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Ingenuity pathway analysis

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https://www.readbyqxmd.com/read/29148176/differential-proteomic-analysis-reveals-protein-networks-and-pathways-that-may-contribute-to-helicobacter-pylori-fkbp-type-ppiase-associated-gastric-diseases
#1
Yanmei Zhu, Yuehua Gong, Aodi Li, Moye Chen, Dan Kang, Jun Liu, Yuan Yuan
PURPOSE: Though Helicobacter pylori (H. pylori) has been classified as class I carcinogen, key virulence factor generated by H. pylori that causes gastric cancer remains to be fully determined. Recently, we identified a gastric cancer-associated H. pylori gene, peptidylprolyl isomerase-FK506 binding protein (PPIase-FKBP), and showed that PPIase-FKBP was capable of inducing oncogenic transformation of gastric epithelial cells. But its mechanism was unclear. EXPERIMENTAL DESIGN: We carried out a comparative proteomic analysis of human gastric epithelial cells that either express PPIase-FKBP or green fluorescent protein (GFP) using two-dimensional (2-D) gel electrophoresis and then matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS)...
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29147886/peromyscus-leucopus-mouse-brain-transcriptome-response-to-powassan-virus-infection
#2
Luwanika Mlera, Kimberly Meade-White, Eric Dahlstrom, Rachel Baur, Kishore Kanakabandi, Kimmo Virtaneva, Stephen F Porcella, Marshall E Bloom
Powassan virus (POWV) is a tick-borne Flavivirus responsible for life-threatening encephalitis in North America and some regions of Russia. The ticks that have been reported to transmit the virus belong to the Ixodes species, and they feed on small-to-medium-sized mammals, such as Peromyscus leucopus mice, skunks, and woodchucks. We previously developed a P. leucopus mouse model of POWV infection, and the model is characterized by a lack of clinical signs of disease following intraperitoneal or intracranial inoculation...
November 16, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/29145837/molecular-network-based-analysis-of-the-mechanism-of-liver-injury-induced-by-volatile-oils-from-artemisiae-argyi-folium
#3
Hongjie Liu, Sha Zhan, Yan Zhang, Yan Ma, Liang Chen, Lingxiu Chen, Hanqiu Dong, Min Ma, Zhe Zhang
BACKGROUND: Volatile oils from Artemisiae argyi folium (VOAAF) is reported with hepatotoxicity, but the underlying mechanism is still unclear. METHODS: In the present study this molecular mechanism was explored with the Ingenuity Pathway Analysis (IPA). The chemical components of the VOAAF were searched in the database, and their target proteins were all identified in the PubChem, while drug-induced liver injury (DILI) genes were searched in the PubMed gene databases...
November 16, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/29143255/pcb-exposure-and-potential-future-cancer-incidence-in-slovak-children-an-assessment-from-molecular-finger-printing-by-ingenuity-pathway-analysis-ipa%C3%A2-derived-from-experimental-and-epidemiological-investigations
#4
Somiranjan Ghosh, Christopher A Loffredo, Partha S Mitra, Tomas Trnovec, Lubica Palkovicova Murinova, Eva Sovcikova, Eric P Hoffman, Kepher H Makambi, Sisir K Dutta
The risk of cancer due to PCB exposure in humans is highly debated. In eastern Slovakia, high exposure of the population to organochlorines (especially PCBs) was associated with various disease and disorder pathways, viz., endocrine disruption, metabolic disorder & diabetes, and cancer, thereby disturbing several cellular processes, including protein synthesis, stress response, and apoptosis. We have evaluated a Slovak cohort (45-month children, at lower and higher levels of PCB exposure from the environment) for disease and disorder development to develop early disease cancer biomarkers that could shed new light on possible mechanisms for the genesis of cancers under such chemical exposures, and identify potential avenues for prevention...
November 15, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29137633/bi-directional-exosome-driven-intercommunication-between-the-hepatic-niche-and-cancer-cells
#5
Nikolina Dioufa, Amanda M Clark, Bo Ma, Colin H Beckwitt, Alan Wells
BACKGROUND: Our understanding of the multiple roles exosomes play during tumor progression is still very poor and the contribution of the normal tissue derived exosomes in distant seeding and tumor outgrowth has also not been widely appreciated. METHODS: Using our all-human liver microphysiological system (MPS) platform as a model to closely recapitulate the early metastatic events, we isolated exosomes from both tumor cells and liver microenvironment. RESULTS: We observed that while priming of the hepatic niche (HepN) with MDA-231 breast cancer derived exosomes facilitated seeding of the cancer cells in the liver, subsequent tumor outgrowth was diminished; this was consistent with increased entry into dormancy...
