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proteomics pathway ontology

Biao Suo, Hua Yang, Yuexia Wang, Haipeng Lv, Zhen Li, Chao Xu, Zhilu Ai
When frozen, Staphylococcus aureus survives in a sublethally injured state. However, S. aureus can recover at a suitable temperature, which poses a threat to food safety. To elucidate the resuscitation mechanism of freezing survived S. aureus , we used cells stored at -18°C for 90 days as controls. After resuscitating the survived cells at 37°C, the viable cell numbers were determined on tryptic soy agar with 0.6% yeast extract (TSAYE), and the non-injured-cell numbers were determined on TSAYE supplemented with 10% NaCl...
2018: Frontiers in Microbiology
Cynthia Kankeu, Kylie Clarke, Delphi Van Haver, Kris Gevaert, Francis Impens, Anna Dittrich, H Llewelyn Roderick, Egle Passante, Heinrich J Huber
The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis...
May 17, 2018: Molecular omics
Yunping Xue, Pengfei Xu, Sujuan Xu, Kai Xue, Lingling Xu, Jie Chen, Juan Xu, Xiaoyan Shi, Qian Li, Lin Gu
BACKGROUND/AIMS: Ovarian endometriosis (OvE) is ovarian cyst that is lined with endometrial tissue. They are found in 17-44% of women with endometriosis. Their clinical manifestations include pelvic pain, dysmenorrhea, dyspareunia, and infertility. Although the incidence of OvE has increased yearly, the exact pathogenesis of OvE is still unclear. We used peptidomics, an emerging branch of proteomics, to identify differentially expressed peptides in order to determine the possible roles of these peptides in the pathogenesis of OvE...
May 9, 2018: Cellular Physiology and Biochemistry
Pallab Bhowmick, Yassene Mohammed, Christoph H Borchers
Motivation: Multiple Reaction Monitoring (MRM)-based targeted proteomics is increasingly being used to study the molecular basis of disease. When combined with an internal standard, MRM allows absolute quantification of proteins in virtually any type of sample but the development and validation of an MRM assay for a specific protein is laborious. Therefore, several public repositories now host targeted proteomics MRM assays, including NCI's Clinical Proteomic Tumor Analysis Consortium assay portals, PeptideAtlas SRM Experiment Library, SRMAtlas, PanoramaWeb, and PeptideTracker, with all of which contain different levels of information...
May 14, 2018: Bioinformatics
Hassan Peyvandi, Ali Asghar Peyvandi, Akram Safaei, Mona Zamanian Azodi, Mostafa Rezaei-Tavirani
The most common malignant neoplasm of the head and neck region is laryngeal cancer which presents a significant international health problem. The present study aims to screen potential proteins related to laryngeal cancer by network analysis to further understanding disease pathogenesis and biomarker discovery. Differentially expressed proteins were extracted from literatures of laryngeal cancer that compare proteome profiling of patient›s tissue with healthy controls. The PPI network analyzed for up and down regulated proteins with Cytoscape Version 3...
2018: Iranian Journal of Pharmaceutical Research: IJPR
Xin Qian, Zhiming Zhao, Wei Shang, Zhihan Xu, Beibei Zhang, Hui Cai
Rheumatoid arthritis (RA) is an autoimmune disease, which is characterized by inflammatory synovitis, and the subsequent destruction of articular cartilage and bone. Sinomenine is a traditional Chinese medicine, which has been employed as a clinical treatment for RA for several years in China. The present study investigated the anti‑arthritic effects of sinomenine on Sprague‑Dawley rats with collagen‑induced arthritis (CIA). The differentially expressed proteins in serum were measured by proteomic analysis in order to generate a differentially expressed protein network...
May 3, 2018: Molecular Medicine Reports
Xavier M Teitsma, Johannes W G Jacobs, Arno N Concepcion, Attila Pethö-Schramm, Michelle E A Borm, Jacob M van Laar, Johannes W J Bijlsma, Floris P J G Lafeber
OBJECTIVES: Previously, we identified networks of co-expressed genes related to achieving sustained drug-free remission (sDFR). The aim of the present exploratory analysis was to identify inflammatory proteins associated with achieving sDFR and their enriched biological pathways, and compare these pathways with those found in the previous transcriptomic analyses. METHODS: Serum samples were used from 60 patients who participated in the U-Act-Early trial and were treated-to-target with tocilizumab plus methotrexate, or tocilizumab or methotrexate; 37 achieved sDFR (≥3 months drug-free) and 23 did not (controls)...
