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https://www.readbyqxmd.com/read/28098900/endothelial-microparticles-activate-endothelial-cells-to-facilitate-the-inflammatory-response
#1
Yiyun Liu, Ruyuan Zhang, Hongping Qu, Jun Wu, Lei Li, Yaoqing Tang
Endothelial microparticles (EMPs) and endothelial cells (ECs) are involved in the pathophysiological mechanisms of sepsis and septic shock. EMPs are small vesicles released by ECs and are considered biomarkers for endothelial cell function and mediators for intercellular information exchange. However, the effect of EMPs on their parental ECs remains unknown. The present study collected tumor necrosis factor‑α‑derived EMPs and detected the proinflammatory cytokines released from unstimulated and EMP‑stimulated ECs by proteome profiler array...
January 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098518/a-4-nitroquinoleneoxide-induced-pleurotus-eryngii-mutant-variety-increases-pin1-expression-in-rat-brain
#2
Yoonhwa Jeong, Mina Jung, Myeung Ju Kim, Cheol Ho Hwang
To develop Pleurotus eryngii varieties with improved medicinal qualities, protoplasts of P. eryngii were mutagenized using 4-nitroquinoleneoxide. The effects of the resulting variant mushrooms on a human cell were evaluated by applying their aqueous extracts to the human hepatoma cell line, HepG2, in vitro and examining any alteration in the proteomes of the treated HepG2. The P. eryngii mutant, NQ2A-12, was selected for its effects on increasing the expression level of Pin1 in HepG2. Pin1 is one of the peptidyl-prolyl cis-trans isomerases known to play an important role in repressing Alzheimer's disease pathogenesis...
January 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28098439/understanding-the-proteomes-using-non-proteomics-approaches-expanding-the-scope-of-proteomics
#3
EDITORIAL
Lucie Kalvodova
No abstract text is available yet for this article.
January 2017: Proteomics
https://www.readbyqxmd.com/read/28098335/not-an-exception-to-the-rule-the-functional-significance-of-intrinsically-disordered-protein-regions-in-enzymes
#4
Shelly DeForte, Vladimir N Uversky
Intrinsically disordered protein regions (IDPRs) are remarkably common and have unique and important biological functions. Enzymes have long been considered an exception to the rule of protein intrinsic disorder due to the structural requirements for catalysis. Although functionally significant IDPRs have been described in several enzymes, there has been no study quantifying the extent of this phenomenon. We have conducted a multilevel computational analysis of missing regions in X-ray crystal structures in the PDB and predicted disorder in 66 representative proteomes...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28098164/uncovering-the-sumoylation-and-ubiquitylation-crosstalk-in-human-cells-using-sequential-peptide-immunopurification
#5
Frédéric Lamoliatte, Francis P McManus, Ghizlane Maarifi, Mounira K Chelbi-Alix, Pierre Thibault
Crosstalk between the SUMO and ubiquitin pathways has recently been reported. However, no approach currently exists to determine the interrelationship between these modifications. Here, we report an optimized immunoaffinity method that permits the study of both protein ubiquitylation and SUMOylation from a single sample. This method enables the unprecedented identification of 10,388 SUMO sites in HEK293 cells. The sequential use of SUMO and ubiquitin remnant immunoaffinity purification facilitates the dynamic profiling of SUMOylated and ubiquitylated proteins in HEK293 cells treated with the proteasome inhibitor MG132...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097710/comparative-evaluation-of-label-free-quantification-methods-for-shotgun-proteomics
#6
Julia A Bubis, Lev I Levitsky, Mark V Ivanov, Irina A Tarasova, Mikhail V Gorshkov
RATIONALE: Label-free quantification (LFQ) is a popular strategy for shotgun proteomics. A variety of LFQ algorithms have been developed recently. However, a comprehensive comparison of the most commonly used LFQ methods is still rare, in part due to a lack of clear metrics for their evaluation and an annotated and quantitatively well-characterized data set. METHODS: Five LFQ methods were compared: spectral counting based algorithms SIN , emPAI, and NSAF, and approaches relying on the extracted ion chromatogram (XIC) intensities, MaxLFQ and Quanti...
January 18, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28097686/context-characterization-of-amino-acid-homorepeats-using-evolution-position-and-order
#7
Pablo Mier, Gregorio Alanis-Lobato, Miguel A Andrade-Navarro
Amino acid repeats, or homorepeats, are low complexity protein motifs consisting of tandem repetitions of a single amino acid. Their presence and relative number vary in different proteomes, and some studies have tried to address this variation, proteome by proteome. In this work, we present a full characterization of amino acid homorepeats across evolution. We studied the presence and differential usage of each possible homorepeat in proteomes from various taxonomic groups, using clusters of very similar proteins to eliminate redundancy...