November 14, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29137139/deduction-of-novel-genes-potentially-involved-in-osteoblasts-of-rheumatoid-arthritis-using-next-generation-sequencing-and-bioinformatic-approaches
#6
Yi-Jen Chen, Wei-An Chang, Ya-Ling Hsu, Chia-Hsin Chen, Po-Lin Kuo
The role of osteoblasts in peri-articular bone loss and bone erosion in rheumatoid arthritis (RA) has gained much attention, and microRNAs are hypothesized to play critical roles in the regulation of osteoblast function in RA. The aim of this study is to explore novel microRNAs differentially expressed in RA osteoblasts and to identify genes potentially involved in the dysregulated bone homeostasis in RA. RNAs were extracted from cultured normal and RA osteoblasts for sequencing. Using the next generation sequencing and bioinformatics approaches, we identified 35 differentially expressed microRNAs and 13 differentially expressed genes with potential microRNA-mRNA interactions in RA osteoblasts...
November 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29136834/comparative-proteomics-of-cancer-stem-cells-in-osteosarcoma-using-ultra-high-performance-liquid-chromatography-and-orbitrap-fusion-mass-spectrometer
#7
Zhihui Zhong, Sifeng Mao, Haifeng Lin, Jin-Ming Lin, Jianhua Lin
Osteosarcoma is the most common malignant tumour found in bones, and it has a poor prognosis. For improved therapy, it is significant to have a deep understanding of the proteomics changes in the cancer stem cells (CSCs) of osteosarcoma. Therefore, a comparative proteomics approach based on ultra-high-performance liquid chromatography coupled to an Orbitrap Fusion mass spectrometer (UHPLC-Orbitrap Fusion MS) was established to investigate the key molecular changes between CSCs and non-CSCs in human osteosarcoma HOS cells...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29133875/heart-function-and-thoracic-aorta-gene-expression-profiling-studies-of-ginseng-combined-with-different-herbal-medicines-in-enos-knockout-mice
#8
Yuchen Qian, Pan Li, Bin Lv, Xiaoqing Jiang, Ting Wang, Han Zhang, Xiaoying Wang, Xiumei Gao
Ginseng, a popular herbal remedy, is often used in combination with other drugs to achieve the maximum therapeutic response. Shenfu (SFI) and Shenmai injection (SMI) have been widely used to treat cardiovascular disease in China. Our study explored the cardiovascular protection of SFI and SMI in eNOS knockout mice to investigate the differences and similarities of the two ginseng-combinations. Transthoracic echocardiography was performed to evaluate the left ventricular structure and function at baseline and 3, 7, and 14 days after drug administration...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126925/comparative-transcriptomic-characterization-of-a-new-mib-mutant-allele-mib-nn2002-in-zebrafish
#9
Keng Po Lai, Jing-Woei Li, Chia-Hao Hsu, May-Su You, Ting-Fung Chan, William Ka Fai Tse, Yun-Jin Jiang
mib(nn2002), identified from an allele screen, shows early segmentation defect and severe cell death phenotypes, which are different from those of other described mib mutant alleles. We have previously reported its defects in somitogenesis and identified its origin of mutation, a large deletion in LG2. The report here is a continuous study, where we applied the bioinformatics analysis to profile the genetic background of mib(nn2002) mutants. By comparing the transcriptomic data of mib(nn2002) mutants with those of AB wild-type, a total of 1945 differentially expressed genes were identified, including 685 up- and 1260 down-regulated genes...
November 7, 2017: Gene
https://www.readbyqxmd.com/read/29126429/rna-sequencing-analysis-of-lung-primary-fibroblast-response-to-eosinophil-degranulation-products-predicts-downstream-effects-on-inflammation-tissue-remodeling-and-lipid-metabolism
#10
Stephane Esnault, Ksenija Bernau, Elizabeth E Torr, Yury A Bochkov, Nizar N Jarjour, Nathan Sandbo
BACKGROUND: The association of eosinophils with inflammation and tissue remodeling is at least partially due to their release of toxic granule proteins and other mediators, including cytokines. Tissue remodeling and consequent functional defects are affected by activity of connective tissue fibroblasts. Exaggerated fibroblast activation, accumulation and change of phenotype may lead to fibrosis and loss of tissue function. So far, little information has been reported on how eosinophils affect inflammation and tissue remodeling via the activation of fibroblasts...
