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Journal of Proteomics

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https://www.readbyqxmd.com/read/28823580/potential-mechanisms-of-calcium-dependent-regulation-of-the-mammalian-cell-cycle-revealed-by-comprehensive-unbiased-label-free-nlc-ms-ms-quantitative-proteomics
#1
Anna Kwasnik, Alex von Kriegsheim, Andrew Irving, Stephen R Pennington
Calcium (Ca(2+)) controls progression through the mammalian cell cycle by engaging a diverse range of molecular pathways. While the essential role of spatio-temporal Ca(2+) signalling in the cell cycle is well established, the precise mechanisms by which it regulates cell cycle entry and progression through G1 are not particularly well understood. Here, high-resolution label-free semi-quantitative nLC-MS/MS analysis has been used to support a highly reproducible unbiased analysis of Ca(2+) influx dependent growth factor induced protein expression early in G1 in human fibroblasts...
August 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28821459/clinical-multi-omics-strategies-for-the-effective-cancer-management
#2
REVIEW
Byong Chul Yoo, Kyung-Hee Kim, Sang Myung Woo, Jae Kyung Myung
Cancer is a global health issue as a multi-factorial complex disease, and early detection and novel therapeutic strategies are required for more effective cancer management. With the development of systemic analytical -omics strategies, the therapeutic approach and study of the molecular mechanisms of carcinogenesis and cancer progression have moved from hypothesis-driven targeted investigations to data-driven untargeted investigations focusing on the integrated diagnosis, treatment, and prevention of cancer in individual patients...
August 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28802583/cytoskeleton-and-nuclear-lamina-affection-in-recessive-osteogenesis-imperfecta-a-functional-proteomics-perspective
#3
Assunta Gagliardi, Roberta Besio, Chiara Carnemolla, Claudia Landi, Alessandro Armini, Mona Aglan, Ghada Otaify, Samia A Temtamy, Antonella Forlino, Luca Bini, Laura Bianchi
Osteogenesis imperfecta (OI) is a collagen-related disorder associated to dominant, recessive or X-linked transmission, mainly caused by mutations in type I collagen genes or in genes involved in type I collagen metabolism. Among the recessive forms, OI types VII, VIII, and IX are due to mutations in CRTAP, P3H1, and PPIB genes, respectively. They code for the three components of the endoplasmic reticulum complex that catalyzes 3-hydroxylation of type I collagen α1Pro986. Under-hydroxylation of this residue leads to collagen structural abnormalities and results in moderate to lethal OI phenotype, despite the exact molecular mechanisms are still not completely clear...
August 9, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28802582/label-free-quantitative-proteomic-analysis-of-lactobacillus-fermentum-ncdc-400-during-bile-salt-exposure
#4
Gurjeet Kaur, Syed Azmal Ali, Sudarshan Kumar, Ashok Kumar Mohanty, Pradip Behare
Lactobacillus fermentum NCDC 400 is a commonly used and a comprehensively studied probiotic organism. The distinctive capability to endure the harsh environment of the gastrointestinal tract owing to the presence of bile salts in gastric juice facilitates gut microbiota, especially the probiotic organisms to transiently inhabit the host gut. In the present study, Label-Free Quantification (LFQ) approach has been employed to analyze the expression pattern of Lactobacillus fermentum NCDC 400 strain proteins, under bile acid stress, using high-resolution mass spectrometer connected to nano-liquid chromatography (LC) system...
August 9, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28797668/salinity-stress-enhancing-basal-and-induced-immune-responses-in-striped-catfish-pangasianodon-hypophthalmus-sauvage
#5
Mélodie Schmitz, Tamar Ziv, Arie Admon, Sébastien Baekelandt, Syaghalirwa N M Mandiki, Maëlenn L'Hoir, Patrick Kestemont
In the Mekong Delta, striped catfish are faced with chronic salinity stress related to saltwater intrusion induced by global climatic changes. In this study, striped catfish juveniles were submitted to a prolonged salinity stress (up to 10ppt) over three weeks followed by infection with a virulent bacterial strain, Edwardsiella ictaluri. Osmoregulatory parameters were investigated. In addition, a label free quantitative proteomics workflow was performed on kidneys. The workflow consisted of an initial global profiling of relative peptide abundances (by LC/MS, peak area quantification based on extracted ion currents), followed by identification (by MS/MS)...
