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https://www.readbyqxmd.com/read/28199731/proteomic-profiling-analysis-reveals-a-link-between-experimental-autoimmune-uveitis-and-complement-activation-in-rats
#1
Dadong Guo, Bing Hu, Hongying Tang, Yuanyuan Sun, Bin Liu, Qingmei Tian, Hongsheng Bi
Uveitis is an autoimmune disease that usually damages the vision function, leading to poor visual quality in patients. As an autoimmune ocular inflammatory disease, the pathogenesis of uveitis is associated with abnormal expression of some proteins and aberrant regulation of multiple signaling pathways. Nevertheless, the detailed mechanism remains unclear. In this study, we induced an experimental autoimmune uveitis (EAU) model in rats. We determined the levels of C3a and membrane attack complex C5b-9 (soluble C5b-9, sC5b-9) in both plasma and aqueous humor, identified the differentially expressed proteins in plasma by liquid chromatography-tandem mass spectrometry, and employed bioinformatics algorithms to analyze differentially expressed proteins in EAU rat plasma...
February 15, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28150236/bioinformatics-analysis-of-protein-phosphorylation-in-plant-systems-biology-using-p3db
#2
Qiuming Yao, Dong Xu
Protein phosphorylation is one of the most pervasive protein post-translational modification events in plant cells. It is involved in many plant biological processes, such as plant growth, organ development, and plant immunology, by regulating or switching signaling and metabolic pathways. High-throughput experimental methods like mass spectrometry can easily characterize hundreds to thousands of phosphorylation events in a single experiment. With the increasing volume of the data sets, Plant Protein Phosphorylation DataBase (P3DB, http://p3db...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28141873/proteomic-and-transcriptomic-study-of-brain-microvessels-in-neonatal-and-adult-mice
#3
Baptiste Porte, Clémence Chatelain, Julie Hardouin, Céline Derambure, Yasmine Zerdoumi, Michèle Hauchecorne, Nicolas Dupré, Soumeya Bekri, Bruno Gonzalez, Stéphane Marret, Pascal Cosette, Philippe Leroux
Infants born before 29 weeks gestation incur a major risk of preterm encephalopathy and subependymal/intracerebral/intraventricular haemorrhage. In mice, an ontogenic window of haemorrhage risk was recorded up to 5 days after birth in serpine1 knock-out animals. Using proteome and transcriptome approaches in mouse forebrain microvessels, we previously described the remodelling of extracellular matrix and integrins likely strengthening the vascular wall between postnatal day 5 (P5) and P10. Haemorrhage is the ultimate outcome of vessel damage (i...
2017: PloS One
https://www.readbyqxmd.com/read/28139890/pharmacogenomics-of-17-alpha-hydroxyprogesterone-caproate-for-recurrent-preterm-birth-a-case-control-study
#4
T A Manuck, W S Watkins, M S Esplin, J Biggio, R Bukowski, S Parry, H Zhan, H Huang, W Andrews, G Saade, Y Sadovsky, U M Reddy, J Ilekis, M Yandell, M W Varner, L B Jorde
OBJECTIVE: To compare maternal genotypes between women with and without significant prolongation of pregnancy in the setting of 17-alpha hydroxyprogesterone caproate (17-P) administration for the prevention of recurrent preterm birth (PTB). DESIGN: Case-control. SETTING: Three tertiary-care centres across the USA. POPULATION: Women (n = 99) with ≥ 1 prior singleton spontaneous PTB, receiving 17-P. METHODS: Women were classified as having successful prolongation of pregnancy during the 17-P treated pregnancy, in two ways: (1) Definition A: success/non-success based on difference in gestational age at delivery between 17-P-treated and untreated pregnancies (success: delivered ≥ 3 weeks later with 17-P) and (2) Definition B: success/non-success based on reaching term (success: delivered at term with 17-P)...
