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Journal of Proteomics

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https://www.readbyqxmd.com/read/29223802/proteogenomic-insights-into-uranium-tolerance-of-a-chernobyl-s-microbacterium-bacterial-isolate
#1
Gallois Nicolas, Alpha-Bazin Béatrice, Ortet Philippe, Barakat Mohamed, Piette Laurie, Long Justine, Berthomieu Catherine, Armengaud Jean, Chapon Virginie
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance...
December 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29223801/the-external-face-of-candida-albicans-a-proteomic-view-of-the-cell-surface-and-the-extracellular-environment
#2
Ana Gil-Bona, Ahinara Amador-García, Concha Gil, Lucia Monteoliva
The cell surface and secreted proteins are the initial points of contact between Candida albicans and the host. Improvements in protein extraction approaches and mass spectrometers have allowed researchers to obtain a comprehensive knowledge of these external subproteomes. In this paper, we review the published proteomic studies that have examined C. albicans extracellular proteins, including the cell surface proteins or surfome and the secreted proteins or secretome. The use of different approaches to isolate cell wall and cell surface proteins, such as fractionation approaches or cell shaving, have resulted in different outcomes...
December 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29208510/differential-impacts-of-individual-and-combined-exposures-of-deoxynivalenol-and-zearalenone-on-the-heparg-human-hepatocyte-proteome
#3
Marie-Caroline Smith, Emma Timmins-Schiffman, Monika Coton, Emmanuel Coton, Nolwenn Hymery, Brook L Nunn, Stéphanie Madec
Numerous surveys have highlighted the natural co-occurrence of deoxynivalenol (DON) and zearalenone (ZEA) mycotoxins in food and feed. Nevertheless, data regarding cellular mechanisms involved in response to their individual and simultaneous exposures are lacking. In this study, in order to analyze how low mycotoxin doses could impact cellular physiology and homeostasis, proteomic profiles of proliferating human hepatocytes (HepaRG) exposed for 1h and 24h to low DON and ZEA cytotoxicity levels (0.2 and 20μM respectively), alone or in combination, were analyzed by LC-MS/MS...
December 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29199152/low-level-hg2-exposure-modulates-the-b-cell-cytoskeletal-phosphoproteome
#4
Nicholas J Carruthers, Allen J Rosenspire, Joseph A Caruso, Paul M Stemmer
Exposure of Wehi-231 B-cells to Hg2+ for 5min resulted in concentration dependent changes in protein phosphorylations. Phosphorylation was quantified using mass spectrometry to analyze TiO2 and anti-pTyr antibody selected phosphopeptides from Wehi-231 digests. The most frequent and largest amplitude responses to Hg2+ exposure were increased phosphorylation although a decrease was observed for 1% of phosphoproteins detected in the untreated cells. A subset of proteins responded with an increase in phosphorylation to Hg2+ exposure at low micromolar concentrations...
November 30, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29199151/gender-influence-on-the-salivary-protein-profile-of-finishing-pigs
#5
Ana M Gutiérrez, Ana Montes, Cándido Gutiérrez-Panizo, Pablo Fuentes, Ernesto De La Cruz-Sánchez
A study on gender differences in the normal range of biomarkers in porcine saliva samples has the scope for further attention. In the present study, the salivary protein profiles of age-matched healthy male and female finishing pigs were compared. The levels of salivary adenosine deaminase (ADA) activity, haptoglobin (Hp) and C-reactive protein (CRP) have been quantified in 32 male and 32 female pigs to ensure the presence of gender effect on the median levels of salivary biomarkers. Moreover, the total salivary protein content was quantified and compared...
November 30, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29199150/peroxiredoxin-2-and-zinc-alpha-2-glycoprotein-as-potentially-combined-novel-salivary-biomarkers-for-early-detection-of-oral-squamous-cell-carcinoma-using-proteomic-approaches
#6
Chukkris Heawchaiyaphum, Chamsai Pientong, Pensiri Phusingha, Patravoot Vatanasapt, Supannee Promthet, Jureerut Daduang, Watchareporn Teeramatwanich, Bunkerd Kongyingyoes, Jureeporn Chuerduangphui, Tipaya Ekalaksananan
No effective screening method is available for oral squamous cell carcinoma (OSCC) that is recognized to influence by environmental factors as well as human papillomavirus (HPV) and Epstein-Barr virus (EBV). Therefore, we sought to identify salivary biomarkers for screening of OSCC with or without HPV and/or EBV infection. Saliva, lesion and oral exfoliated cells were collected from OSCC patients and cancer-free controls (CFCs) and grouped depending on their HPV- and EBV-infection status. Salivary protein was precipitated and subjected to 2-dimensional gel electrophoresis...
