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proteomics pathway ontology

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https://www.readbyqxmd.com/read/29151691/parallel-mrna-proteomics-and-mirna-expression-analysis-in-cell-line-models-of-the-intestine
#1
Finbarr O'Sullivan, Joanne Keenan, Sinead Aherne, Fiona O'Neill, Colin Clarke, Michael Henry, Paula Meleady, Laura Breen, Niall Barron, Martin Clynes, Karina Horgan, Padraig Doolan, Richard Murphy
AIM: To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. METHODS: Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array...
November 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29149484/comparative-analysis-of-proteomes-between-diabetic-and-normal-human-sperm-insights-into-the-effects-of-diabetes-on-male-reproduction-based-on-the-regulation-of-mitochondria-related-proteins
#2
Tian An, Yue-Fen Wang, Jia-Xian Liu, Yan-Yun Pan, Yu-Fei Liu, Zhong-Chen He, Fang-Fang Mo, Jun Li, Li-Hua Kang, Yu-Jie Gu, Bo-Han Lv, Si-Huan Gao, Guang-Jian Jiang
This study sought to identify sources of the reduced fertility of men with type 2 diabetes mellitus. Significant reductions in semen volume, sperm concentration, and total sperm count were observed in diabetic individuals, while transmission electron microscopy revealed that the structure of mitochondria in the tail of sperm from diabetic patients was damaged. Proteins potentially associated with these sperm defects were identified using proteomics. Isobaric tagging for relative and absolute quantitation labeling and high-performance liquid chromatography-tandem mass spectrometry allowed us to identify 357 proteins significantly differentially expressed in diabetic versus control semen (>1...
November 17, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29121109/itraq-based-quantitative-proteomic-analysis-in-vernalization-treated-faba-bean-vicia-faba-l
#3
Yun-Ying Cao, Xiao-Chun Bian, Mo-Xian Chen, Li-Ru Xia, Jianhua Zhang, Fu-Yuan Zhu, Chun-Fang Wu
Vernalization is classically defined as the induction of flowering process by exposure of the plants to a prolonged cold condition. Normally, it is considered as a precondition of flowering. Vicia faba, commonly known as faba bean, belongs to family Fabaceae. It is one of the plant species that has been cultivated in the earliest human settlements. In this study, an iTRAQ-LC-MS/MS-based quantitative proteomic analysis has been conducted to compare the vernalized faba bean seedlings and its corresponding control...
2017: PloS One
https://www.readbyqxmd.com/read/29113319/comparative-proteomic-analysis-of-virulent-and-avirulent-strains-of-toxoplasma-gondii-reveals-strain-specific-patterns
#4
Dong-Hui Zhou, Ze-Xiang Wang, Chun-Xue Zhou, Shuai He, Hany M Elsheikha, Xing-Quan Zhu
Research exploring the proteome of Toxoplasma gondii oocysts has gained momentum over the past few years. However, little is known about the oocyst's protein repertoires that contribute to differential virulence among T. gondii strains. Here, we used isobaric tag for relative and absolute quantitation-based proteomic analysis of oocysts of two T. gondii strains exhibiting the virulent PYS (ToxoDB#9) phenotype versus the less virulent PRU (Type II, ToxoDB#1) phenotype. Our aim was to determine protein expression patterns that contribute to the virulence of a particular phenotype...
October 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/29107696/the-potential-mechanism-for-hydroxysafflor-yellow-a-attenuating-blood-brain-barrier-dysfunction-via-tight-junction-signaling-pathways-excavated-by-an-integrated-serial-affinity-chromatography-and-shotgun-proteomics-analysis-approach
#5
Yanni Lv, Longsheng Fu
Our previous studies elucidated that hydroxysafflor yellow A (HSYA) exerted anti-inflammatory effects against ischemia stroke by inhibiting TLR4 pathway-mediated signaling transduction. However, only several targets were verified in that limited work. The integrated method of serial affinity chromatography (SAC) and shotgun proteomics analysis (SPA) might be an alternative approach for exploring a potential therapeutic role. SAC was induced to extract specific binding proteins in the brain tissue of 2 h of ischemia stroke mice via HSYA affinity matrices...
