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Liao Peng, De-Yi Luo
PURPOSE: To identify keys genes and elucidate miRNA-mRNA regulatory networks in Bladder smooth muscle cell (BSMC) response to mechanical stimuli. METHODS: Human BSMCs, seeded on a silicone membrane, were subjected to mechanical stretch or without stretch. Microarray was used to analyze the differential expression of mRNAs and miRNAs between human BSMCs under mechanical stretch and control static control group. Differentially expressed genes(DEGs) and miRNAs (DEMs) in these two groups were identified...
November 15, 2017: World Journal of Urology
Hojjat-Allah Abbaszadeh, Ali Asghar Peyvandi, Yousef Sadeghi, Akram Safaei, Mona Zamanian-Azodi, Maryam Sadat Khoramgah, Mostafa Rezaei-Tavirani
Introduction: Periodontitis is a set of inflammatory disorders characterized by periodontal attachment loss and alveolar bone resorption. Because of deficiency in periodontitis mechanical therapy, this study was aimed to explore the molecular influence of the erbiumdoped: yttrium aluminum garnet (Er:YAG) laser and cyclosporin A (CsA) on human gingival fibroblasts (HGFs) for improvement in periodontal diseases therapy. Methods: We focused on articles that studied the proteome profiles of HGFs after treatment with laser irradiation and application of CsA...
2017: Journal of Lasers in Medical Sciences
Reza Karbalaei, Mehran Piran, Mostafa Rezaei-Tavirani, Hamid Asadzadeh-Aghdaei, Mohammad Hossein Heidari
Aim: Analysis reconstruction networks from two diseases, IBD and NASH and their relationship, based on systems biology methods. Background: IBD and NASH are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on co-existence of these two diseases. In addition, they have some similar risk factors such as age, obesity, and insulin resistance. Therefore, systems biology approach can help to discover their relationship...
2017: Gastroenterology and Hepatology From Bed to Bench
Liang Wei, Qi Wang, Yanfei Zhang, Cheng Yang, Hongxin Guan, Yiming Chen, Zhiyang Sun
Intracranial aneurysm (IA) is a devastating disease, the pathogenesis of which remains to be elucidated. The present study aimed to determine the molecular mechanism of IA and to identify potential therapeutic targets using bioinformatics analysis. The GSE54083 dataset, which includes data from patients with ruptured IA and superficial temporal artery controls, was downloaded from the Gene Expression Omnibus, and differentially expressed genes (DEGs) were identified in the ruptured IA samples using the limma package in R...
November 3, 2017: Molecular Medicine Reports
Zheng-Lun Zhu, Qiu-Meng Yang, Chen Li, Jun Chen, Min Xiang, Ming-Min Chen, Min Yan, Zheng-Gang Zhu
The aim of the current study was to identify potential biomarkers of childhood obesity, and investigate molecular mechanisms and candidate agents in order to improve therapeutic strategies for childhood obesity. The GSE9624 gene expression profile was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in omental adipose tissues were analyzed with limma package by comparing samples from obese and normal control children. Two‑way hierarchical clustering was applied using the pheatmap package...
October 27, 2017: Molecular Medicine Reports
Wei Sun, Zeting Qiu, Wenqi Huang, Minghui Cao
Oral tongue squamous cell carcinoma (OTSCC) has a high incidence and is associated with a high mortality rate. Studies regarding the potential molecular mechanism of OTSCC in the tumor microenvironment (TME) are required. The present study aimed to perform bioinformatic analysis to identify important nodes, clusters and functional pathways during tongue carcinogenesis in the TME. After downloading the gene expression data of GSE42780, differentially expressed genes (DEGs) among carcinoma, dysplastic and normal samples in epithelia and fibroblasts were identified using the affy and limma packages with R version 3...
October 20, 2017: Molecular Medicine Reports
Bingli Zheng, Jie Peng, Ablikim Mollayup, Ahmat Bakri, Lei Guo, Jianjiang Zheng, Hui Xu
Pancreatic cancer (PC) is associated with high mortality rates and poor prognoses. Pancreatic adenocarcinoma is the most common type of PC, and almost all cases of pancreatic adenocarcinoma are pancreatic ductal adenocarcinoma (PDAC). The aim of the current study was to reveal the genes involved in the prognosis of PDAC. Five datasets, including GSE71729 (145 PDAC samples and 46 normal samples), GSE15471 (39 PDAC samples and 39 normal samples), GSE1542 (24 PDAC samples and 25 normal samples), GSE28735 (45 PDAC samples and 45 normal samples) and GSE62452 (69 PDAC samples and 69 normal samples) were downloaded from the Gene Expression Omnibus database...
