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proteomics pathway ontology

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https://www.readbyqxmd.com/read/29321808/itraq-based-proteomic-analysis-to-identify-the-molecular-mechanism-of-zhibai-dihuang-granule-in-the-yin-deficiency-heat-syndrome-rats
#1
Chang-Ming Liu, Jing Chen, Su Yang, Ting-Ting Jiang, Zhong-Liang Chen, Hui-Hui Tu, Lian-Gen Mao, Yu-Ting Hu, Lin Gan, Zhong-Jie Li, Ji-Cheng Li
Background: Zhibai Dihuang Granule (ZDG) is a traditional Chinese medicine which has been used to treat Yin-deficiency-heat (YDH) syndrome for thousands of years in China. However, little work has been conducted to explore the molecular mechanism of ZDG in YDH syndrome, and the processes of YDH syndrome prevention and treatment have been developed slowly. The present study was aimed to explore the therapeutic mechanism of ZDG on YDH syndrome. Methods: The YDH syndrome rats were induced by hot Chinese herbs, then treated by ZDG orally for 1 week...
2018: Chinese Medicine
https://www.readbyqxmd.com/read/29317699/inflammatory-proteomic-network-analysis-of-statin-treated-and-lipopolysaccharide-activated-macrophages
#2
Abu Hena M Kamal, Jayanta K Chakrabarty, S M Nashir Udden, Md Hasan Zaki, Saiful M Chowdhury
A significant component of immune biology research is the investigation of protein encoding genes that play central roles in contributing inflammatory response. A gel-free quantitative bottom-up proteomics study was performed on immune cell macrophages after the combined treatment of lipopolysaccharide (LPS) and statin drugs using mass spectrometry and a detailed bioinformatics analyses were conducted. Systematic bioinformatics analysis was applied for discovering novel relationships among proteins and effects of statin and lipopolysaccharide in macrophage cells...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29299995/mirna-and-proteomic-dysregulation-in-non-small-cell-lung-cancer-in-response-to-cigarette-smoke
#3
Niraj Babu, Jayshree Advani, Hitendra S Solanki, Krishna Patel, Ankit P Jain, Aafaque Ahmad Khan, Aneesha Radhakrishnan, Nandini A Sahasrabuddhe, Premendu Prakash Mathur, Bipin Nair, T S Keshava Prasad, Xiaofei Chang, David Sidransky, Harsha Gowda, Aditi Chatterjee
BACKGROUND: Dysregulation of miRNAs is associated with the development of non-small cell lung cancer (NSCLC). It is imperative to study the dysregulation of miRNAs by cigarette smoke which will affect their targets, either leading to the overexpression of oncoproteins or downregulation of tumor suppressor proteins. OBJECTIVE AND METHODS: In this study, we carried out miRNA sequencing and SILAC-based proteomic analysis of H358 cells chronically exposed to cigarette smoke condensate...
January 3, 2018: MicroRNA
https://www.readbyqxmd.com/read/29287759/comparative-proteomics-analysis-of-trichinella-spiralis-muscle-larvae-exposure-to-albendazole-sulfoxide-stress
#4
Ruo Yu Peng, Hui Jun Ren, Chun Li Zhang, Pin Lv, Gao Hui Wei, Zhong Quan Wang, Jing Cui, Liang Ming
The drug albendazole (ABZ) has a positive effect against Trichinella spiralis infection and has been used for the treatment and prevention of trichinellosis in both humans and animals. However, the molecular mechanism of ABZ's effects on T. spiralis remains unknown now. Albendazole sulfoxide (ABZSO) is the main intermediary metabolic product of ABZ, and often used as a substitute of ABZ for the metabolism and bioavailability researches. Herein, isobaric tagging reagents for relative and absolute quantification (iTRAQ)-based LC-MS/MS analysis was used to identify the effect of ABZSO on the proteome of T...