October 28, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/29094729/chinese-herbal-formula-fuzheng-huayu-alleviates-ccl4-induced-liver-fibrosis-in-rats-a-transcriptomic-and-proteomic-analysis
#6
Shu Dong, Fei-Fei Cai, Qi-Long Chen, Ya-Nan Song, Yang Sun, Bin Wei, Xiao-Yan Li, Yi-Yang Hu, Ping Liu, Shi-Bing Su
Liver fibrosis is a consequence of chronic liver disease that can progress to liver cirrhosis or even hepatocarcinoma. Fuzheng Huayu (FZHY), a Chinese herbal formula, has been shown to exert anti-fibrotic effects. To better understand the molecular mechanisms underlying the anti-fibrotic effects of FZHY, we analyzed transcriptomic and proteomic combination profiles in CCl4-induced liver fibrosis in rats, which were treated with extracted FZHY powder (0.35 g/kg/d, ig) for 3 weeks. We showed that FZHY administration significantly improved liver function, alleviated hepatic inflammatory and fibrotic changes, and decreased the hydroxyproline content in the livers of CCl4-treated rats...
November 2, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/29080277/proteomic-profiling-of-follicle-fluids-after-superstimulation-in-one-month-old-lambs
#7
Y Wu, J Lin, B Han, L Wang, Y Chen, M Liu, J Huang
Follicular fluid (FF) accumulates in the antrum of the ovarian follicle. In addition, FF provides the microenvironment for oocyte development, oocyte maturation and competence, which are acquired during follicular development. Superstimulatory treatment of 1-month-old lambs can achieve synchronous development of numerous growing follicles. However, these growing follicles are unable to completely mature and ovulate. Furthermore, the oocytes exhibit lower competence compared with those of ewes. In this study, we utilized an isobaric tag for relative and absolute quantification (iTRAQ)-based proteomics analysis and compare protein composition between pre-pubertal and adult superstimulated follicle FF in sheep...
October 28, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/29075250/itraq-proteomic-analysis-reveals-that-metabolic-pathways-involving-energy-metabolism-are-affected-by-tea-tree-oil-in-botrytis-cinerea
#8
Jiayu Xu, Xingfeng Shao, Yingying Wei, Feng Xu, Hongfei Wang
Tea tree oil (TTO) is a volatile essential oil obtained from the leaves of the Australian tree Melaleuca alternifolia by vapor distillation. Previously, we demonstrated that TTO has a strong inhibitory effect on Botrytis cinerea. This study investigates the underlying antifungal mechanisms at the molecular level. A proteomics approach using isobaric tags for relative and absolute quantification (iTRAQ) was adopted to investigate the effects of TTO on B. cinerea. A total of 718 differentially expression proteins (DEPs) were identified in TTO-treated samples, 17 were markedly up-regulated and 701 were significantly down-regulated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29069483/protein-profile-of-mouse-ovarian-follicles-grown-in-vitro
#9
Amandine Anastácio, Kenny A Rodriguez-Wallberg, Solenne Chardonnet, Cédric Pionneau, Christian Fédérici, Teresa Almeida Santos, Catherine Poirot
STUDY QUESTION: Could the follicle proteome be mapped by identifying specific proteins that are common or differ between three developmental stages from the secondary follicle to the antrum-like stage? SUMMARY ANSWER: From a total of 1401 proteins identified in the follicles, 609 were common to the three developmental stages investigated and 444 were found uniquely at one of the stages. WHAT IS KNOWN ALREADY: The importance of the follicle as a functional structure has been recognized; however, up-to-date the proteome of the whole follicle has not been described...
October 23, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/29063586/protein-expression-during-early-stages-of-bone-regeneration-under-hydrophobic-and-hydrophilic-titanium-domes-a-pilot-study
#10
E Calciolari, N Mardas, X Dereka, A K Anagnostopoulos, G T Tsangaris, N Donos
BACKGROUND AND OBJECTIVES: There is significant evidence that, during the early stages of osseointegration, moderately rough hydrophilic (SLActive) surfaces can accelerate osteogenesis and increase bone-to-implant contact in comparison to hydrophobic (SLA) surfaces. However, very little is known regarding the molecular mechanisms behind the influence that surface chemistry modifications to increase hydrophilicity determine on bone healing. The aim of this study was to describe for the first time the proteins and related signalling pathways expressed during early osseous healing stages under SLA and SLActive titanium domes for guided bone regeneration...
