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miRNA prediction

Rahul Agrawal, Tina P Dale, Mohammed A Al-Zubaidi, Prit Benny Malgulwar, Nicholas R Forsyth, Ritu Kulshreshtha
MicroRNAs are reported to have a crucial role in the regulation of self-renewal and differentiation of stem cells. Hypoxia has been identified as a key biophysical element of the stem cell culture milieu however, the link between hypoxia and miRNA expression in stem cells remains poorly understood. We therefore explored miRNA expression in hypoxic human embryonic and mesenchymal stem cells (hESCs and hMSCs). A total of 50 and 76 miRNAs were differentially regulated by hypoxia (2% O2) in hESCs and hMSCs, respectively, with a negligible overlap of only three miRNAs...
2016: PloS One
M Drozdzik, S Oswald
Orally administered drugs must pass through the intestinal wall and then through the liver before reaching systemic circulation. During this process drugs are subjected to different processes that may determine the therapeutic value. The intestinal barrier with active drug metabolizing enzymes and drug transporters in enterocytes plays an important role in the determination of drug bioavailability. Accumulating information demonstrates variable distribution of drug metabolizing enzymes and transporters along the human gastrointestinal tract (GI), that creates specific barrier characteristics in different segments of the GI...
October 24, 2016: Current Medicinal Chemistry
Dorothee Hartmann, Jan Fiedler, Kristina Sonnenschein, Annette Just, Angelika Pfanne, Karina Zimmer, Janet Remke, Ariana Foinquinos, Malte Butzlaff, Katharina Schimmel, Lars Maegdefessel, Denise Hilfiker-Kleiner, Nico Lachmann, Andreas Schober, Natali Froese, Joerg Heineke, Johann Bauersachs, Sandor Batkai, Thomas Thum
BACKGROUND: -The transcription factor GATA2 orchestrates the expression of many endothelial-specific genes illustrating its crucial importance for endothelial cell function. The capacity of this transcription factor in orchestrating endothelial important microRNAs (miRNAs/miR) is unknown. METHODS: -Endothelial GATA2 was functionally analyzed in human endothelial cells in vitro. Endogenous siRNA-mediated knockdown and lentiviral-based overexpression were applied to decipher capacity of GATA2 in regulating cell viability and capillary formation...
October 25, 2016: Circulation
Wei Zhao, Xiaohui Zhang, Jia Liu, Bei Sun, Hua Tang, Hong Zhang
Metformin was demonstrated to have effects on breast cancer, and microRNA-27a (miR-27a) is a prognostic marker for breast cancer progression and patient survival. AMPKα2 was found to be a suppressor in breast cancer MCF-7 cells. Therefore, the present study aimed to explain this phenomenon in regards to the relationship between microRNAs (miRNAs) and their target genes and to predict how AMPKα2 may be a downstream target gene of miR-27a, thus exploring the new mechanism of metformin in the treatment of breast cancer regarding miRNAs...
October 24, 2016: Oncology Reports
Song Xu, Xiao-Ming Yi, Zheng-Yu Zhang, Jing-Ping Ge, Wen-Quan Zhou
MicroRNAs (miRNAs) are a class of small, well-conserved, non-coding RNAs that are increasingly identified as diagnostic and prognostic biomarkers in a number of cancers. Deregulated miR‑129 is closely associated with tumorigenesis and cancer progression. However, the potential role of miR‑129 in prostate cancer remains largely elusive. The present study investigated the role of miR‑129 as a prognostic biomarker for tumor progression and clinical prognosis in prostate cancer patients. The examined prostate cancer tissues exhibited a significant reduction in miR‑129 expression compared with the normal tissues (P=0...
October 19, 2016: Molecular Medicine Reports
Liangliang Quan, Yang Wang, Jiulong Liang, Tao Qiu, Hongyi Wang, Ye Zhang, Yu Zhang, Qiang Hui, Kai Tao
In the present study, we aimed to reveal the molecular mechanisms responsible for the differentiation of human adipose tissue-derived stem cells (hASCs) into myocytes and osteoblasts. Microarray data GSE37329 were obtained from the Gene Expression Omnibus database, including three hASC cell lines from healthy donors, two osteogenic lineages and two myogenic lineages from the in vitro‑induction of hASCs. Differentially expressed genes (DEGs) in the two lineages were firstly screened. Subsequently, the underlying functions of the two sets of DEGs were investigated by Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, followed by protein-protein interaction (PPI) network construction...
October 25, 2016: International Journal of Molecular Medicine
Changlong Gu, Bo Liao, Xiaoying Li, Keqin Li
Prediction and confirmation of the presence of disease-related miRNAs is beneficial to understand disease mechanisms at the miRNA level. However, the use of experimental verification to identify disease-related miRNAs is expensive and time-consuming. Effective computational approaches used to predict miRNA-disease associations are highly specific. In this study, we develop the Network Consistency Projection for miRNA-Disease Associations (NCPMDA) method to reveal the potential associations between miRNAs and diseases...