October 20, 2017: Molecular Medicine Reports
Anping Wang, Guibin Zhang
The differentially expressed genes between glioblastoma (GBM) cells and normal human brain cells were investigated to performed pathway analysis and protein interaction network analysis for the differentially expressed genes. GSE12657 and GSE42656 gene chips, which contain gene expression profile of GBM were obtained from Gene Expression Omniub (GEO) database of National Center for Biotechnology Information (NCBI). The 'limma' data packet in 'R' software was used to analyze the differentially expressed genes in the two gene chips, and gene integration was performed using 'RobustRankAggreg' package...
November 2017: Oncology Letters
Junxiu Sheng, Jinyao Zhao, Qiuhong Xu, Linlin Wang, Wenjing Zhang, Yang Zhang
Colorectal cancer is the third most common type of cancer and the fourth leading cause of cancer-associated mortality worldwide. Serine/arginine-rich splicing factor 1 (SRSF1) is a well-characterized oncogenic factor that promotes tumorigenesis by controlling a number of alternative splicing events. However, there is limited network analysis, from a global aspect, to study the effect of SRSF1 on colorectal cancer. In the present study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of available gene regulation data from The Cancer Genome Atlas database revealed the enriched functions and signaling pathways of SRSF1...
November 2017: Oncology Letters
Francesca De Filippis, Eugenio Parente, Teresa Zotta, Danilo Ercolini
The different pipelines that may be used in 16S rRNA gene profiling of bacterial communities are known to have a significant impact on alpha and beta diversity measures and this may prevent direct comparison of results obtained in studies using different bioinformatic approaches to analyse raw sequences. To evaluate the feasibility of meta-studies on food bacterial communities, we compared four analysis procedures, varying in OTU picking and taxonomy assignment strategies. A closed reference OTU picking resulted in the most divergent results in terms of both alpha and beta diversity, compared to open reference methods...
October 27, 2017: International Journal of Food Microbiology
Gang Zheng, Qianlei Zheng, Qianwei Xu
Cerebral small vessel disease (CSVD) primarily affects the perforating cerebral arterioles and capillaries, and results in injury to subcortical grey and white matter. Despite advances in determining the genetic basis of CSVD, the molecular mechanisms underlying the development and progression of CSVD remain unclear. The present study aimed to identify significant signaling pathways associated with CSVD based on differential pathway network analysis. Combining CSVD microarray data with human protein-protein interaction data and data from the Reactome pathway database, pathway interactions were constructed using the Spearman's correlation coefficient strategy...
November 2017: Experimental and Therapeutic Medicine
Shuang Yang, Xinxin Zhang, Jinxin Wang, Shang Wang, Yu Pan, Juhong Zhang, Jinghui Xi
Rapid cold hardening (RCH) is a central physiological adaptation in which brief chilling significantly enhances the cold tolerance ability of insects. However, the mechanism of rapid cold stress response remains unknown for rice water weevils. To elucidate the mechanism, a comparative proteomic analysis was applied with two-dimensional gel electrophoresis (2-DE) between RCH and control treatment samples. A total of 21 protein spots were found to be up-regulated in rice water weevil adults for the RCH condition...
November 2, 2017: Gene
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
Heather Wiedenhoft, Lauren Hayashi, Allison B Coffin
Inner ear hair cell death leads to sensorineural hearing loss and can be a direct consequence of aminoglycoside antibiotic treatment. Aminoglycosides such as gentamicin are effective therapy for serious Gram-negative bacterial infections such as some forms of meningitis, pneumonia, and sepsis. Aminoglycosides enter hair cells through mechanotransduction channels at the apical end of hair bundles and initiate intrinsic cell death cascades, but the precise cell signaling that leads to hair cell death is incompletely understood...