October 24, 2017: Journal of Periodontal Research
https://www.readbyqxmd.com/read/29054504/proteomics-in-plasma-of-ovariectomized-rats-and-those-exposed-to-estradiol-valerate
#11
Hai Jiang, Wenpei Bai, Wenjuan Wang, Ke Wang, Jing Jia, Jing Zhang, He Diao, Lihua Qin
The menopausal period, an inevitable physiological process for women, is frequently associated with physiological and psychological dysfunction attributable to substantial fluctuation and gradual decrease in female hormones induced by ovarian failure, leading to corresponding symptoms and diseases that impact multiple systems in the body to varying degrees. As prior studies have focused primarily on menopausal syndrome-related pathophysiological changes and hormone replacement therapy effects, here we approached menopausal disease incidence risk and pathogenesis through systemic plasma proteomics analysis...
October 17, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29046343/complement-activation-in-peritoneal-dialysis-induced-arteriolopathy
#12
Maria Bartosova, Betti Schaefer, Justo Lorenzo Bermejo, Silvia Tarantino, Felix Lasitschka, Stephan Macher-Goeppinger, Peter Sinn, Bradley A Warady, Ariane Zaloszyc, Katja Parapatics, Peter Májek, Keiryn L Bennett, Jun Oh, Christoph Aufricht, Franz Schaefer, Klaus Kratochwill, Claus Peter Schmitt
Cardiovascular disease (CVD) is the leading cause of increased mortality in patients with CKD and is further aggravated by peritoneal dialysis (PD). Children are devoid of preexisting CVD and provide unique insight into specific uremia- and PD-induced pathomechanisms of CVD. We obtained peritoneal specimens from children with stage 5 CKD at time of PD catheter insertion (CKD5 group), children with established PD (PD group), and age-matched nonuremic controls (n=6/group). We microdissected omental arterioles from tissue layers not directly exposed to PD fluid and used adjacent sections of four arterioles per patient for transcriptomic and proteomic analyses...
October 18, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29033837/dioscin-inhibits-hsc-t6-cell-migration-via-adjusting-sdc-4-expression-insights-from-itraq-based-quantitative-proteomics
#13
Lianhong Yin, Yan Qi, Youwei Xu, Lina Xu, Xu Han, Xufeng Tao, Shasha Song, Jinyong Peng
Hepatic stellate cells (HSCs) migration, an important bioprocess, contributes to the development of liver fibrosis. Our previous studies have found the potent activity of dioscin against liver fibrosis by inhibiting HSCs proliferation, triggering the senescence and inducing apoptosis of activated HSCs, but the molecular mechanisms associated with cell migration were not clarified. In this work, iTRAQ (isobaric tags for relative and absolution quantitation)-based quantitative proteomics study was carried out, and a total of 1566 differentially expressed proteins with fold change ≥2...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28979670/quantitative-proteomics-analysis-of-mitochondrial-proteins-in-lung-adenocarcinomas-and-normal-lung-tissue-using-itraq-and-tandem-mass-spectrometry
#14
Wei Li, Xuede Zhang, Wei Wang, Ruiying Sun, Boxuan Liu, Yuefeng Ma, Wei Zhang, Li Ma, Yaofeng Jin, Shuanying Yang
Lung adenocarcinoma is the most common type of lung cancer. Unfortunately, lung adenocarcinoma has a poor prognosis and the pathogenesis remains unclear. Mitochondria are important mediators of tumorigenesis. However, the proteomics profile of lung adenocarcinoma mitochondrial proteins has not been elucidated. In this study, we investigated differences in the mitochondrial protein profiles between lung adenocarcinomas and normal tissue. Laser capture microdissection (LCM) was used to isolate the target cells from lung adenocarcinomas and normal tissue...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28975715/data-independent-acquisition-based-quantitative-proteomic-analysis-reveals-potential-biomarkers-of-kidney-cancer
#15
Yimeng Song, Lijun Zhong, Juntuo Zhou, Min Lu, Tianying Xing, Lulin Ma, Jing Shen
PURPOSE: Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. EXPERIMENTAL DESIGN: Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition...