January 18, 2017: Proteins
https://www.readbyqxmd.com/read/28097685/cartilage-oligomeric-matrix-protein-comp-neo-epitope-in-the-synovial-fluid-of-horses-with-acute-lameness-a-new-biomarker-for-the-early-stages-of-osteoarthritis
#8
E Skiöldebrand, S Ekman, L MattssonHultén, E Svala, K Björkman, A Lindahl, A Lundqvist, P Önnerfjord, C Sihlbom, U Rüetschi
BACKGROUND: Clinical tools to diagnose the early changes of osteoarthritis (OA) that occur in the articular cartilage are lacking. OBJECTIVES: We sought to identify and quantify a novel cartilage oligomeric matrix protein (COMP) neo-epitope in the synovial fluid from the joints of healthy horses and those with different stages of OA. STUDY DESIGN: In vitro quantitative proteomics and assay development with application in synovial fluids samples obtained from biobanks of well-characterised horses...
January 17, 2017: Equine Veterinary Journal
https://www.readbyqxmd.com/read/28097537/optimization-of-a-new-aerodynamic-cylindrical-faims-device-for-small-molecule-analysis
#9
Randy W Purves, Satendra Prasad, Michael Belford, Albert Vandenberg, Jean-Jacques Dunyach
The implementation of an aerodynamic mechanism to improve ion sampling between nanoelectrospray (n-ESI) and FAIMS was recently reported for proteomic analyses. This investigation explores the new FAIMS interface for small molecule analysis at high liquid flow rates and includes an examination of key differences in ionization between heated-ESI (HESI) and n-ESI. The sheath gas, critical for desolvation with HESI, affects FAIMS operation as higher FAIMS gas flow rates are required to achieve sufficient desolvation...
January 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28097424/analysis-of-the-spleen-proteome-of-chickens-infected-with-reticuloendotheliosis-virus
#10
Mei Xue, Yan Zhao, Shunlei Hu, Xingming Shi, Hongyu Cui, Yunfeng Wang
Infection with reticuloendotheliosis virus (REV), a gammaretrovirus in the family Retroviridae, can result in immunosuppression and subsequent increased susceptibility to secondary infections. In the present study, we identified differentially expressed proteins in the spleens of chickens infected with the REV-A HLJ07I strain, using two-dimensional gel electrophoresis on samples from time points coinciding with different phases of the REV life cycle. Differentially expressed proteins were identified using one-dimensional liquid chromatography electrospray ionization tandem mass spectrometry (1D LC ESI MS/MS)...
January 17, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28097378/-molecular-pathogenesis-of-duchenne-muscular-dystrophy-related-fibrosis
#11
K Ohlendieck, D Swandulla
Progressive myofibrosis plays a key role in Duchenne muscular dystrophy. The dystrophic loss of contractile cells triggers a relatively nonspecific restructuring of the surrounding mesenchyme. The increase in connective and fatty tissue leads to muscular weakness and is therefore of critical importance for the cellular pathogenesis of muscular dystrophy. The systematic biochemical analysis of fibrosis using comparative proteomics has identified a number of extracellular matrix proteins that are indirectly involved in muscular dystrophy...
January 17, 2017: Der Pathologe
https://www.readbyqxmd.com/read/28097087/identification-of-the-vascular-endothelial-growth-factor-signalling-pathway-by-quantitative-proteomic-analysis-of-rat-condylar-cartilage
#12
Liting Jiang, Yinyin Xie, Li Wei, Qi Zhou, Xing Shen, Xinquan Jiang, Yiming Gao
Angiogenesis mediated by vascular endothelial growth factor (VEGF) is known to play an important role in regulating cartilage remodelling and endochondral ossification. However, the details of how VEGF signalling mechanisms affect condyle remodelling in response to alterations in functional loading remains unclear. To explore this, eighty 16-day-old male SD rats were divided into two equal groups which were fed either a soft/powdery diet or a hard diet for 4 weeks; the stiffness of the diet results in alteration of mastication force and hence temporomandibular joint (TMJ) development...