January 31, 2017: BJOG: An International Journal of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28126595/global-proteome-and-phospho-proteome-analysis-of-merlin-deficient-meningioma-and-schwannoma-identifies-pdlim2-as-a-novel-therapeutic-target
#5
Kayleigh Bassiri, Sara Ferluga, Vikram Sharma, Nelofer Syed, Claire L Adams, Edwin Lasonder, C Oliver Hanemann
Loss or mutation of the tumour suppressor Merlin predisposes individuals to develop multiple nervous system tumours, including schwannomas and meningiomas, sporadically or as part of the autosomal dominant inherited condition Neurofibromatosis 2 (NF2). These tumours display largely low grade features but their presence can lead to significant morbidity. Surgery and radiotherapy remain the only treatment options despite years of research, therefore an effective therapeutic is required. Unbiased omics studies have become pivotal in the identification of differentially expressed genes and proteins that may act as drug targets or biomarkers...
January 18, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28122643/identification-of-potential-saliva-and-tear-biomarkers-in-primary-sj%C3%A3-gren-s-syndrome-utilising-the-extraction-of-extracellular-vesicles-and-proteomics-analysis
#6
Lara A Aqrawi, Hilde Kanli Galtung, Beate Vestad, Reidun Øvstebø, Bernd Thiede, Shermin Rusthen, Alix Young, Eduarda M Guerreiro, Tor Paaske Utheim, Xiangjun Chen, Øygunn Aass Utheim, Øyvind Palm, Janicke Liaaen Jensen
BACKGROUND: There is a long-lasting need for non-invasive, more accurate diagnostic techniques when evaluating primary Sjögren's syndrome (pSS) patients. Incorporation of additional diagnostics involving screening for disease-specific biomarkers in biological fluid is a promising concept that requires further investigation. In the current study we aimed to explore novel disease biomarkers in saliva and tears from pSS patients. METHODS: Liquid chromatography-mass spectrometry (LC-MS) was performed on stimulated whole saliva and tears from 27 pSS patients and 32 healthy controls, and salivary and tear proteomic biomarker profiles were generated...
January 25, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28120393/proteomic-analyses-of-changes-in-synechococcus-sp-pcc7942-following-uv-c-stress
#7
Xi Peng, Jie Yang, Yang Gao
UV-C's effects on the physiological and biochemical processes of cyanobacteria have been well characterized. However, the molecular mechanisms of cyanobacteria's tolerance to UV-C still needs further investigation. This research attempts to decode the variation in protein abundances in cyanobacteria after UV-C stress. Different expression levels of proteins in the cytoplasm of Synechococcus sp. PCC7942 under UV-C stress were investigated by using a comparative proteomic approach. Forty-seven UV-C-regulated proteins were identified by MALDI-TOF analysis and classified by Gene Ontology (GO)...
January 25, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28116073/protein-profiling-of-plasma-proteins-in-dairy-cows-with-subclinical-hypocalcaemia
#8
Ziling Fan, Shi Shu, Chuchu Xu, Xinhuan Xiao, Gang Wang, Yunlong Bai, Cheng Xia, Ling Wu, Hongyou Zhang, Chuang Xu, Wei Yang
Subclinical hypocalcaemia (SH) is an important metabolic disease in dairy cows that has a serious impact on production performance. The objective of this study was to investigate novel aspects of pathogenesis using proteomics technology to identify proteins that are differentially expressed in diseased and healthy animals. Dairy cows were divided into an SH group (T, n = 10) and a control group (C, n = 10) based on plasma calcium concentration. A total of 398 differentially expressed proteins were identified, of which 265 proteins were overlapped in the two parallel experiments...
2017: Irish Veterinary Journal
https://www.readbyqxmd.com/read/28049027/an-integrated-shotgun-proteomics-and-bioinformatics-approach-for-analysis-of-brain-proteins-from-mcao-model-using-serial-affinity-chromatograph-with-four-active-ingredients-from-shengmai-preparations-as-ligands
#9
Xiao-Xue Fan, Fang Li, Yan-Ni Lv, Yu Zhang, Jun-Ping Kou, Bo-Yang Yu
Identification and validation of disease-relevant target proteins for natural products is an essential component of modern pharmaceutical research. In the present study, an integrated shotgun proteomics and bioinformatics approach was established to profile the interaction of active small molecules derived from ShengMai preparations (SMXZF) with hundreds of endogenously expressed proteins from middle cerebral artery occlusion (MCAO) model. Affinity-based proteomic strategies for isolation and identification of targets for the bioactive components is a classic, but still powerful approach...
