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https://www.readbyqxmd.com/read/29679077/proteome-wide-analysis-of-cysteine-oxidation-reveals-metabolic-sensitivity-to-redox-stress
#1
Jiska van der Reest, Sergio Lilla, Liang Zheng, Sara Zanivan, Eyal Gottlieb
Reactive oxygen species (ROS) are increasingly recognised as important signalling molecules through oxidation of protein cysteine residues. Comprehensive identification of redox-regulated proteins and pathways is crucial to understand ROS-mediated events. Here, we present stable isotope cysteine labelling with iodoacetamide (SICyLIA), a mass spectrometry-based workflow to assess proteome-scale cysteine oxidation. SICyLIA does not require enrichment steps and achieves unbiased proteome-wide sensitivity. Applying SICyLIA to diverse cellular models and primary tissues provides detailed insights into thiol oxidation proteomes...
April 20, 2018: Nature Communications
https://www.readbyqxmd.com/read/29679008/improving-wood-properties-for-wood-utilization-through-multi-omics-integration-in-lignin-biosynthesis
#2
Jack P Wang, Megan L Matthews, Cranos M Williams, Rui Shi, Chenmin Yang, Sermsawat Tunlaya-Anukit, Hsi-Chuan Chen, Quanzi Li, Jie Liu, Chien-Yuan Lin, Punith Naik, Ying-Hsuan Sun, Philip L Loziuk, Ting-Feng Yeh, Hoon Kim, Erica Gjersing, Todd Shollenberger, Christopher M Shuford, Jina Song, Zachary Miller, Yung-Yun Huang, Charles W Edmunds, Baoguang Liu, Yi Sun, Ying-Chung Jimmy Lin, Wei Li, Hao Chen, Ilona Peszlen, Joel J Ducoste, John Ralph, Hou-Min Chang, David C Muddiman, Mark F Davis, Chris Smith, Fikret Isik, Ronald Sederoff, Vincent L Chiang
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old)...
April 20, 2018: Nature Communications
https://www.readbyqxmd.com/read/29678861/the-tomato-mitogen-activated-protein-kinase-slmpk1-is-as-a-negative-regulator-of-the-high-temperature-stress-response
#3
Haidong Ding, Jie He, Yuan Wu, Xiao-Xia Wu, Cailin Ge, Yijun Wang, Silin Zhong, Edgar Peiter, Jian-Sheng Liang, Weifeng Xu
High temperature (HT) stress is a major environmental stress that limits plant growth and development. Mitogen-activated protein kinase (MAPK) cascades play key roles in plant growth and stress signaling, but their involvement in the HT stress response are poorly understood. Here, we describe a 47-kDa MBP-phosphorylated protein (p47-MBPK) activated in tomato (Solanum lycopersicum) leaves under HT, and identify it as SlMPK1 by MS/MS analysis. Silencing of SlMPK1 in transgenic tomato plants resulted in enhanced tolerance to HT, while overexpression resulted in reduced tolerance...
April 20, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29678717/a-tandem-mass-tag-tmt-proteomic-analysis-during-the-early-phase-of-experimental-pancreatitis-reveals-new-insights-in-the-disease-pathogenesis
#4
Violeta García-Hernández, Carmen Sánchez-Bernal, Domitille Schvartz, José J Calvo, Jean-Charles Sanchez, Jesús Sánchez-Yagüe
Changes in the protein expression occurring within the initiation phase of acute pancreatitis (AP) might be vital in the development of this complex disease. However, the exact mechanisms involved in the onset of AP remains elusive and most of our knowledge about the pathobiology of AP comes from animal models. We performed in a rat pancreatitic model a high-throughput shotgun proteomic profiling of the soluble and whole membrane fractions from the pancreas during the early phase of cerulein (Cer)-induced AP...
April 17, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29678203/quantitative-shotgun-proteomics-distinguishes-wound-healing-biomarker-signatures-in-common-carp-skin-mucus-in-response-to-ichthyophthirius-multifiliis
#5
Mona Saleh, Gokhlesh Kumar, Abdel-Azeem Abdel-Baki, Mohamed A Dkhil, Mansour El-Matbouli, Saleh Al-Quraishy
Ichthyophthirius multifiliis is a ciliated protozoan parasite recognized as one of the most pathogenic diseases of wild and cultured freshwater fish. Fish skin mucus plays a significant role against invading pathogens. However, the protein-based modulation against infection with I. multifiliis, of host fish at this barrier is unknown. Thus, we investigated the skin mucus proteome of common carp using a shotgun proteomic approach at days 1 and 9 after I. multifiliis exposure. We identified 25 differentially expressed proteins in infected carp skin mucus...