August 7, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28782717/in-silico-approaches-for-unveiling-novel-glycobiomarkers-in-cancer
#6
Rita Azevedo, André M N Silva, Celso A Reis, Lúcio Lara Santos, José Alexandre Ferreira
Glycosylation is one of the most common and dynamic post-translational modification of cell surface and secreted proteins. Cancer cells display unique glycosylation patterns that decisively contribute to drive oncogenic behavior, including disease progression and dissemination. Moreover, alterations in glycosylation are often responsible for the creation of protein signatures holding significant biomarker value and potential for targeted therapeutics. Accordingly, many analytical protocols have been outlined for the identification of abnormally glycosylated proteins by mass spectrometry...
August 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28782718/merging-in-silico-and-in-vitro-salivary-protein-complex-partners-using-the-string-database-a-tutorial
#7
Karla Tonelli Bicalho Crosara, Eduardo Buozi Moffa, Yizhi Xiao, Walter Luiz Siqueira
Protein-protein interaction is a common physiological mechanism for protection and actions of proteins in an organism. The identification and characterization of protein-protein interactions in different organisms is necessary to better understand their physiology and to determine their efficacy. In a previous in vitro study using mass spectrometry, we identified 43 proteins that interact with histatin 1. Six previously documented interactors were confirmed and 37 novel partners were identified. In this tutorial, we aimed to demonstrate the usefulness of the STRING database for studying protein-protein interactions...
August 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28780057/top-down-mass-spectrometric-immunoassay-for-human-insulin-and-its-therapeutic-analogs
#8
Dobrin Nedelkov, Eric E Niederkofler, Paul E Oran, Scott Peterman, Randall W Nelson
Measurement of insulin and its therapeutic analogs is important in diabetes, hypoglycemia, sports anti-doping and toxicology. Commercial insulin immunoassays fail to detect commonly prescribed insulin analogs. Because of their unique sequences and masses, these analogs are readily measured and distinguished with mass spectrometric (MS) assays. Reviewed here is an insulin mass spectrometric immunoassay (MSIA) that combines micro-scale immunoaffinity capture with sensitive MS detection of insulin and its therapeutic analogs...
August 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28774858/a-comparative-intracellular-proteomic-profiling-of-pseudomonas-aeruginosa-strain-asp-53-grown-on-pyrene-or-glucose-as-sole-source-of-carbon-and-identification-of-some-key-enzymes-of-pyrene-biodegradation-pathway
#9
Ashis K Mukherjee, Pabitra Bhagowati, Bhim Bahadur Biswa, Abhishek Chanda, Bhargab Kalita
Pseudomonas aeruginosa strain ASP-53, isolated from a petroleum oil-contaminated soil sample, was found to be an efficient degrader of pyrene. PCR amplification of selected hydrocarbon catabolic genes (alkB gene, which encodes for monooxygenase, and the C12O, C23O, and PAH-RHDα genes encoding for the dioxygenase enzyme) from the genomic DNA of P. aeruginosa strain ASP-53 suggested its hydrocarbon degradation potential. The GC-MS analysis demonstrated 30.1% pyrene degradation by P. aeruginosa strain ASP-53 after 144h of incubation at pH6...
July 31, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28757466/identification-of-serum-proteome-signature-of-irritable-bowel-syndrome-potential-utility-of-the-tool-for-early-diagnosis-and-patient-s-stratification
#10
Athanasios Tsigaridas, Athanassios K Anagnostopoulos, Aggeliki Papadopoulou, Stamatia Ioakeim, Anna Vaiopoulou, Ioannis S Papanikolaou, Nikos Viazis, George Karamanolis, Gerasimos J Mantzaris, George T Tsangaris, Maria Gazouli
Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder with high incidence, and great heterogeneity of symptoms. Numerous factors are correlated with IBS development; however, the pathophysiology is not yet clear. In addition, there is no appropriate diagnostic tool available. The aim of this study was the identification of protein expression alterations in IBS patients compared to healthy individuals. Serum samples from 30 IBS patients (10 with IBS-Diarrhea, 10 IBS-Constipation and 10 IBS-Mixed) and 10 healthy individuals were subjected to proteomic analysis by 2-dimensional gel electrophoresis...