October 4, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28971515/serum-proteomic-assessment-of-the-progression-of-fracture-healing
#16
Amira I Hussein, Christian Mancini, Kyle E Lybrand, Margaret E Cooke, Heather E Matheny, Brenna L Hogue, Paul Tornetta, Louis C Gerstenfeld
A targeted proteomic analysis of murine serum over a 35-day course of fracture healing was carried out to determine if serum proteomic changes could be used to monitor the biological progression of fracture healing. Transverse, closed femoral fractures where generated and stabilized with intramedullary fixation. A single stranded DNA aptamer-based multiplexed proteomic approach was used to assay 1310 proteins. The transcriptomic profiles for genes matching the 1310 proteins were obtained by microarray analysis of callus mRNA...
October 2, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28946568/protein-expression-profiling-in-the-hippocampus-after-focal-cerebral-ischemia-injury-in-rats
#17
Lichan He, Rui He, Ruihua Liang, Yi Li, Xiaoqiang Li, Chuqiao Li, Suping Zhang
In this study, we aimed to explore protein expression profiles in the hippocampus of rats after the induction of focal ischemia injury. Forty SD male rats were randomly divided into 4 groups, with ten rats per group: the control, Day 3, Day 7, and Day 14 after the ischemia injury surgery. Focal cortical ischemia was induced in thirty rats by photothrombosis of the cortical microvessels. After surgery, the induction of ischemia was confirmed by the measurement of infarct size using 2,3,5-triphenyltetrazolium chloride (TTC) staining...
September 20, 2017: Journal of Integrative Neuroscience
https://www.readbyqxmd.com/read/28944995/comparative-analysis-of-serum-proteome-in-congenital-scoliosis-patients-with-tbx6-haploinsufficiency-a-first-report-pointing-to-lipid-metabolism
#18
Qiankun Zhu, Nan Wu, Gang Liu, Yangzhong Zhou, Sen Liu, Jun Chen, Jiaqi Liu, Yuzhi Zuo, Zhenlei Liu, Weisheng Chen, Yixin Chen, Jia Chen, Mao Lin, Yanxue Zhao, Yang Yang, Shensgru Wang, Xu Yang, Yufen Ma, Jian Wang, Xiaoli Chen, Jianguo Zhang, Jianxiong Shen, Zhihong Wu, Guixing Qiu
Congenital scoliosis (CS) is a three-dimensional deformity of the spine affecting quality of life. We have demonstrated TBX6 haploinsufficiency is the most important contributor to CS. However, the pathophysiology at the protein level remains unclear. Therefore, this study was to explore the differential proteome in serum of CS patients with TBX6 haploinsufficiency. Sera from nine CS patients with TBX6 haploinsufficiency and nine age- and gender-matched healthy controls were collected and analysed by isobaric tagged relative and absolute quantification (iTRAQ) labelling coupled with mass spectrometry (MS)...
September 25, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28926933/itraq-based-quantitative-proteomic-analysis-reveals-cold-responsive-proteins-involved-in-leaf-senescence-in-upland-cotton-gossypium-hirsutum-l
#19
Xuewei Zheng, Shuli Fan, Hengling Wei, Chengcheng Tao, Qiang Ma, Qifeng Ma, Siping Zhang, Hongbin Li, Chaoyou Pang, Shuxun Yu
Premature leaf senescence occurs in the ultimate phase of the plant, and it occurs through a complex series of actions regulated by stress, hormones and genes. In this study, a proteomic analysis was performed to analyze the factors that could induce premature leaf senescence in two cotton cultivars. We successfully identified 443 differential abundant proteins (DAPs) from 7388 high-confidence proteins at four stages between non-premature senescence (NS) and premature senescence (PS), among which 158 proteins were over-accumulated, 238 proteins were down-accumulated at four stages, and 47 proteins displayed overlapped accumulation...
September 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28918527/alterations-in-epididymal-proteomics-and-antioxidant-activity-of-mice-exposed-to-fluoride
#20
Zilong Sun, Sujuan Li, Yuxiang Yu, Hongyu Chen, Mohammad Mehdi Ommati, Ram Kumar Manthari, Ruiyan Niu, Jundong Wang
It is well known that high fluoride results in low fertility. Epididymis is the important place for spermatozoa maturation, which is essential for successful fertilization. In the previous studies, fluoride was reported to damage the epididymal structure of mouse and rabbit. However, the mechanism underlying sodium fluoride (NaF)-induced epididymal toxicity has not yet been well elucidated. The aim of this study is to explore the global protein alterations in epididymis of mice exposed to NaF using the iTRAQ technique...
September 16, 2017: Archives of Toxicology
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