2017: Frontiers in Cellular Neuroscience
Enhao Fang, Xiuqing Zhang, Kang Shao
BACKGROUND: Breast cancer (BC) is the second most common cause of death from cancer in women in the United States. As the molecular mechanism of BC has not yet been completely discovered, identification of hub genes and pathways of this disease is of importance for revealing molecular mechanism of breast cancer initiation and progression. OBJECTIVE: This study aimed to identify potential biomarkers and survival analysis of hub genes for BC treatment. METHODS: The differentially expressed genes (DEGs) between breast cancer and normal cells were screened using microarray data obtained from the Gene Expression Omnibus (GEO) database...
October 13, 2017: Cancer Biomarkers: Section A of Disease Markers
Janet Sultana, Marco Calabró, Ricard Garcia-Serna, Carmen Ferrajolo, Concetta Crisafulli, Jordi Mestres, Gianluca Trifirò'
INTRODUCTION: Antipsychotic (AP) safety has been widely investigated. However, mechanisms underlying AP-associated pneumonia are not well-defined. AIM: The aim of this study was to investigate the known mechanisms of AP-associated pneumonia through a systematic literature review, confirm these mechanisms using an independent data source on drug targets and attempt to identify novel AP drug targets potentially linked to pneumonia. METHODS: A search was conducted in Medline and Web of Science to identify studies exploring the association between pneumonia and antipsychotic use, from which information on hypothesized mechanism of action was extracted...
2017: PloS One
Nani Wang, Guizhi Zhao, Yang Zhang, Xuping Wang, Lisha Zhao, Pingcui Xu, Dan Shou
BACKGROUND Osteoporosis is a complex bone disorder with a genetic predisposition, and is a cause of health problems worldwide. In China, Curculigo orchioides (CO) has been widely used as a herbal medicine in the prevention and treatment of osteoporosis. However, research on the mechanism of action of CO is still lacking. The aim of this study was to identify the absorbable components, potential targets, and associated treatment pathways of CO using a network pharmacology approach. MATERIAL AND METHODS We explored the chemical components of CO and used the five main principles of drug absorption to identify absorbable components...
October 27, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Akram Safaei, Mostafa Rezaei Tavirani, Mona Zamanian Azodi, Alireza Lashay, Seyed Farzad Mohammadi, Mohamad Ghasemi Broumand, Ali Asghar Peyvandi, Farshad Okhovatian, Hassan Peyvandi, Mohammad Rostami Nejad
Introduction: Diabetic retinopathy (DR) is a serious microvascular complication of diabetes which can cause vision loss or blindness ultimately. Non enzymatic glycation of proteins leads to advanced glycation end products (AGEs) in DR. Since laser therapy is a well-established method, in this study, protein-protein interaction (PPI) network is applied for protein targets in DR disease in rats treated by laser. Methods: In this study, we focused on articles that investigated and compared the proteome profiles of DR rats with healthy control and also DR rats before and after laser therapy...
2017: Journal of Lasers in Medical Sciences
Anshika N Singh, Neeti Sharma
Prostate cancer (PCa), a multifocal clinically heterogeneous disease, is the most commonly diagnosed non-cutaneous neoplasm in men worldwide. The epigenome of PCa is a typical representation of catastrophic model of epigenetic alterations during tumorigenesis and its progression. Alterations in methylation patterns in tumor suppressors, cell cycle, oncogenes and metabolism-related genes are the most commonly observed epigenetic alterations in PCa. In this study, we have developed a computational strategy to identify methylated biomarker signature panels as potential targets of PCa by screening >160 genes reported to be epigenetically dysregulated, and shortlisted 26 differentially methylated genes (DMGs) that significantly contribute to oncogenesis...
2017: OncoTargets and Therapy
Govindaraj Saravanan, Theivendren Panneer Selvam, Veerachamy Alagarsamy, Selvaraj Kunjiappan, Shrinivas D Joshi, Murugan Indhumathy, Pandurangan Dinesh Kumar
Background We designed to synthesize a number of 2-(2-(substituted benzylidene) hydrazinyl)-N-(4-((3-(phenyl imino)-3,4-dihydro quinoxalin-2(1 H)-ylidene)amino) phenyl) acetamide S1-S13 with the hope to obtain more active and less toxic anti-microbial and anti-TB agents. Methods A series of novel quinoxaline Schiff bases S1-S13 were synthesized from o-phenylenediamine and oxalic acid by a multistep synthesis. In present work, we are introducing graph theoretical analysis to identify drug target. In the connection of graph theoretical analysis, we utilised KEGG database and Cytoscape software...
October 24, 2017: Drug Research
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