April 20, 2018: Veterinary Research
https://www.readbyqxmd.com/read/29678103/ouantitative-proteomic-analysis-of-cellular-responses-to-a-designed-amino-acid-feed-in-a-monoclonal-antibody-producing-chinese-hamster-ovary-cell-line
#6
Fatemeh Torkashvand, Fereidoun Mahboudi, Manouchehr Vossoughi, Elnaz Fatemi, Seyed Masoud Moosavi Basri, Amir Heydari, Behrouz Vaziri
Background: Chinese hamster ovary (CHO) cell line is considered as the most common cell line in the biopharmaceutical industry because of its capability in performing efficient post-translational modifications and producing the recombinant proteins, which are similar to natural human proteins. The optimization of the upstream process via different feed strategies has a great impact on the target molecule expression and yield. Methods: To determine and understand the molecular events beneath the feed effects on the CHO cell, a label-free quantitative proteomic analysis was applied...
April 21, 2018: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/29675946/plasma-proteomics-identifies-a-chemokine-storm-in-idiopathic-multicentric-castleman-disease
#7
Sheila K Pierson, Aaron J Stonestrom, Dustin Shilling, Jason Ruth, Christopher S Nabel, Amrit Singh, Yue Ren, Katie Stone, Hongzhe Li, Frits van Rhee, David C Fajgenbaum
Human Herpesvirus-8 (HHV-8)-negative/idiopathic multicentric Castleman disease (iMCD) is a poorly understood disease involving polyclonal lymphoproliferation with dysmorphic germinal centers, constitutional symptoms, and multi-organ failure. Patients can experience thrombocytopenia, anasarca, reticulin fibrosis, renal dysfunction, organomegaly, and normal immunoglobulin levels, - iMCD-TAFRO. Others experience thrombocytosis, milder effusions, and hypergammaglobulinemia, -iMCD-Not Otherwise Specified (iMCD-NOS)...
April 20, 2018: American Journal of Hematology
https://www.readbyqxmd.com/read/29674748/itraq-based-quantitative-proteomic-analysis-of-embryonic-developmental-stages-in-amur-sturgeon-acipenser-schrenckii
#8
Shubo Jin, Dajiang Sun, Dan Song, Nianmin Wang, Hongtuo Fu, Feng Ji, Ying Zhang
The Amur sturgeon, Acipenser schrenckii, is an important aquaculture species in China with annual production of about 150 thousand tons in 2015. In this study, we investigated the regulatory proteins and pathways affecting embryonic development of Amur sturgeon, by analyzing of the differential proteomes among four embryonic developmental stages using isobaric tags for relative and absolute quantitation (iTRAQ), combined with the analysis of effects of microelements and antioxidants on embryonic development...
April 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29674717/a-proteomics-landscape-of-circadian-clock-in-mouse-liver
#9
Yunzhi Wang, Lei Song, Mingwei Liu, Rui Ge, Quan Zhou, Wanlin Liu, Ruiyang Li, Jingbo Qie, Bei Zhen, Yi Wang, Fuchu He, Jun Qin, Chen Ding
As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a transcription factor (TF) DNA-binding activity-centered multi-dimensional proteomics landscape of the mouse liver, which includes DNA-binding profiles of different TFs, phosphorylation, and ubiquitylation patterns, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portray the hierarchical circadian clock network of this tissue...
April 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29674673/proteomics-studies-on-the-three-larval-stages-of-development-and-metamorphosis-of-babylonia-areolata
#10
Minghui Shen, Guilan Di, Min Li, Jingqiang Fu, Qi Dai, Xiulian Miao, Miaoqin Huang, Weiwei You, Caihuan Ke
The ivory shell, Babylonia areolata, is a commercially important aquaculture species in the southeast coast of mainland China. The middle veliger stage, later veliger stage, and juvenile stage are distinct larval stages in B. areolata development. In this study, we used label-free quantification proteomics analysis of the three developmental stages of B. areolata. We identified a total of 5,583 proteins, of which 1,419 proteins expression level showed significant differential expression. The results of gene ontology enrichment analysis showed that the number of proteins involved in metabolic and cellular processes were the most abundant...