December 26, 2017: Acta Tropica
https://www.readbyqxmd.com/read/29285290/preliminary-quantitative-proteomics-analysis-in-chronic-and-latent-keshan-disease-by-itraq-labeling-approach
#5
Yuxiao Sun, Chuanyu Gao, Xianqing Wang, Yuhao Liu
Keshan disease is a congestive cardiomyopathy. Dietary selenium deficiency combined with additional stressors are recognized to cause the cardiomyopathies. In this study, clinical condition of individuals with different subtypes including chronic and latent were analyzed. ECG abnormalities, chest radiography, echocardiography and blood selenium concentration were assessed. Subsequently, in effort to uncover proteins that were reliably changed in patients, isobaric tags for absolute and relative quantitation technology was applied...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29282749/compared-proteomic-analysis-of-8-and-32-week-old-postnatal-porcine-ovaries
#6
Lin Hou, Jian Wang, Yinjuan Wang, Xiuguo Hua, Ji Wu
Pigs share many anatomical and physiological features with humans, offering a unique and viable model for biomedical research. Tandem mass tag method followed by mass spectrometry analysis was utilized to identify peptides (47,405), proteins (14,701), and protein groups (7634) in ovaries of 8- and 32-week-old postnatal Banna miniature pigs. After annotation and analysis by Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology, the proteins were identified as being involved in hormone metabolic pathways and maintenance, proliferation, and regulation of stem cells...
December 28, 2017: Cell Biochemistry and Function
https://www.readbyqxmd.com/read/29277631/a-proteomic-clock-of-human-pregnancy
#7
Nima Aghaeepour, Benoit Lehallier, Quentin Baca, Ed A Ganio, Ronald J Wong, Mohammad S Ghaemi, Anthony Culos, Yasser Y El-Sayed, Yair J Blumenfeld, Maurice L Druzin, Virginia D Winn, Ronald S Gibbs, Rob Tibshirani, Gary M Shaw, David K Stevenson, Brice Gaudilliere, Martin S Angst
BACKGROUND: Early detection of maladaptive processes underlying pregnancy-related pathologies is desirable, as it will enable targeted interventions ahead of clinical manifestations. The quantitative analysis of plasma proteins features prominently among molecular approaches used to detect deviations from normal pregnancy. However, derivation of proteomic signatures sufficiently predictive of pregnancy-related outcomes has been challenging. An important obstacle hindering such efforts were limitations in assay technology, which prevented the broad examination of the plasma proteome...
December 22, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29245986/plasma-proteomics-reveals-coagulation-inflammation-and-metabolic-shifts-in-h-type-hypertension-patients-with-and-without-acute-ischemic-stroke
#8
Feng Zhou, Lv Zhou, Tie Guo, Nianzhen Wang, Haizhen Hao, Yanhui Zhou, Dan Yu
Systematic profiling of a larger portion of circulating plasma proteome provide opportunities for unbiased discovery of novel markers to improve diagnostic, therapeutic, or predictive accuracy. This study aimed to identify differentially expressed proteins (DEPs) in plasma that could provide overall insight into the molecular changes of both H- type hypertension (HH) and HH-related acute ischemic stroke (AIS). This study used an iTRAQ-based LC-MS/MS proteomics approach to screen for plasma DEPs in HH patients with and without AIS, and controls...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29237571/identification-of-genes-related-to-proliferative-diabetic-retinopathy-through-rwr-algorithm-based-on-protein-protein-interaction-network
#9
Jian Zhang, Yan Suo, Min Liu, Xun Xu
Proliferative diabetic retinopathy (PDR) is one of the most common complications of diabetes and can lead to blindness. Proteomic studies have provided insight into the pathogenesis of PDR and a series of PDR-related genes has been identified but are far from fully characterized because the experimental methods are expensive and time consuming. In our previous study, we successfully identified 35 candidate PDR-related genes through the shortest-path algorithm. In the current study, we developed a computational method using the random walk with restart (RWR) algorithm and the protein-protein interaction (PPI) network to identify potential PDR-related genes...