January 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28096900/ms_histonedb-a-manually-curated-resource-for-proteomic-analysis-of-human-and-mouse-histones
#13
Sara El Kennani, Annie Adrait, Alexey K Shaytan, Saadi Khochbin, Christophe Bruley, Anna R Panchenko, David Landsman, Delphine Pflieger, Jérôme Govin
BACKGROUND: Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28096404/torc1-dependent-sumoylation-of-rpc82-promotes-rna-polymerase-iii-assembly-and-activity
#14
Pierre Chymkowitch, Aurélie Nguéa P, Håvard Aanes, Joseph Robertson, Arne Klungland, Jorrit M Enserink
Maintaining cellular homeostasis under changing nutrient conditions is essential for the growth and development of all organisms. The mechanisms that maintain homeostasis upon loss of nutrient supply are not well understood. By mapping the SUMO proteome in Saccharomyces cerevisiae, we discovered a specific set of differentially sumoylated proteins mainly involved in transcription. RNA polymerase III (RNAPIII) components, including Rpc53, Rpc82, and Ret1, are particularly prominent nutrient-dependent SUMO targets...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096348/transcriptomic-proteomic-and-metabolomic-landscape-of-positional-memory-in-the-caudal-fin-of-zebrafish
#15
Jeremy S Rabinowitz, Aaron M Robitaille, Yuliang Wang, Catherine A Ray, Ryan Thummel, Haiwei Gu, Danijel Djukovic, Daniel Raftery, Jason D Berndt, Randall T Moon
Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified. Here, we quantified the global abundance of transcripts, proteins, and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach, we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions, including development, bioelectric signaling, and amino acid and lipid metabolism...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096192/integrated-physiological-proteomic-and-metabolomic-analysis-of-uv-stress-responses-and-adaptation-mechanisms-in-pinus-radiata
#16
Jesus Pascual, Maria Jesus Canal, Monica Escandon, Monica Meijon, Wolfram Weckwerth, Luis Valledor
Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus sp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner...
January 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28096092/initiation-of-acute-graft-versus-host-disease-by-angiogenesis
#17
Katarina Riesner, Yu Shi, Angela Jacobi, Martin Kraeter, Martina Kalupa, Aleixandria McGearey, Sarah Mertlitz, Steffen Cordes, Jens-Florian Schrezenmeier, Jörg Mengwasser, Sabine Westphal, Daniel Perez-Hernandez, Clemens Schmitt, Gunnar Dittmar, Jochen Guck, Olaf Penack
The inhibition of inflammation-associated angiogenesis ameliorates inflammatory diseases by reducing the recruitment of tissue infiltrating leukocytes. However, it is not known if angiogenesis has an active role during the initiation of inflammation or if it is merely a secondary effect occurring in response to stimuli by tissue infiltrating leukocytes. Here we show that angiogenesis precedes leukocyte infiltration in experimental models of inflammatory bowel disease and acute graft-versus-host disease (GVHD)...
January 17, 2017: Blood
https://www.readbyqxmd.com/read/28096085/improved-orthology-inference-with-hieranoid-2
#18
Mateusz Kaduk, Erik Sonnhammer
MOTIVATION: The initial step in many orthology inference methods is the computationally demanding establishment of all pairwise protein similarities across all analysed proteomes. The quadratic scaling with proteomes has become a major bottleneck. A remedy is offered by the Hieranoid algorithm which reduces the complexity to linear by hierarchically aggregating ortholog groups from InParanoid along a species tree. RESULTS: We have further developed the Hieranoid algorithm in many ways...
January 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28096083/lrssl-predict-and-interpret-drug-disease-associations-based-on-data-integration-using-sparse-subspace-learning
#19
Xujun Liang, Pengfei Zhang, Lu Yan, Ying Fu, Fang Peng, Lingzhi Qu, Meiying Shao, Yongheng Chen, Zhuchu Chen
MOTIVATION: Exploring the potential curative effects of drugs is crucial for effective drug development. Previous studies have indicated that integration of multiple types of information could be conducive to discovering novel indications of drugs. However, how to efficiently identify the mechanism behind drug-disease associations while integrating data from different sources remains a challenging problem. RESULTS: In this research, we present a novel method for indication prediction of both new drugs and approved drugs...
January 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28095989/prolonged-k-deficiency-increases-intracellular-atp-cell-cycle-arrest-and-cell-death-in-renal-tubular-cells
#20
Kedsarin Fong-Ngern, Nardtaya Ausakunpipat, Nilubon Singhto, Kanyarat Sueksakit, Visith Thongboonkerd
BACKGROUND: Chronic potassium (K(+)) deficiency can cause renal damage namely hypokalemic nephropathy with unclear pathogenic mechanisms. In the present study, we investigated expression and functional alterations in renal tubular cells induced by prolonged K(+) deficiency. METHODS: MDCK cells were maintained in normal-K(+) (CNK) (K(+)=5.3mmol/L), low-K(+) (CLK) (K(+)=2.5mmol/L), or K(+)-depleted (CKD) (K(+)=0mmol/L) medium for 10days (n=5 independent cultures/condition)...
January 4, 2017: Metabolism: Clinical and Experimental
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