May 8, 2018: Clinical and Experimental Rheumatology
Julia Steinberg, Roger A Brooks, Lorraine Southam, Sahir Bhatnagar, Theodoros I Roumeliotis, Konstantinos Hatzikotoulas, Eleni Zengini, J Mark Wilkinson, Jyoti S Choudhary, Andrew W McCaskie, Eleftheria Zeggini
Objectives: To identify molecular differences between chondrocytes from osteophytic and articular cartilage tissue from OA patients. Methods: We investigated genes and pathways by combining genome-wide DNA methylation, RNA sequencing and quantitative proteomics in isolated primary chondrocytes from the cartilaginous layer of osteophytes and matched areas of low- and high-grade articular cartilage across nine patients with OA undergoing hip replacement surgery. Results: Chondrocytes from osteophytic cartilage showed widespread differences to low-grade articular cartilage chondrocytes...
May 8, 2018: Rheumatology
Dan Wang, Yong Sun, Lili Chang, Zheng Tong, Quanliang Xie, Xiang Jin, Liping Zhu, Peng He, Hongbin Li, Xuchu Wang
Rubber particle (RP) is a specific organelle for natural rubber biosynthesis (NRB) and storage in rubber tree Hevea brasiliensis. NRB is processed by RP membrane-localized proteins, which were traditionally purified by repeated washing. However, we noticed many proteins in the discarded washing solutions (WS) from RP. Here, we compared the proteome profiles of WS, C-serum (CS) and RP by 2-DE, and identified 233 abundant proteins from WS by mass spectrometry. Many spots on 2-DE gels were identified as different protein species...
May 3, 2018: Journal of Proteomics
Xin-Ying Sun, Qing-Hui Liu, Jie Huang
The isobaric tags for relative and absolute quantitation (iTRAQ) was applied to identify differentially expressed proteins (DEPs) in Litopenaeus vannamei in response to different virulence white spot syndrome virus infection. A total of 2,780 unique peptides corresponding to 754 proteins were identified. The number of significant differentially expressed proteins was 161, including 38 up-regulated ones and 123 down-regulated ones in low-virulence infection library compared with normal-virulence infection library...
May 4, 2018: Letters in Applied Microbiology
Misol Do, Dohyun Han, Joseph Injae Wang, Hyunsoo Kim, Wooil Kwon, Youngmin Han, Jin-Young Jang, Youngsoo Kim
Background: The application of advanced imaging technologies for identifying pancreatic cysts has become widespread. However, accurately differentiating between low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive intraductal papillary mucinous neoplasms (IPMNs) remains a diagnostic challenge with current biomarkers, necessitating the development of novel biomarkers that can distinguish IPMN malignancy. Methods: Cyst fluid samples were collected from nine IPMN patients (3 LGD, 3 HGD, and 3 invasive IPMN) during their pancreatectomies...
2018: Clinical Proteomics
Zhongzan Cao, Ruiming Fan, Bo Meng, Zhe Xing, Mei Liu, Ming Gao, Xinhong Luan
The hypothalamus plays a central role in controlling poultry endocrine and reproductive activities. So far there is limited information focused on the proteome profiles of the hypothalamus from geese during different stages of the egg-laying cycle. In order to identify proteins regulating the egg-laying process of Huoyan geese, we investigated the proteome profiles of the hypothalamus from Huoyan geese during the laying period and pre-laying period by applying an isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic technology...
April 30, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
Zhuoqing Hu, Minqun Du, Wenxiu Lai, Yanlong Liang, Qin Liu, Yilin Mo, Jiaxin Bei, Shuhui Li, Yajun Yang, Jinrong Xu, Liao Cui
BACKGROUND/AIMS: In this study we assessed histomorphometric changes induced by thyroxine (T4) in 3-month-old hyperthyroid male rats and examined whether the potential mechanism of these changes is related to bone changes. METHODS: Rats were classified as either hyperthyroid following administration of 250 µg/kg/day freshly prepared T4 by gavage for 2 months or euthyroid following administration of vehicle alone (n = 8 per group). We measured bone mineral density (BMD), bone biomechanical properties, and bone histomorphometric changes...