February 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28039103/itraq-based-proteome-analysis-of-fluoroquinolone-resistant-staphylococcus-aureus
#10
Van Chi Thai, Teck Kwang Lim, Kim Phuong Uyen Le, Qingsong Lin, Thi Thu Hoai Nguyen
OBJECTIVES: The aim of this study was to compare global protein expression changes during fluoroquinolone (FQ) exposure of Staphylococcus aureus. METHODS: Total protein extracts of wild-type S. aureus ATCC 29213 and six multidrug-resistant (MDR) strains derived from the wild-type under different FQ exposures were analysed using the 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) method combined with LC-MS/MS analysis. Differentially expressed proteins were searched for their Gene Ontology (GO) annotation (UniProt database) and protein-protein interaction network (STRING v...
December 27, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28018404/functional-and-integrative-analysis-of-the-proteomic-profile-of-radish-root-under-pb-exposure
#11
Yan Wang, Liang Xu, Mingjia Tang, Haiyan Jiang, Wei Chen, Wei Zhang, Ronghua Wang, Liwang Liu
Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L(-1)(Pb500) and 1000 mg L(-1)(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification)...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27975291/a-systematic-bioinformatics-approach-to-identify-high-quality-mass-spectrometry-data-and-functionally-annotate-proteins-and-proteomes
#12
Mohammad Tawhidul Islam, Abidali Mohamedali, Seong Beom Ahn, Ishmam Nawar, Mark S Baker, Shoba Ranganathan
In the past decade, proteomics and mass spectrometry have taken tremendous strides forward, particularly in the life sciences, spurred on by rapid advances in technology resulting in generation and conglomeration of vast amounts of data. Though this has led to tremendous advancements in biology, the interpretation of the data poses serious challenges for many practitioners due to the immense size and complexity of the data. Furthermore, the lack of annotation means that a potential gold mine of relevant biological information may be hiding within this data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27941623/identification-of-potential-biomarkers-for-rhegmatogenous-retinal-detachment-associated-with-choroidal-detachment-by-vitreous-itraq-based-proteomic-profiling
#13
Zhifeng Wu, Nannan Ding, Mengxi Yu, Ke Wang, Shasha Luo, Wenjun Zou, Ying Zhou, Biao Yan, Qin Jiang
Rhegmatogenous retinal detachment associated with choroidal detachment (RRDCD) is a complicated and serious type of rhegmatogenous retinal detachment (RRD). In this study, we identified differentially expressed proteins in the vitreous humors of RRDCD and RRD using isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano-liquid chromatography-electrospray ion trap-mass spectrometry-mass spectrometry (nano-LC-ESI-MS/MS) and bioinformatic analysis. Our result shows that 103 differentially expressed proteins, including 54 up-regulated and 49 down-regulated proteins were identified in RRDCD...
December 7, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27927957/the-proteome-of-bloc-1-genetic-defects-identifies-the-arp2-3-actin-polymerization-complex-to-function-downstream-of-the-schizophrenia-susceptibility-factor-dysbindin-at-the-synapse
#14
Avanti Gokhale, Cortnie Hartwig, Amanda H Freeman, Ravi Das, Stephanie A Zlatic, Rachel Vistein, Amelia Burch, Guillemette Carrot, Arielle F Lewis, Sheldon Nelms, Dion K Dickman, Manojkumar A Puthenveedu, Daniel N Cox, Victor Faundez
: Proteome modifications downstream of monogenic or polygenic disorders have the potential to uncover novel molecular mechanisms participating in pathogenesis and/or extragenic modification of phenotypic expression. We tested this idea by determining the proteome sensitive to genetic defects in a locus encoding dysbindin, a protein required for synapse biology and implicated in schizophrenia risk. We applied quantitative mass spectrometry to identify proteins expressed in neuronal cells the abundance of which was altered after downregulation of the schizophrenia susceptibility factor dysbindin (Bloc1s8) or two other dysbindin-interacting polypeptides, which assemble into the octameric biogenesis of lysosome-related organelles complex 1 (BLOC-1)...