November 30, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29199149/ultra-high-mass-multimer-analysis-of-protein-1a-capping-domains-by-a-silicon-nanomembrane-detector
#7
H C Shin, D Deterra, J Park, H Kim, M Nishikiori, Ch Uetrecht, P G Ahlquist, M Arbulu, R H Blick
Conventional time of flight ion detectors are based on secondary electron multipliers encountering a significant loss in detection efficiency, sensitivity and resolution with protein mass above 50kDa. In this work we employ a silicon nanomembrane detector in a Matrix-Assisted Laser Desorption/Ionization coupled to time of flight (MALDI-TOF) mass spectrometer. The operating principle relies on phonon-assisted field emission with excellent performance in the high mass range from 0.001-2MDa. In addition to the analysis of standard proteins the nanomembrane detector (NMD) has the potential for the detection and structural investigation of complex macromolecular assemblies through non-covalent interactions...
November 30, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29197583/evaluation-of-ion-mobility-for-the-separation-of-glycoconjugate-isomers-due-to-different-types-of-sialic-acid-linkage-at-the-intact-glycoprotein-glycopeptide-and-glycan-level
#8
Albert Barroso, Estela Giménez, Albert Konijnenberg, Jaime Sancho, Victoria Sanz-Nebot, Frank Sobott
The study of protein glycosylation can be regarded as an intricate but very important task, making glycomics one of the most challenging and interesting, albeit under-researched, type of "omics" science. Complexity escalates remarkably when considering that carbohydrates can form severely branched structures with many different constituents, which often leads to the formation of multiple isomers. In this regard, ion mobility (IM) spectrometry has recently demonstrated its power for the separation of isomeric compounds...
November 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29197582/label-free-quantitative-proteomic-profiling-of-colon-cancer-cells-identifies-acetyl-coa-carboxylase-alpha-as-antitumor-target-of-citrus-limon-derived-nanovesicles
#9
Stefania Raimondo, Laura Saieva, Marta Cristaldi, Francesca Monteleone, Simona Fontana, Riccardo Alessandro
We have previously isolated exosome-like nanoparticles from Citrus-limon juice, able to inhibit in vitro and in vivo tumor cell growth. In order to deeply understand the mechanism underlying nanovesicle effects, we performed a proteomic profile of treated colorectal cancer cells. Among the proteins differentially expressed after nanovesicle treatment, we found a significant downregulation of the Acetyl-CoA Carboxylase 1 (ACACA) and we demonstrated that silencing ACACA in cancer cells leads to a reduction of cell growth...
November 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29197581/proteomic-analysis-of-bombyx-mori-molting-fluid-insights-into-the-molting-process
#10
Hua-Wei Liu, Luo-Ling Wang, Xin Tang, Zhao-Ming Dong, Peng-Chao Guo, Dong-Chao Zhao, Qing-You Xia, Ping Zhao
Molting is an essential biological process occurring multiple times throughout the life cycle of most Ecdysozoa. Molting fluids accumulate and function in the exuvial space during the molting process. In this study, we used liquid chromatography-tandem mass spectrometry to investigate the molting fluids to analyze the molecular mechanisms of molting in the silkworm, Bombyx mori. In total, 375 proteins were identified in molting fluids from the silkworm at 14-16h before pupation and eclosion, including 12 chitin metabolism-related enzymes, 35 serine proteases, 15 peptidases, and 38 protease inhibitors...
November 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29191748/study-of-a-novel-agent-for-tca-precipitated-proteins-washing-comprehensive-insights-into-the-role-of-ethanol-hcl-on-molten-globule-state-by-multi-spectroscopic-analyses
#11
Balkis Eddhif, Justin Lange, Nadia Guignard, Yann Batonneau, Jonathan Clarhaut, Sébastien Papot, Claude Geffroy-Rodier, Pauline Poinot
Sample preparation for mass spectrometry-based proteomics is a key step for ensuring reliable data. In gel-free experimental workflows, protein purification often starts with a precipitation stage using trichloroacetic acid (TCA). In presence of TCA, proteins precipitate in a stable molten globule state making the pellet difficult to solubilize in aqueous buffer for proteolytic digestion and MS analysis. In this context, the objective of this work was to study the suitability of a novel agent, ethanol/HCl, for the washing of TCA-precipitated proteins...
