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https://www.readbyqxmd.com/read/28339059/proteomic-based-identification-of-hsp70-as-a-tumor-associated-antigen-in-ovarian-cancer
#1
Xin-Xin Liu, Hua Ye, Peng Wang, Liu-Xia Li, Yi Zhang, Jian-Ying Zhang
Ovarian cancer commonly presents without prominent symptoms and is consequently diagnosed at advanced stages with unfavorable prognosis. Novel serological biomarkers for the early detection and clinical management of ovarian cancer are imminently needed. Proteomic-based methods for biomarker discovery are promising strategies implemented in cancer research. The aim of the present study was to identify new tumor antigens from the ovarian cancer cell line SKOV3 and their associated autoantibodies in sera of patients with ovarian cancer employing proteomic-based approaches...
March 24, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28336331/are-neutral-loss-and-internal-product-ions-useful-for-top-down-protein-identification
#2
Kaijie Xiao, Fan Yu, Houqin Fang, Bingbing Xue, Yan Liu, Yunhui Li, Zhixin Tian
Neutral loss and internal product ions have been found to be significant in both peptide and protein tandem mass spectra and they have been proposed to be included in database search and for protein identification. In addition to common canonical b/y ions in collision-based dissociation or c/z ions in electron-based dissociation, inclusion of neutral loss and internal product ions would certainly make better use of tandem mass spectra data; however, their ultimate utility for protein identification with false discovery rate control remains unclear...
March 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28335968/dipentaerythritol-penta-hexa-acrylate-based-highly-cross-linked-hybrid-monolithic-column-preparation-and-its-applications-for-ultrahigh-efficiency-separation-of-proteins
#3
Junqian Ma, Qian Dai, Xueyun Li, Xianghui Zhu, Teng Ma, Xiaoqiang Qiao, Shigang Shen, Xiuhua Liu
In this study, multi-acrylate based dipentaerythritol penta-/hexa-acrylate (DPEPA) was exploited for fabrication of highly cross-linked hybrid monolithic column by copolymerization with polyhedral oligomeric silsesquioxane methacryl substituted (POSS-MA) via a "one-pot" method. The new DPEPA-POSS hybrid monolithic column was respectively characterized by Fourier transform infrared spectrometry, thermogravimetric analysis, scanning electron microscopy and nitrogen adsorption/desorption measurement. When it was used for the separation of amides, thioureas and positional isomers of phenols, ultrahigh column efficiency separation (up to 511,000 N m(-1)) was achieved with excellent selectivity...
April 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28328168/intrastriatal-transplantation-of-human-neural-stem-cells-restores-the-impaired-subventricular-zone-in-parkinsonian-mice
#4
Fuxing Zuo, Feng Xiong, Xia Wang, Xueyuan Li, Renzhi Wang, Wei Ge, Xinjie Bao
Cell replacement therapy using neural stem cells (NSCs) transplantation has recently emerged as a promising method of Parkinson's disease (PD) treatment; however, the underlying mechanisms are not fully understood. To gain new insights into the mechanisms of 6-hydroxydopamine (6-OHDA)-induced lesioning and therapeutic efficacy of human NSCs (hNSCs) transplantation, the striatum (ST) of intrastriatal 6-OHDA-injected parkinsonian mice were unilaterally engrafted with undifferentiated hNSCs. A high-throughput quantitative proteomic approach was used to characterize the proteome profiles of PD-related brain regions such as the SN, ST, olfactory bulb (OB), and subventricular zone (SVZ) in these mice...
March 22, 2017: Stem Cells
https://www.readbyqxmd.com/read/28327990/estimating-the-total-number-of-phosphoproteins-and-phosphorylation-sites-in-eukaryotic-proteomes
#5
Panayotis Vlastaridis, Pelagia Kyriakidou, Anargyros Chaliotis, Yves Van de Peer, Stephen G Oliver, Grigoris D Amoutzias
Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and phosphorylation sites (p-sites), for four eukaryotes (human, mouse, Arabidopsis, and yeast)...