November 10, 2017: Respiratory Research
https://www.readbyqxmd.com/read/29122055/extruded-linseed-alone-or-in-combination-with-fish-oil-modifies-mammary-gene-expression-profiles-in-lactating-goats
#11
Y Faulconnier, L Bernard, C Boby, J Domagalski, Y Chilliard, C Leroux
Nutrition is a major factor that regulates ruminant milk components, particularly its fatty acid (FA) composition, which is an important determinant of milk nutritional quality. In the mammary gland, milk component biosynthesis involves a large number of genes under nutritional regulation that are not well understood. Thus, the objective of the present study was to evaluate the effects of extruded linseeds (EL) alone or in combination with fish oil (ELFO) on goat mammary gene expression. In total, 14 goats were fed one of the following three diets: a natural grassland hay basal diet (CTRL) alone, CTRL supplemented with 530 g/day of EL, or 340 g/day of EL plus 39 g/day of fish oil (ELFO)...
November 10, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29121074/proteome-profiling-in-the-aorta-and-kidney-of-type-1-diabetic-rats
#12
Moustafa Al Hariri, Mohamad Elmedawar, Rui Zhu, Miran A Jaffa, Jingfu Zhao, Parvin Mirzaei, Adnan Ahmed, Firas Kobeissy, Fuad N Ziyadeh, Yehia Mechref, Ayad A Jaffa
Diabetes is associated with a number of metabolic and cardiovascular risk factors that contribute to a high rate of microvascular and macrovascular complications. The risk factors and mechanisms that contribute to the development of micro- and macrovascular disease in diabetes are not fully explained. In this study, we employed mass spectrometric analysis using tandem LC-MS/MS to generate a proteomic profile of protein abundance and post-translational modifications (PTM) in the aorta and kidney of diabetic rats...
2017: PloS One
https://www.readbyqxmd.com/read/29115597/quantitative-proteomic-study-of-the-plasma-reveals-acute-phase-response-and-lxr-rxr-and-fxr-rxr-activation-in-the-chronic-unpredictable-mild-stress-mouse-model-of-depression
#13
Chuangchuang Yang, Chanjuan Zhou, Jie Li, Zhi Chen, Haiyang Shi, Wensong Yang, Yinhua Qin, Lin Lü, Libo Zhao, Liang Fang, Haiyang Wang, Zicheng Hu, Peng Xie
Major depressive disorder is a severe neuropsychiatric disease that negatively impacts the quality of life of a large portion of the population. However, the molecular mechanisms underlying depression are still unclear. The pathogenesis of depression involves several brain regions. However, most previous studies have focused only on one specific brain region. Plasma and brain tissues exchange numerous components through the blood‑brain barrier. Therefore, in the present study, plasma samples from control (CON) mice and mice subjected to chronic unpredictable mild stress (CUMS) were used to investigate the molecular pathogenesis of depression, and the association between the peripheral circulation and the central nervous system...
October 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29115543/the-screening-and-analysis-of-protein-signatures-and-signaling-associated-with-chemoresistance-based-on-protein-pathway-array-technology-in-gastric-cancer
#14
Guodong Lian, Leping Li, Fei Ye, Daguang Wang, Jinglei Liu, Yulong Shi, Changqing Jing, Jian Suo, David Y Zhang, Man Chen
The present study was aimed to identify proteins associated with signaling pathways involved in chemoresistance, and establish a predictive model for chemoresistance in gastric cancer patients after radical surgery. A total of 140 clinically-staged III gastric cancer samples from patients after D2 radical gastrectomy were enrolled in the present study. Protein Pathway Array (PPA) and 286 antibodies were used to assess the protein expression in tumor tissues of patients. The Significance Analysis of Microarray (SAM) software and clustering and discriminant analysis were used to identify differentially expressed proteins between chemosensitive and chemoresistant subsets, and a predictive model for chemoresistance was established using the independent predictive factors...
November 6, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29111329/exosomes-derived-from-pancreatic-cancer-cells-induce-activation-and-profibrogenic-activities-in-pancreatic-stellate-cells
#15
Atsushi Masamune, Naoki Yoshida, Shin Hamada, Tetsuya Takikawa, Tatsuhide Nabeshima, Tooru Shimosegawa
Pancreatic cancer cells (PCCs) interact with pancreatic stellate cells (PSCs), which play a pivotal role in pancreatic fibrogenesis, to develop the cancer-conditioned tumor microenvironment. Exosomes are membrane-enclosed nanovesicles, and have been increasingly recognized as important mediators of cell-to-cell communications. The aim of this study was to clarify the effects of PCC-derived exosomes on cell functions in PSCs. Exosomes were isolated from the conditioned medium of Panc-1 and SUIT-2 PCCs. Human primary PSCs were treated with PCC-derived exosomes...