November 27, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29191747/peptide-fingerprinting-of-the-sea-anemone-heteractis-magnifica-mucus-revealed-neurotoxins-kunitz-type-proteinase-inhibitors-and-a-new-%C3%AE-defensin-%C3%AE-amylase-inhibitor
#12
Oksana Sintsova, Irina Gladkikh, Victoria Chausova, Margarita Monastyrnaya, Stanislav Anastyuk, Oleg Chernikov, Ekaterina Yurchenko, Dmitriy Aminin, Marina Isaeva, Elena Leychenko, Emma Kozlovskaya
Sea anemone mucus, due to its multiple and vital functions, is a valuable substance for investigation of new biologically active peptides. In this work, compounds of Heteractis magnifica mucus were separated by multistage liquid chromatography and resulting fractions were analyzed by MALDI-TOF MS. Peptide maps constructed according to the molecular masses and hydrophobicity showed presence of 326 both new and known peptides. Several major peptides from mucus were identified, including the sodium channel toxin RpII isolated earlier from H...
November 27, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29191746/proteomics-analysis-to-understand-the-aba-stimulation-of-wound-suberization-in-kiwifruit
#13
Xueyuan Han, Wenjing Lu, Xiaopeng Wei, Li Li, Linchun Mao, Yuying Zhao
Quick suberin-based healing after wounding played a protective role for plant to prevent further damage. In this study, the stimulative effect of exogenous abscisic acid (ABA) on wound suberization in postharvest kiwifruit was evaluated through suberin staining with toluidine blue O as well as the determination of suberin phenolics and aliphatics in wound tissue. Furthermore, to reveal the regulatory involvement of ABA in wound suberization, comparative quantitative proteomics and transcriptomics analyses based on iTRAQ and qRT-PCR technique were performed...
November 27, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29180046/proteomics-in-cardiovascular-diseases-unveiling-sex-and-gender-differences-in-the-era-of-precision-medicine
#14
Roberta Baetta, Marta Pontremoli, Alma Martinez Fernandez, Corinne M Spickett, Cristina Banfi
Cardiovascular diseases (CVDs) represent the most important cause of mortality in women and in men. Contrary to the long-standing notion that the effects of the major risk factors on CVD outcomes are the same in both sexes, recent evidence recognizes new, potentially independent, sex/gender-related risk factors for CVDs, and sex/gender-differences in the clinical presentation of CVDs have been demonstrated. Furthermore, some therapeutic options may not be equally effective and safe in men and women. In this context, proteomics offers an extremely useful and versatile analytical platform for biomedical researches that expand from the screening of early diagnostic and prognostic biomarkers to the investigation of the molecular mechanisms underlying CDVs...
November 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29180045/unraveling-the-human-protein-atlas-of-metastatic-melanoma-in-the-course-of-ultraviolet-radiation-derived-photo-therapy
#15
Eumorphia G Konstantakou, Athanassios D Velentzas, Athanasios K Anagnostopoulos, Aikaterini F Giannopoulou, Ema Anastasiadou, Issidora S Papassideri, Gerassimos E Voutsinas, George Th Tsangaris, Dimitrios J Stravopodis
To explore the photo-therapeutic capacity of UV radiation in solid tumors, we herein employed an nLC-MS/MS technology to profile the proteomic landscape of irradiated WM-266-4 human metastatic-melanoma cells. Obtained data resulted in proteomic catalogues of 5982 and 7280 proteins for UVB- and UVC-radiation conditions, respectively, and indicated the ability of UVB/C-radiation forms to eliminate metastatic-melanoma cells through induction of synergistically operating programs of apoptosis and necroptosis. However, it seems that one or more WM-266-4 cell sub-populations may escape from UV-radiation's photo-damaging activity, acquiring, besides apoptosis tolerance, an EMT phenotype that likely offers them the advantage of developing resistance to certain chemotherapeutic drugs...