December 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29228584/combination-of-calr-and-pdia3-is-a-potential-prognostic-biomarker-for-non-small-cell-lung-cancer
#10
Ke Wang, Hao Li, Ruo Chen, Yang Zhang, Xiu-Xuan Sun, Wan Huang, Huijie Bian, Zhi-Nan Chen
Proteomic-based approaches for biomarker discovery are promising strategies used in cancer research. In this study, we performed quantitative proteomic analysis on 16 paired samples of non-small cell lung cancer (NSCLC) and adjacent non-tumor lung tissues using label-free quantitative proteomics and liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS) to identify differentially expressed proteins. A total of 91 proteins were differentially expressed in NSCLC compared with adjacent non-tumor lung tissues among 4047 identified proteins (fold change > 1...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29222758/differential-proteomics-based-on-2d-difference-in-gel-electrophoresis-and-tandem-mass-spectrometry-for-the-elucidation-of-biological-processes-in-antibiotic-producer-bacterial-strains
#11
Giuseppe Gallo, Andrea Scaloni
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29207638/jolkinolide-b-induces-apoptosis-of-colorectal-carcinoma-through-ros-er-stress-ca2-mitochondria-dependent-pathway
#12
Jing Zhang, Yang Wang, Ye Zhou, Qing-Yu He
Colorectal carcinoma (CRC) remains one of the leading causes of death in cancer-related diseases. In this study, we aimed to investigate the anticancer effect of Jolkinolide B (JB), a bioactive diterpenoid component isolated from the dried roots of Euphorbia fischeriana Steud, on CRC cells and its underlying mechanisms. We found that JB suppressed the cell viability and colony formation of CRC cells, HT29 and SW620. Annexin V/PI assay revealed that JB induced apoptosis in CRC cells, which was further confirmed by the increased expression of cleaved-caspase3 and cleaved-PARP...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29197581/proteomic-analysis-of-bombyx-mori-molting-fluid-insights-into-the-molting-process
#13
Hua-Wei Liu, Luo-Ling Wang, Xin Tang, Zhao-Ming Dong, Peng-Chao Guo, Dong-Chao Zhao, Qing-You Xia, Ping Zhao
Molting is an essential biological process occurring multiple times throughout the life cycle of most Ecdysozoa. Molting fluids accumulate and function in the exuvial space during the molting process. In this study, we used liquid chromatography-tandem mass spectrometry to investigate the molting fluids to analyze the molecular mechanisms of molting in the silkworm, Bombyx mori. In total, 375 proteins were identified in molting fluids from the silkworm at 14-16h before pupation and eclosion, including 12 chitin metabolism-related enzymes, 35 serine proteases, 15 peptidases, and 38 protease inhibitors...
November 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29169324/a-post-gene-silencing-bioinformatics-protocol-for-plant-defence-gene-validation-and-underlying-process-identification-case-study-of-the-arabidopsis-thaliana-npr1
#14
Rosita E Yocgo, Ephifania Geza, Emile R Chimusa, Gaston K Mazandu
BACKGROUND: Advances in forward and reverse genetic techniques have enabled the discovery and identification of several plant defence genes based on quantifiable disease phenotypes in mutant populations. Existing models for testing the effect of gene inactivation or genes causing these phenotypes do not take into account eventual uncertainty of these datasets and potential noise inherent in the biological experiment used, which may mask downstream analysis and limit the use of these datasets...
November 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29166853/proteomic-insight-into-fruit-set-of-cucumber-cucumis-sativus-l-suggests-the-cues-of-hormone-independent-parthenocarpy
#15
Ji Li, Jian Xu, Qin-Wei Guo, Zhe Wu, Ting Zhang, Kai-Jing Zhang, Chun-Yan Cheng, Pin-Yu Zhu, Qun-Feng Lou, Jin-Feng Chen
BACKGROUND: Parthenocarpy is an excellent agronomic trait that enables crops to set fruit in the absence of pollination and fertilization, and therefore to produce seedless fruit. Although parthenocarpy is widely recognized as a hormone-dependent process, hormone-insensitive parthenocarpy can also be observed in cucumber; however, its mechanism is poorly understood. To improve the global understanding of parthenocarpy and address the hormone-insensitive parthenocarpy shown in cucumber, we conducted a physiological and proteomic analysis of differently developed fruits...
November 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29164074/systemic-responses-of-multidrug-resistant-pseudomonas-aeruginosa-and-acinetobacter-baumannii-following-exposure-to-the-antimicrobial-peptide-cathelicidin-bf-imply-multiple-intracellular-targets
#16
Cunbao Liu, Bin Shan, Jialong Qi, Yanbing Ma
Cathelicidin-BF, derived from the banded krait (Bungarus fasciatus), is a typically cationic, amphiphilic and α-helical antimicrobial peptide (AMP) with 30 amino acids that exerts powerful effects on multidrug-resistant (MDR) clinical isolates, including Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae, but whether it targets plasma membranes or intracellular targets to kill bacteria is still controversial. In the present study, we demonstrated that the disruption of bacterial membranes with high concentrations of cathelicidin-BF was the cause of bacterial death, as with conventional antibiotics at high concentrations...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29151691/parallel-mrna-proteomics-and-mirna-expression-analysis-in-cell-line-models-of-the-intestine
#17
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
#18
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
#19
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
#20
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
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