July 28, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28757465/mini-encyclopaedia-of-the-wound-healing-opportunities-for-integrating-multi-omic-approaches-into-medical-practice
#11
Lara Stolzenburg-Veeser, Olga Golubnitschaja
Wound healing is a highly complex life-important repair process triggered by plenty of local and/or systemic organ and tissue damaging events, such as an acute surgical invasion, accidental organ and tissue damages, acute and chronic diseases, aggressive local and systemic therapeutic approaches (e.g. irradiation and systemic chemotherapy). Individual health condition determines over the quality of wound healing. Impaired wound healing, in turn, may lead, for example, to post-surgical complications frequently observed in elderly, chronic ulcers in diabetic patients, hindered and ineffective pain management, etc...
July 28, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28757464/an-online-2d-reversed-phase-reversed-phase-chromatographic-method-for-sensitive-and-robust-plasma-protein-quantitation
#12
Vincent R Richard, Dominik Domanski, Andrew J Percy, Christoph H Borchers
Offline high-pH reversed-phase fractionation is widely used to reduce sample complexity in proteomic workflows. This is due to the semi-orthogonality and high peak resolution of the two separations. Offline 2D fractionation, however, is low throughput and requires several manual manipulations and is prone to sample losses. To address these issues, we developed an online two dimensional high-pH - low-pH reversed-phase-reversed-phase LC-MRM (2D RPRP) method whereby hundreds of peptides can be quantified in a single LC-MS/MS injection...
July 27, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28755913/comparative-proteomics-of-matrix-fractions-between-pimpled-and-normal-chicken-eggshells
#13
Zhangguo Liu, Lingzi Song, Lizhi Lu, Xianfu Zhang, Fuming Zhang, Kehua Wang, Robert J Linhardt
Eggshell matrix can be dissociated into three matrix fractions: acid-insoluble matrix (M1), water-insoluble matrix (M2) and acid-water facultative-soluble matrix (M3). Matrix fractions from pimpled and normal eggshells were compared using label-free proteomic method to understand the differences among three matrix fractions and the proteins involved with eggshell quality. A total of 738 and 600 proteins were identified in the pimpled and normal calcified eggshells, respectively. Both eggshells showed a combined proteomic inventory of 769 proteins...
July 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28755912/examination-of-pathways-involved-in-leukemia-inhibitory-factor-lif-induced-cell-growth-arrest-using-label-free-proteomics-approach
#14
Syed Azmal Ali, Gurjeet Kaur, Ashok Kumar Mohanty, Sudarshan Kumar
Leukemia inhibitory factor (LIF) is a multifunctional highly glycosylated protein, synthesized and secreted in various body tissues. Besides the abundance in multiple organs, the molecular mechanism underlying the LIF interactions for cell survival and polarity is poorly understood. In the present study, high-resolution LC-MS/MS based LFQ approach identified 2083 proteins with the overall PSM as 16,032. This proteomics data reviles that LIF promotes the AKT-mTOR signaling pathway. It induces cell growth arrest by an intracellular pathways loop to increase the half-life of the cell...
July 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28755911/itraq-proteomic-analysis-of-the-interactions-between-bombyx-mori-nuclear-polyhedrosis-virus-and-silkworm
#15
Wei-Tao Dong, Long-Fei Xiao, Jun-Jie Hu, Xin-Xu Zhao, Ji-Xing Liu, Yong Zhang
The silkworm hemolymph is an important defense system against bacteria and viruses. In this study, silkworms were infected with Bombyx mori nuclear polyhedrosis virus to investigate the subsequent immune response at the protein level. Proteomes were analyzed before and after infection using isobaric tags for relative and absolute quantitation and LC-MS. A total of 456 differentially expressed proteins were identified, of which 179 were upregulated and 193 were downregulated. Changes in expression were validated by western blot for several proteins...