January 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28327659/the-immunosuppressant-mycophenolic-acid-alters-nucleotide-and-lipid-metabolism-in-an-intestinal-cell-model
#6
Svenja Heischmann, Monika Dzieciatkowska, Kirk Hansen, Dieter Leibfritz, Uwe Christians
The study objective was to elucidate the molecular mechanisms underlying the negative effects of mycophenolic acid (MPA) on human intestinal cells. Effects of MPA exposure and guanosine supplementation on nucleotide concentrations in LS180 cells were assessed using liquid chromatography-mass spectrometry. Proteomics analysis was carried out using stable isotope labeling by amino acids in cell culture combined with gel-based liquid chromatography-mass spectrometry and lipidome analysis using (1)H nuclear magnetic resonance spectroscopy...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327460/comprehensive-proteomic-characterization-of-stem-cell-derived-extracellular-matrices
#7
Héloïse Ragelle, Alexandra Naba, Benjamin L Larson, Fangheng Zhou, Miralem Prijić, Charles A Whittaker, Amanda Del Rosario, Robert Langer, Richard O Hynes, Daniel G Anderson
In the stem-cell niche, the extracellular matrix (ECM) serves as a structural support that additionally provides stem cells with signals that contribute to the regulation of stem-cell function, via reciprocal interactions between cells and components of the ECM. Recently, cell-derived ECMs have emerged as in vitro cell culture substrates to better recapitulate the native stem-cell microenvironment outside the body. Significant changes in cell number, morphology and function have been observed when mesenchymal stem cells (MSC) were cultured on ECM substrates as compared to standard tissue-culture polystyrene (TCPS)...
March 7, 2017: Biomaterials
https://www.readbyqxmd.com/read/28326926/potential-protein-biomarkers-for-burning-mouth-syndrome-discovered-by-quantitative-proteomics
#8
Eoon Hye Ji, Cynthia Diep, Tong Liu, Hong Li, Robert Merrill, Diana Messadi, Shen Hu
Burning mouth syndrome (BMS) is a chronic pain disorder characterized by severe burning sensation in normal looking oral mucosa. Diagnosis of BMS remains to be a challenge to oral healthcare professionals because the method for definite diagnosis is still uncertain. In this study, a quantitative saliva proteomic analysis was performed in order to identify target proteins in BMS patients' saliva that may be used as biomarkers for simple, non-invasive detection of the disease. By using isobaric tags for relative and absolute quantitation labeling and liquid chromatography-tandem mass spectrometry to quantify 1130 saliva proteins between BMS patients and healthy control subjects, we found that 50 proteins were significantly changed in the BMS patients when compared to the healthy control subjects ( p ≤ 0...
January 2017: Molecular Pain
https://www.readbyqxmd.com/read/28326073/rhoptry-protein-5-rop5-is-a-key-virulence-factor-in-neospora-caninum
#9
Lei Ma, Jing Liu, Muzi Li, Yong Fu, Xiao Zhang, Qun Liu
Neospora caninum, of the Apicomplexa phylum, is a common cause of abortions in cattle and nervous system dysfunction in dogs. Rhoptry proteins of Apicomplexa play an important role in virulence. The objectives of this study were to study functions of NcROP5 in N. caninum by deleting the NcROP5 gene from the wild Nc-1 strain. We selected NcROP5 in ToxoDB and successfully constructed an NcROP5 gene-deleted vector, pTCR-NcROP5-CD KO. Then we screened the NcROP5 knockout strains (ΔNcROP5) at the gene, protein and transcription levels...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28325852/extended-multiplexing-of-tmt-labeling-reveals-age-and-high-fat-diet-specific-proteome-changes-in-mouse-epididymal-adipose-tissue
#10
Deanna L Plubell, Phillip A Wilmarth, Yuqi Zhao, Alexandra M Fenton, Jessica Minnier, Ashok P Reddy, John Klimek, Xia Yang, Larry L David, Nathalie Pamir
The lack of high-throughput methods to analyze the adipose tissue protein composition limits our understanding of the protein networks responsible for age and diet related metabolic response. We have developed an approach using multiple-dimension liquid chromatography tandem mass spectrometry and extended multiplexing (24 biological samples) with TMT labeling to analyze proteomes of epididymal adipose tissues isolated from mice fed either low or high fat diet for a short or a long-term, and from mice that aged on low vs...
March 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28317950/in-vivo-identification-of-potential-uranium-protein-targets-in-zebrafish-ovaries-after-chronic-waterborne-exposure
#11
Y Eb-Levadoux, S Frelon, O Simon, C Arnaudguilhem, R Lobinski, S Mounicou
Ecotoxicological studies have indicated the reprotoxicity of uranium (U) in zebrafish, but its molecular mechanisms remain unclear. Due to the non-covalent nature of U-protein complexes, canonical proteomics approaches are often not relevant as they usually use denaturating reagents or solvents. In this study, non-denaturating (ND) methods were used to obtain insight into the nature of U potential targets in ovaries of reproduced and non-reproduced zebrafish after 20 days of exposure to an environmentally relevant U concentration (20 μg L(-1))...
March 20, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28317605/use-of-foodomics-for-control-of-food-processing-and-assessing-of-food-safety
#12
D Josić, Ž Peršurić, D Rešetar, T Martinović, L Saftić, S Kraljević Pavelić
Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28317598/corrigendum-to-proteomics-method-to-quantify-the-percentage-of-cow-goat-and-sheep-milks-in-raw-materials-for-dairy-products-j-dairy-sci-99-9483-9492
#13
Q Chen, X Ke, J S Zhang, S Y Lai, F Fang, W M Mo, Y P Ren
No abstract text is available yet for this article.