April 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29674526/galectin-3-downregulates-antioxidant-peroxiredoxin-4-in-human-cardiac-fibroblasts-a-new-pathway-to-induce-cardiac-damage
#11
Jaime Ibarrola, Vanessa Arrieta, Rafael Sádaba, Ernesto Martínez-Martínez, Amaia García-Peña, Virginia Alvarez, Amaya Fernández-Celis, Alicia Gainza, Enrique Santamaría, Joaquin Fernández-Irigoyen, Victoria Cachofeiro, Guillermo Zalba, Renaud Fay, Patrick Rossignol, Natalia López-Andrés
Galectin-3 (Gal-3) is increased in heart failure (HF) and promotes cardiac fibrosis and inflammation. We investigated whether Gal-3 modulates oxidative stress in human cardiac fibroblasts, in experimental animal models and in human aortic stenosis (AS). Using proteomics and immunodetection approaches, we have identified that Gal-3 down-regulated the anti-oxidant peroxiredoxin-4 (Prx-4) in cardiac fibroblasts. In parallel, Gal-3 increased peroxide, nitrotyrosine, malondialdehyde and N-carboxymethyl-lysine levels and decreased total antioxidant capacity...
April 19, 2018: Clinical Science (1979-)
https://www.readbyqxmd.com/read/29673699/the-phosphorylated-redox-proteome-of-chlamydomonas-reinhardtii-revealing-novel-means-for-regulation-of-protein-structure-and-function
#12
Evan W McConnell, Emily G Werth, Leslie M Hicks
Post-translational modifications (PTMs) are covalent modifications to protein residues which may alter both conformation and activity, thereby modulating signaling and metabolic processes. While PTMs have been largely investigated independently, examination into how different modification interact, or crosstalk, will reveal a more complete understanding of the reciprocity of signaling cascades across numerous pathways. Combinatorial reversible thiol oxidation and phosphorylation in eukaryotes is largely recognized, but rigorous approaches for experimental discovery are underdeveloped...
April 4, 2018: Redox Biology
https://www.readbyqxmd.com/read/29673528/genomics-and-proteomic-techniques
#13
Jonathan Z Pan
Although general anesthesia induced by inhaled anesthetics produces definitive phenotypes (e.g., loss of mobility, amnesia, analgesia), the underlying targets of these drugs are still not clear. Genomics and proteomic techniques are discussed for measurement of global transcriptional and translational changes after inhaled anesthetic exposures. The current discussion focuses primarily on the genomic and proteomic technical methodology. We also include a discussion of network and pathway analyses for data interpretation after identification of the targets...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29671811/shape-shifted-red-blood-cells-a-novel-red-blood-cell-stage
#14
Verónica Chico, Sara Puente-Marin, Iván Nombela, Sergio Ciordia, María Carmen Mena, Begoña Carracedo, Alberto Villena, Luis Mercado, Julio Coll, María Del Mar Ortega-Villaizan
Primitive nucleated erythroid cells in the bloodstream have long been suggested to be more similar to nucleated red cells of fish, amphibians, and birds than the red cells of fetal and adult mammals. Rainbow trout Ficoll-purified red blood cells (RBCs) cultured in vitro undergo morphological changes, especially when exposed to stress, and enter a new cell stage that we have coined shape-shifted RBCs (shRBCs). We have characterized these shRBCs using transmission electron microscopy (TEM) micrographs, Wright⁻Giemsa staining, cell marker immunostaining, and transcriptomic and proteomic evaluation...
April 19, 2018: Cells
https://www.readbyqxmd.com/read/29671787/proteomic-identification-of-the-galectin-1-involved-molecular-pathways-in-urinary-bladder-urothelial-carcinoma
#15
Chien-Feng Li, Kun-Hung Shen, Lan-Hsiang Chien, Cheng-Hao Huang, Ting-Feng Wu, Hong-Lin He
Among various heterogeneous types of bladder tumors, urothelial carcinoma is the most prevalent lesion. Some of the urinary bladder urothelial carcinomas (UBUCs) develop local recurrence and may cause distal invasion. Galectin-1 de-regulation significantly affects cell transformation, cell proliferation, angiogenesis, and cell invasiveness. In continuation of our previous investigation on the role of galectin-1 in UBUC tumorigenesis, in this study, proteomics strategies were implemented in order to find more galectin-1-associated signaling pathways...
