reflects in vivo organ physiology and their functional properties. Organoids have been established from several organs, such as the intestine, prostate, brain, liver, kidney and pancreas. With recent advances in high-throughput and -omics profiling technologies, it is now possible to study the mechanisms of cellular organisation at the systems level. It is therefore not surprising that these methods are now used to characterize organoids at the transcriptomic, proteomic, chromatin state and transcription factor DNA-binding levels...
June 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28643898/identification-of-cross-reactive-b-cell-epitopes-between-bos-d-9-0101-bos-taurus-and-gly-m-5-0101-glycine-max-by-epitope-mapping-maldi-tof-ms
#16
Ángela María Candreva, Mario Ferrer-Navarro, Silvia Bronsoms, Alejandra Quiroga, Renata Curciarello, Ana Cauerhff, Silvana Petruccelli, Guillermo Horacio Docena, Sebastián Alejandro Trejo
Exposure to cow's milk constitutes one of the most common causes of food allergy. In addition, exposure to soy proteins has become relevant in a restricted proportion of milk allergic pediatric patients treated with soy formulae as a dairy substitute, because of the cross-allergenicity described between soy and milk proteins . We have previously identified several cross-reactive allergens between milk and soy that may explain this intolerance. The purpose of the present work was to identify epitopes in the purified αS1-casein and the recombinant soy allergen Gly m 5...
June 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28627733/response-of-renal-tubular-cells-to-differential-types-and-doses-of-calcium-oxalate-crystals-integrative-proteome-network-analysis-and-functional-investigations
#17
Arada Vinaiphat, Siripat Aluksanasuwan, Juthatip Manissorn, Suchitra Sutthimethakorn, Visith Thongboonkerd
We have previously identified changes in the cellular proteome of renal tubular cells induced by low-dose (100 μg/ml) and high-dose (1,000 μg/ml) calcium oxalate monohydrate (COM) and dihydrate (COD) crystals. However, the functional significance of such expression data remained unclear. In this study, we performed comparative analyses and functional investigations of four proteomic datasets to define potential mechanisms by which renal tubular cells responded to differential crystal types and doses. The data showed that high-dose induced greater changes than low-dose, whereas COM induced more changes than COD...
June 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28627015/small-proteins-encoded-by-unannotated-orfs-are-rising-stars-of-the-proteome-confirming-shortcomings-in-genome-annotations-and-current-vision-of-an-mrna
#18
REVIEW
Vivian Delcourt, Antanas Staskevicius, Michel Salzet, Isabelle Fournier, Xavier Roucou
Short ORF-encoded peptides and small proteins in eukaryotes have been hiding in the shadow of large proteins for a long time. Recently, improved identifications in MS-based proteomics and ribosome profiling resulted in the detection of large numbers of small proteins. The variety of functions of small proteins is also emerging. It seems to be the right time to reflect on why small proteins remained invisible. In addition to the obvious technical challenge of detecting small proteins, they were mostly forgotten from annotations and they escaped detection because they were not sought...
June 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28621911/different-roles-of-cd4-cd8-and-%C3%AE-%C3%AE-t-lymphocytes-in-naive-and-vaccinated-chickens-during-s-enteritidis-infection
#19
Zuzana Sekelova, Ondrej Polansky, Hana Stepanova, Radek Fedr, Marcela Faldynova, Ivan Rychlik, Lenka Vlasatikova
Lymphocytes represent the key antigen-specific leukocyte subpopulation. Despite their importance in mounting an immune response, an unbiased description of proteins expressed by chicken lymphocytes has not been presented. In this study we therefore intravenously infected chickens with Salmonella Enteritidis, sorted CD4, CD8 and γδ T-lymphocytes from the spleen by flow cytometry and determined the proteome of each population by LC-MS/MS. CD4 T-lymphocyte characteristic proteins included ubiquitin SUMO-like domain and BAR domain containing proteins...
June 16, 2017: Proteomics
https://www.readbyqxmd.com/read/28618117/itraq-based-proteomics-of-sunflower-cultivars-differing-in-resistance-to-parasitic-weed-orobanche-cumana
#20
Chong Yang, Ling Xu, Na Zhang, Faisal Islam, Wenjian Song, Luyang Hu, Dan Liu, Xiaonan Xie, Weijun Zhou
Orobanche cumana is an obligate root parasite causing severe damage to many economically important crops, including sunflowers worldwide. For efficient control measures, it is necessary to understand the resistant mechanism during interaction at molecular level. The present study emphasizes on comparative proteomics to investigate the mechanistic basis of compatible and incompatible interaction of O. cumana with resistant (JY207) and susceptible (TK0409) sunflowers. More than 3500 proteins were identified from two cultivars by iTRAQ analysis...
June 15, 2017: Proteomics
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