December 7, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27896924/detailed-tail-proteomic-analysis-of-axolotl-ambystoma-mexicanum-using-an-mrna-seq-reference-database
#15
Turan Demircan, Ilknur Keskin, Seda Nilgün Dumlu, Nilüfer Aytürk, Mahmut Erhan Avşaroğlu, Emel Akgün, Gürkan Öztürk, Ahmet Tarık Baykal
Salamander axolotl has been emerging as an important model for stem cell research due to its powerful regenerative capacity. Several advantages, such as the high capability of advanced tissue, organ, and appendages regeneration, promote axolotl as an ideal model system to extend our current understanding on the mechanisms of regeneration. Acknowledging the common molecular pathways between amphibians and mammals, there is a great potential to translate the messages from axolotl research to mammalian studies...
January 2017: Proteomics
https://www.readbyqxmd.com/read/27878450/mass-spectrometry-based-proteomics-profiling-of-human-monocytes
#16
Yong Zeng, Fei-Yan Deng, Wei Zhu, Lan Zhang, Hao He, Chao Xu, Qing Tian, Ji-Gang Zhang, Li-Shu Zhang, Hong-Gang Hu, Hong-Wen Deng
Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged...
February 2017: Protein & Cell
https://www.readbyqxmd.com/read/27862958/nicotine-induced-protein-expression-profiling-reveals-mutually-altered-proteins-across-four-human-cell-lines
#17
Joao A Paulo, Steven P Gygi
Mass spectrometry-based proteomic strategies can profile the expression level of proteins in response to external stimuli. Nicotine affects diverse cellular pathways, however, the nicotine-induced alterations on the global proteome across human cell lines have not been fully elucidated. We measured perturbations in protein levels resulting from nicotine treatment in four cell lines-HEK, HeLa, PaSC, and SH-SY5Y-in a single experiment using tandem mass tags (TMT10-plex) and high-resolution mass spectrometry. We quantified 8590 proteins across all cell lines...
January 2017: Proteomics
https://www.readbyqxmd.com/read/27836980/proteome-profiling-outperforms-transcriptome-profiling-for-coexpression-based-gene-function-prediction
#18
Jing Wang, Zihao Ma, Steven A Carr, Philipp Mertins, Hui Zhang, Zhen Zhang, Daniel W Chan, Matthew J C Ellis, R Reid Townsend, Richard D Smith, Jason E McDermott, Xian Chen, Amanda G Paulovich, Emily S Boja, Mehdi Mesri, Christopher R Kinsinger, Henry Rodriguez, Karin D Rodland, Daniel C Liebler, Bing Zhang
Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC)...
January 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27809461/differentially-expressed-serum-proteins-associated-with-calcium-regulation-and-hypocalcemia-in-dairy-cows
#19
Shi Shu, Yunlong Bai, Gang Wang, Xinhuan Xiao, Ziling Fan, Jiang Zhang, Chang Zhao, Yang Zhao, Cheng Xia, Hongyou Zhang
Hypocalcemia is an important metabolic disease of dairy cows during the transition period, although the effect of hypocalcemia on biological function in dairy cows remains unknown. In this study, proteomic, mass spectrum, bioinformatics and western blotting were employed to identify differentially expressed proteins related to serum Ca concentration. Serum samples from dairy cows were collected at three time points: 3rd days before calving (day -3), the day of calving (day 0), and 3rd days after calving (day +3)...
November 3, 2016: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/27791462/deregulation-of-focal-adhesion-formation-and-cytoskeletal-tension-due-to-loss-of-a-type-lamins
#20
Tobias D J Corne, Tom Sieprath, Jonathan Vandenbussche, Danahe Mohammed, Mariska Te Lindert, Kris Gevaert, Sylvain Gabriele, Katarina Wolf, Winnok H De Vos
The nuclear lamina mechanically integrates the nucleus with the cytoskeleton and extracellular environment and regulates gene expression. These functions are exerted through direct and indirect interactions with the lamina's major constituent proteins, the A-type lamins, which are encoded by the LMNA gene. Using quantitative stable isotope labeling-based shotgun proteomics we have analyzed the proteome of human dermal fibroblasts in which we have depleted A-type lamins by means of a sustained siRNA-mediated LMNA knockdown...
October 28, 2016: Cell Adhesion & Migration
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