April 19, 2018: Cellular Physiology and Biochemistry
Xiang Liu, Yijun Song, Zhengguang Guo, Wei Sun, Juntao Liu
Amniotic fluid contains large amounts of proteins produced by amnion epithelial cells, fetal tissues, fetal excretions and placental tissues; thus, it is an important potential source of biomarkers for identifying fetal pathologies. In this study, a pooled AF sample from 7 healthy volunteers was used to provide a comprehensive profile of normal human AF proteome using immunoaffinity depletion of 14 high-abundance proteins. Each individual AF sample was used to analyze inter-individual variations with iTRAQ method...
April 20, 2018: Journal of Proteomics
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
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
Ting Zhao, Jie Wu, Xiaohui Liu, Lei Zhang, Gang Chen, Haojie Lu
The histological typing of thymic epithelial tumours (TETs) still remains a challenge for surgical pathologists, especially when encountering borderline cases mainly focused on spindle cell types (including type A, atypical type A (aA), AB, and B3). A systematic proteomics analysis of TETs was performed using isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS). In total, 6479 and 6305 proteins were identified and quantified, respectively...
April 12, 2018: Analyst
Shulin Chen, Juan Chen, Fu Hou, Yigao Feng, Ruiqi Zhang
BACKGROUND: Spike architecture mutants in tetraploid wheat (Triticum turgidum L., 2n = 28, AABB) have a distinct morphology, with parts of the rachis node producing lateral meristems that develop into ramified spikelete (RSs) or four-rowed spikelete (FRSs). The genetic basis of RSs and FRSs has been analyzed, but little is known about the underlying developmental mechanisms of the lateral meristem. We used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a quantitative proteomic analysis of immature spikes harvested from tetraploid near-isogenic lines of wheat with normal spikelete (NSs), FRSs, and RSs and investigated the molecular mechanisms of lateral meristem differentiation and development...
April 2, 2018: BMC Genomics
Antigoni Manousopoulou, Annette Hayden, Massimiliano Mellone, Diana J Garay-Baquero, Cory H White, Fergus Noble, Monette Lopez, Gareth J Thomas, Timothy J Underwood, Spiros D Garbis
BACKGROUND: Cancer-associated fibroblasts (CAFs) form the major stromal component of the tumour microenvironment (TME). The present study aimed to examine the proteomic profiles of CAFs vs. normal fibroblasts (NOFs) from patients with oesophageal adenocarcinoma to gain insight into their pro-oncogenic phenotype. METHODS: CAFs/NOFs from four patients were sub-cultured and analysed using quantitative proteomics. Differentially expressed proteins (DEPs) were subjected to bioinformatics and compared with published proteomics and transcriptomics  datasets...
March 29, 2018: British Journal of Cancer
Florian Schlotter, Arda Halu, Shinji Goto, Mark C Blaser, Simon C Body, Lang H Lee, Hideyuki Higashi, Daniel M DeLaughter, Joshua D Hutcheson, Payal Vyas, Tan Pham, Maximillian A Rogers, Amitabh Sharma, Christine E Seidman, Joseph Loscalzo, Jonathan G Seidman, Masanori Aikawa, Sasha A Singh, Elena Aikawa
Background -No pharmacological therapy exists for calcific aortic valve disease (CAVD), which confers a dismal prognosis without invasive valve replacement. The search for therapeutics and early diagnostics is challenging since CAVD presents in multiple pathological stages. Moreover, it occurs in the context of a complex, multi-layered tissue architecture, a rich and abundant extracellular matrix phenotype, and a unique, highly plastic and multipotent resident cell population. Methods -A total of 25 human stenotic aortic valves obtained from valve replacement surgeries were analyzed by multiple modalities, including transcriptomics and global unlabeled and label-based tandem-mass-tagged proteomics...
March 27, 2018: Circulation
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