October 27, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29108742/gene-expression-analysis-reveals-chronic-low-level-exposure-to-the-pesticide-diazinon-affects-psychological-disorders-gene-sets-in-the-adult-rat
#16
Claire Y Savy, Ann E Fitchett, Peter G Blain, Christopher M Morris, Sarah J Judge
Chronic low level exposure to organophosphate (OPs) pesticides in adulthood has been linked to adverse neurobehavioural deficits and psychological disorder symptoms, although this remains a contentious issue. The OP-induced biological changes that could underlie these effects are unclear. We assessed gene expression changes following chronic low level exposure to diazinon, a pesticide with a high dietary exposure risk. Adult male rats were orally exposed to diazinon (0, 1, 2mg/kg, 5days a week for 12 weeks)...
November 3, 2017: Toxicology
https://www.readbyqxmd.com/read/29100313/g2-m-checkpoint-plays-a-vital-role-at-the-early-stage-of-hcc-by-analysis-of-key-pathways-and-genes
#17
Li Yin, Cuifang Chang, Cunshuan Xu
The present study was designed to explore the molecular mechanism at the early stage of hepatocarcinoma (HCC) and identify the candidate genes and pathways changed significantly. We downloaded the gene expression file dataset GSE6764 from GEO, adopted the Robust Multi-array Average (RMA) algorithm to preprocess the raw file. 797 differentially expressed genes (DEGs) were screened out based on the SAM method using R language. Ingenuity Pathway Analysis (IPA) was used to perform canonical pathway analysis in order to calculate the most significantly changed pathways and predict the upstream regulators...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29099282/dna-methylation-and-obesity-traits-an-epigenome-wide-association-study-the-regicor-study
#18
Sergi Sayols-Baixeras, Isaac Subirana, Alba Fernández-Sanlés, Mariano Sentí, Carla Lluís-Ganella, Jaume Marrugat, Roberto Elosua
Obesity is associated with increased risk of several diseases and has become epidemic. Obesity is highly heritable but the genetic variants identified by genome-wide association studies explain only limited variability. Epigenetics could contribute to explain the missing variability. The study aim was to discover differential methylation patterns related to obesity. We designed an epigenome-wide association study with a discovery phase in a subsample of 641 REGICOR study participants, validated by analysis of 2,515 participants in the Framingham Offspring Study...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29095204/improvement-of-blood-brain-barrier-integrity-in-traumatic-brain-injury-and-hemorrhagic-shock-following-treatment-with-valproic-acid-and-fresh-frozen-plasma
#19
Vahagn C Nikolian, Simone E Dekker, Ted Bambakidis, Gerald A Higgins, Isabel S Dennahy, Patrick E Georgoff, Aaron M Williams, Anuska V Andjelkovic, Hasan B Alam
OBJECTIVE: Combined traumatic brain injury and hemorrhagic shock are highly lethal. Following injuries, the integrity of the blood-brain barrier can be impaired, contributing to secondary brain insults. The status of the blood-brain barrier represents a potential factor impacting long-term neurologic outcomes in combined injuries. Treatment strategies involving plasma-based resuscitation and valproic acid therapy have shown efficacy in this setting. We hypothesize that a component of this beneficial effect is related to blood-brain barrier preservation...
October 31, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/29092904/analysis-of-orp2-knockout-hepatocytes-uncovers-a-novel-function-in-actin-cytoskeletal-regulation
#20
Henriikka Kentala, Annika Koponen, Annukka M Kivelä, Robert Andrews, ChunHei Li, You Zhou, Vesa M Olkkonen
ORP2 is implicated in cholesterol transport, triglyceride metabolism, and adrenocortical steroid hormone production. We addressed ORP2 function in hepatocytes by generating ORP2-knockout (KO) HuH7 cells by CRISPR-Cas9 gene editing, followed by analyses of transcriptome, F-actin morphology, migration, adhesion, and proliferation. RNA sequencing of ORP2-KO cells revealed >2-fold changes in 579 mRNAs. The Ingenuity Pathway Analysis (IPA) uncovered alterations in the following functional categories: cellular movement, cell-cell signaling and interaction, cellular development, cellular function and maintenance, cellular growth and proliferation, and cell morphology...
November 1, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
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