July 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28751243/changes-in-protein-abundance-and-activity-induced-by-drought-during-generative-development-of-winter-barley-hordeum-vulgare-l
#16
Gabriela Gołębiowska-Pikania, Przemysław Kopeć, Ewa Surówka, Franciszek Janowiak, Monika Krzewska, Ewa Dubas, Anna Nowicka, Joanna Kasprzyk, Agnieszka Ostrowska, Sabina Malaga, Tomasz Hura, Iwona Żur
The present study investigated drought-induced changes in proteome profiles of ten DH lines of winter barley, relatively varied in water deficit tolerance level. Additionally, the parameters describing the functioning of the photosynthetic apparatus and the activity of the antioxidative system were analysed. Water deficit (3-week growth in soil with water content reduced to ca. 35%) induced significant changes in leaf water relations and reduced photosynthetic activity, probably due to decreased stomatal conductance...
July 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28739510/differential-proteomics-reveals-s100-a11-as-a-key-factor-in-aldosterone-induced-collagen-expression-in-human-cardiac-fibroblasts
#17
Ernesto Martínez-Martínez, Jaime Ibarrola, Mercedes Lachén-Montes, Amaya Fernández-Celis, Frederic Jaisser, Enrique Santamaría, Joaquín Fernández-Irigoyen, Natalia López-Andrés
Aldosterone (Aldo) could induce cardiac fibrosis, a hallmark of heart disease. Aldo direct effects on collagen production in cardiac fibroblasts remain controversial. Our aim is to characterize changes in the proteome of adult human cardiac fibroblasts treated with Aldo to identify new proteins altered that might be new therapeutic targets in cardiovascular diseases. Aldo increased collagens expressions in human cardiac fibroblasts. Complementary, using a quantitative proteomic approach, 30 proteins were found differentially expressed between control and Aldo-treated cardiac fibroblasts...
July 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28739511/revisiting-venom-of-the-sea-anemone-stichodactyla-haddoni-omics-techniques-reveal-the-complete-toxin-arsenal-of-a-well-studied-sea-anemone-genus
#18
Bruno Madio, Eivind A B Undheim, Glenn F King
More than a century of research on sea anemone venoms has shown that they contain a diversity of biologically active proteins and peptides. However, recent omics studies have revealed that much of the venom proteome remains unexplored. We used, for the first time, a combination of proteomic and transcriptomic techniques to obtain a holistic overview of the venom arsenal of the well-studied sea anemone Stichodactyla haddoni. A purely search-based approach to identify putative toxins in a transcriptome from tentacles regenerating after venom extraction identified 508 unique toxin-like transcripts grouped into 63 families...
July 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28739509/proteomic-analysis-of-the-secretome-of-human-bone-marrow-derived-mesenchymal-stem-cells-primed-by-pro-inflammatory-cytokines
#19
Elisa Maffioli, Simona Nonnis, Roberta Angioni, Fabiana Santagata, Bianca Calì, Lucia Zanotti, Armando Negri, Antonella Viola, Gabriella Tedeschi
Mesenchymal stem cells (MSC) represent an impressive opportunity in term of regenerative medicine and immunosuppressive therapy. Although it is clear that upon transplantation MSC exert most of their therapeutic effects through the secretion of bioactive molecules, the effects of a pro-inflammatory recipient environment on MSC secretome have not been characterized. In this study, we used a label free mass spectrometry based quantitative proteomic approach to analyze how pro-inflammatory cytokines modulate the composition of the human MSC secretome...
July 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28735093/stable-isotope-labeling-by-fatty-acids-in-cell-culture-silfac-coupled-with-isotope-pattern-dependent-mass-spectrometry-for-global-screening-of-lipid-hydroperoxide-mediated-protein-modifications
#20
Ryo Takahashi, Shuhei Fujioka, Tomoyuki Oe, Seon Hwa Lee
Lipid hydroperoxide-mediated modifications of proteins are receiving increasing attention because of their possible involvement in various degenerative diseases. These biological effects are attributed to the ability of lipid peroxidation-derived aldehydes to react with the nucleophilic sites of proteins. Here we describe a methodology involving metabolic labeling coupled with mass spectrometry-based proteomic analysis that enables global screening of lipid hydroperoxide-mediated protein modifications in a cell system...
July 20, 2017: Journal of Proteomics
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