November 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29175092/differences-in-resistance-to-nitrogen-and-phosphorus-deficiencies-explain-male-biased-populations-of-poplar-in-nutrient-deficient-habitats
#16
Haifeng Song, Yanbao Lei, Sheng Zhang
In most forest soils, the availability of nitrogen (N) and phosphorus (P) nutrients is low and unable to meet the requirement of tree growth. In the past decades, sex-based differences in poplar have been investigated in morphology and physiology. Proteomic techniques provide new insights into sex-specific differences at the molecular level. This review gives a comparative overview of the effects of N and P deficiencies on poplar physiological and proteomic characteristics. Male poplars are more efficient at photosynthesis and nutrient usage than females...
November 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29175091/phosphoprotein-dige-profiles-reflects-blast-differentiation-cytogenetic-risk-stratification-flt3-npm1-mutations-and-therapy-response-in-acute-myeloid-leukaemia
#17
Rakel Brendsdal Forthun, Elise Aasebø, Josef Daniel Rasinger, Siv Lise Bedringaas, Frode Berven, Frode Selheim, Øystein Bruserud, Bjørn Tore Gjertsen
Acute myeloid leukaemia (AML) is an aggressive blood cancer characterized by a distinct block in differentiation of myeloid progenitors, recurrent chromosomal translocations and gene mutations of which >50% involve signal transduction through dysregulated kinases and phosphatases. In search for novel protein biomarkers for disease stratification we investigated the phosphoproteome in leukaemic cells from 62 AML patients at time of diagnosis using immobilized metal-affinity chromatography, protein separation by two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry before validation by selected reaction monitoring (SRM)...
November 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29157724/differential-n-glycan-patterns-identified-in-lung-adenocarcinoma-by-n-glycan-profiling-of-formalin-fixed-paraffin-embedded-ffpe-tissue-sections
#18
Xiaoning Wang, Zaian Deng, Chuncui Huang, Tong Zhu, Jiatao Lou, Lin Wang, Yan Li
N-glycan profiling is a powerful approach for analyzing the functional relationship between N-glycosylation and cancer. Current methods rely on either serum or fresh tissue samples; however, N-glycan patterns may differ between serum and tissue, as the proteins of serum originate from a variety of tissues. Furthermore, fresh tissue samples are difficult to ship and store. Here, we used a profiling method based on formalin-fixed paraffin-embedded (FFPE) tissue sections from lung adenocarcinoma patients. We found that our method was highly reproducible...
November 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29155091/dynamic-molecular-events-associated-to-plasmodium-berghei-gametogenesis-through-proteomic-approach
#19
Carlos H S Garcia, Delphine Depoix, Rayner M L Queiroz, Jaques M F Souza, Wagner Fontes, Marcelo V de Sousa, Marlon D M Santos, Paulo C Carvalho, Philippe Grellier, Sébastien Charneau
Plasmodium mature sexual cycle occurs in the vector mosquitoes and ensures the transmission to a new host. Gametogenesis takes place within minutes in the vector midgut. Gametocytes have to complete a deep nuclear reorganization, quick differentiation, and in the case of male gametocytes, intracytoplasmic flagellum assembly that results in free-swimming microgametes required for macrogamete fertilization. In efforts to improve our knowledge of molecular mechanisms involved in gamete morphogenesis, we carried out a nanoLC/MSMS based quantitative proteomic analysis throughout the xanthurenic acid-induced gametogenesis of the rodent parasite P...
November 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29155090/proteome-and-phosphoproteome-analysis-of-commensally-induced-dendritic-cell-maturation-states
#20
Ali Giray Korkmaz, Todor Popov, Loulou Peisl, Marius Cosmin Codrea, Sven Nahnsen, Alexander Steimle, Ana Velic, Boris Macek, Martin von Bergen, Joerg Bernhardt, Julia-Stefanie Frick
Dendritic cells (DCs) can shape the immune system towards an inflammatory or tolerant state depending on the bacterial antigens and the environment they encounter. In this study we provide a proteomic catalogue of differentially expressed proteins between distinct DC maturation states, brought about by bacteria that differ in their endotoxicity. To achieve this, we have performed proteomics and phosphoproteomics on murine DC cultures. Symbiont and pathobiont bacteria were used to direct dendritic cells into a semi-mature and fully-mature state, respectively...
November 15, 2017: Journal of Proteomics
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