April 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29671274/an-internal-standard-for-assessing-phosphopeptide-recovery-from-metal-ion-oxide-enrichment-strategies
#16
Joao A Paulo, Jose Navarrete-Perea, Alison R Erickson, Jeffrey Knott, Steven P Gygi
Phosphorylation-mediated signaling pathways have major implications in cellular regulation and disease. However, proteins with roles in these pathways are frequently less abundant and phosphorylation is often sub-stoichiometric. As such, the efficient enrichment, and subsequent recovery of phosphorylated peptides, is vital. Mass spectrometry-based proteomics is a well-established approach for quantifying thousands of phosphorylation events in a single experiment. We designed a peptide internal standard-based assay directed toward sample preparation strategies for mass spectrometry analysis to understand better phosphopeptide recovery from enrichment strategies...
April 18, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29670521/the-prenylflavonoid-xanthohumol-reduces-alzheimer-like-changes-and-modulates-multiple-pathogenic-molecular-pathways-in-the-neuro2a-app-swe-cell-model-of-ad
#17
Xianfeng Huang, Jing Wang, Xiao Chen, Pan Liu, Shujin Wang, Fangchen Song, Zaijun Zhang, Feiqi Zhu, Xinfeng Huang, Jianjun Liu, Guoqiang Song, Peter S Spencer, Xifei Yang
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that has proved refractory to drug treatment. Given evidence of neuroprotection in animal models of ischemic stroke, we assessed the prenylflavonoid xanthohumol from the Common Hop ( Humulus lupulus L.) for therapeutic potential in murine neuroblastoma N2a cells stably expressing human Swedish mutant amyloid precursor protein (N2a/APP), a well-characterized cellular model of AD. The ELISA and Western-blot analysis revealed that xanthohumol (Xn) inhibited Aβ accumulation and APP processing, and that Xn ameliorated tau hyperphosphorylation via PP2A, GSK3β pathways in N2a/APP cells...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29670063/identification-of-the-candidate-proteins-related-to-oleic-acid-accumulation-during-peanut-arachis-hypogaea-l-seed-development-through-comparative-proteome-analysis
#18
Hao Liu, Haifen Li, Jianzhong Gu, Li Deng, Li Ren, Yanbin Hong, Qing Lu, Xiaoping Chen, Xuanqiang Liang
Peanuts ( Arachis hypogaea L.) are an important oilseed crop, containing high contents of protein and fatty acids (FA). The major components of FA found in peanut oil are unsaturated FAs, including oleic acid (OA, C18:1) and linoleic acid (LOA, C18:2). Moreover, the high content of OA in peanut oil is beneficial for human health and long-term storage due to its antioxidant activity. However, the dynamic changes in proteomics related to OA accumulation during seed development still remain largely unexplored...
April 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29670056/isolation-and-identification-of-putative-protein-substrates-of-the-aaa-molecular-chaperone-clpb-from-the-pathogenic-spirochaete-leptospira-interrogans
#19
Joanna Krajewska, Zbigniew Arent, Michal Zolkiewski, Sabina Kędzierska-Mieszkowska
Bacterial ClpB is an ATP-dependent Hsp100 chaperone that reactivates aggregated proteins in cooperation with the DnaK chaperone system and promotes survival of bacteria under stress conditions. A large number of publications also indicate that ClpB supports the virulence of bacteria, including a pathogenic spirochaete Leptospira interrogans responsible for leptospirosis in both animals and humans. However, the exact role of ClpB in bacterial pathogenicity remains poorly characterized. It can be assumed that ClpB, due to its role as the molecular chaperone, mediates refolding of essential bacterial proteins, including the known virulence factors, which may become prone to aggregation under infection-induced stresses...
April 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29669898/multi-omics-analysis-of-thermal-stress-response-in-a-zooxanthellate-cnidarian-reveals-the-importance-of-associating-with-thermotolerant-symbionts
#20
Maha J Cziesielski, Yi Jin Liew, Guoxin Cui, Sebastian Schmidt-Roach, Sara Campana, Claudius Marondedze, Manuel Aranda
Corals and their endosymbiotic dinoflagellates of the genus Symbiodinium have a fragile relationship that breaks down under heat stress, an event known as bleaching. However, many coral species have adapted to high temperature environments such as the Red Sea (RS). To investigate mechanisms underlying temperature adaptation in zooxanthellate cnidarians we compared transcriptome- and proteome-wide heat stress response (24 h at 32°C) of three strains of the model organism Aiptasia pallida from regions with differing temperature profiles; North Carolina (CC7), Hawaii (H2) and the RS...
April 25, 2018: Proceedings. Biological Sciences
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