April 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28317313/profiling-of-antioxidative-enzyme-expression-induced-by-various-food-components-using-targeted-proteome-analysis
#14
Sven Bartenbacher, Christiane Östreicher, Monika Pischetsrieder
SCOPE: A method was developed for targeted proteome analysis of the expression profile of a set of antioxidative enzymes in rat macrophages and applied to screen the antioxidative potential of several food components/foods. METHODS AND RESULTS: Expression profiles of heme oxygenase 1, peroxiredoxin 1, thioredoxin reductase 1, glutathione reductase, glutathione-S transferase P1, and superoxide dismutase 1 were analyzed by nanoLC-MS/MS in selected scheduled reaction monitoring (sSRM) mode monitoring 2-3 peptides per protein and 3 transitions per peptide...
March 20, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28316883/middle-pleistocene-protein-sequences-from-the-rhinoceros-genus-stephanorhinus-and-the-phylogeny-of-extant-and-extinct-middle-late-pleistocene-rhinocerotidae
#15
Frido Welker, Geoff M Smith, Jarod M Hutson, Lutz Kindler, Alejandro Garcia-Moreno, Aritza Villaluenga, Elaine Turner, Sabine Gaudzinski-Windheuser
BACKGROUND: Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis)...
2017: PeerJ
https://www.readbyqxmd.com/read/28316149/detecting-alternatively-spliced-transcript-isoforms-from-single-molecule-long-read-sequences-without-a-reference-genome
#16
Xiaoxian Liu, Wenbin Mei, Pamela S Soltis, Douglas E Soltis, W Brad Barbazuk
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq(™) data for isoform-level transcriptome analysis, including the study of AS and gene fusion. We applied Iso-Seq(™) to investigate AS in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living angiosperms. Our data show that, compared with RNA-Seq data, the Iso-Seq(™) platform provides better recovery on large transcripts, new gene locus identification, and gene model correction...
March 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28315482/modes-of-antibacterial-action-of-curcumin-under-dark-and-light-conditions-a-toxicoproteomics-approach
#17
Ilya Shlar, Samir Droby, Victor Rodov
Curcumin is a potent natural food-grade antimicrobial compound. Exposure to light further enhances its antimicrobial capacity. Proteomic methods were used in this study for investigating the mechanistic aspects of the antibacterial curcumin effects in the dark and upon illumination. Escherichia coli cells exposed to water-dispersible curcumin-methyl-β-cyclodextrin inclusion complex under dark and light conditions were compared with the non-treated cells kept under the same illumination regimes. Curcumin treatment in the dark evoked adaptive responses aimed at mitigation of oxidative stress, DNA protection, proteostasis, modulation of redox state via changing NADH level, and gasotransmitter (H2S and NH3) biosynthesis...
March 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28315252/profiling-of-protease-cleavage-sites-by-proteome-derived-peptide-libraries-and-quantitative-proteomics
#18
Chia-Yi Chen, Bettina Mayer, Oliver Schilling
Biochemical profiling of active site specificity is a crucial step to characterize proteases, which play key roles in health and disease. Here, we present a protocol using proteome-derived peptide libraries in combination with quantitative proteomics to simultaneously identify cleavage motifs N- and C-terminal to the scissile peptide bond. First, bacterial or eukaryotic cell lysate is used to generate peptide libraries. Without further chemical modification, peptide libraries are then split into control and treated (incubate with active protease) aliquots...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315251/fpps-fast-profiling-of-protease-specificity
#19
Matej Vizovišek, Robert Vidmar, Marko Fonović
Profiling of protease specificity is crucial for characterization of these important enzymes that play numerous roles in health and disease. In the past, several proteomic methods have been developed that enable profiling of protease specificities. Although able to identify thousands of protease cleavage events, these degradomics approaches are often time consuming and methodologically challenging, which limits their application to specialized proteomic groups or the laboratories that initially introduced them...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315248/proc-tel-profiling-of-protein-c-termini-by-enzymatic-labeling
#20
Wenwen Duan, Guoqiang Xu
Proteins are frequently processed by proteases in cell signaling pathways to perform their biological functions in response to environmental stimuli. Identification of the exact cleavage sites provides necessary information for the study of their biological functions. Although proteomic approaches for profiling of protein N-termini have been developed extensively in the past few years, the N-terminal profiling strategy has its inherent disadvantages. Therefore, C-terminal profiling approaches might be a complementary approach for the identification of protein cleavages although it has similar shortcomings as N-terminal profiling methods...
2017: Methods in Molecular Biology
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