October 25, 2016: Scientific Reports
Chunjin Li, Lu Chen, Yun Zhao, Shuxiong Chen, Lulu Fu, Yanwen Jiang, Shan Gao, Zhuo Liu, Fengge Wang, Xiaoling Zhu, Jiahui Rao, Jing Zhang, Xu Zhou
Polycystic ovary syndrome (PCOS) causes female subfertility with ovarian disorders and may be associated with increased rate of early-pregnancy failure. Rat PCOS models were established using letrozole to understand the uterine pathogenesis of PCOS. The differential expression of microRNAs (miRNAs) was observed in rat uterus with PCOS. After estrous cycles were disrupted, significantly abnormal ovarian morphology and hormone level were observed in rats with PCOS. A total of 148 miRNAs differentially expressed were identified in the uterus from the letrozole-induced rat model compared with the control...
October 21, 2016: Gene
Suli Huang, Ziquan Lv, Yi Guo, Lu Li, Yanwei Zhang, Li Zhou, Binyao Yang, Shuang Wu, Ying Zhang, Changhui Xie, Shanshan Li, Jinquan Cheng
Circulating microRNAs (miRNAs) are emerging as novel disease biomarkers. Using a miRNA microarray, we previously showed that the whole blood level of let-7e-5p was significantly higher in ischemic stroke patients than in control subjects. However, the association between let-7e-5p expression and the occurrence of ischemic stroke remains unknown. In this study, we validated the expression levels of let-7e-5p in two case-control populations using miRNA TaqMan assays and further investigated the potential targets of let-7e-5p...
2016: PloS One
D F Paulo, A M L Azeredo-Espin, L E C Canesin, R Vicentini, A C M Junqueira
MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression through post-transcriptional regulation. Here, we report the identification and characterization of miRNAs in two closely related screwworm flies with different feeding habits: Cochliomyia hominivorax and Cochliomyia macellaria. The New World screwworm, C. hominivorax, is an obligatory parasite of warm-blooded vertebrates, whereas the secondary screwworm, C. macellaria, is a free-living organism that feeds on decaying organic matter. Here, the small RNA transcriptomes of adults and third-instar larvae of both species were sequenced...
October 24, 2016: Insect Molecular Biology
Parthiban Subramanian, In-Chan Choi, Vimalraj Mani, Junhyung Park, Sathiyamoorthy Subramaniyam, Kang-Hyun Choi, Joon-Soo Sim, Chang-Muk Lee, Ja Choon Koo, Bum-Soo Hahn
In this study, we investigated global changes in miRNAs of Meloidogyne incognita throughout its life cycle. Small RNA sequencing resulted in approximately 62, 38, 38, 35, and 39 Mb reads in the egg, J2, J3, J4, and female stages, respectively. Overall, we identified 2724 known and 383 novel miRNAs (read count > 10) from all stages, of which 169 known and 13 novel miRNA were common to all the five stages. Among the stage-specific miRNAs, miR-286 was highly expressed in eggs, miR-2401 in J2, miR-8 and miR-187 in J3, miR-6736 in J4, and miR-17 in the female stages...
October 21, 2016: International Journal of Molecular Sciences
Chang Youn Lee, Sunhye Shin, Jiyun Lee, Hyang-Hee Seo, Kyu Hee Lim, Hyemin Kim, Jung-Won Choi, Sang Woo Kim, Seahyung Lee, Soyeon Lim, Ki-Chul Hwang
Stem cell therapy using adult stem cells, such as mesenchymal stem cells (MSCs) has produced some promising results in treating the damaged heart. However, the low survival rate of MSCs after transplantation is still one of the crucial factors that limit the therapeutic effect of stem cells. In the damaged heart, oxidative stress due to reactive oxygen species (ROS) production can cause the death of transplanted MSCs. Apoptosis signal-regulating kinase 1 (ASK1) has been implicated in the development of oxidative stress-related pathologic conditions...
October 20, 2016: International Journal of Molecular Sciences
Zhongping Xu, Monal Sharma, Andrew Gelman, Ramsey Hachem, Thalachallour Mohanakumar
BACKGROUND: MicroRNAs (miRNAs) were recently identified as modulators of immune responses after human lung transplantation (LTx). This study was undertaken to assess the contribution of miRNAs to the pathogenesis of primary graft dysfunction (PGD) after LTx. METHODS: Of the 39 recipients, 14 (35.9%) developed Grade 3 PGD (i.e., severe PGD) within the first 72 hours of LTx. The remaining 25 recipients (64.1%) had Grade 2 or less PGD, and served as the control group...
September 12, 2016: Journal of Heart and Lung Transplantation
Ruirui Han, Qianqian Sun, Jianbo Wu, Pengyuan Zheng, Guoqiang Zhao
BACKGROUND: As the end product of the bacterial fermentation of dietary fiber in the colonic lumen, sodium butyrate (NaBt) has been reported to exert antitumor effects on colorectal cancer (CRC). In addition to functioning as a histone deacetylase (HDAC) inhibitor, NaBt also regulates the expression of microRNAs (miRNAs) to inhibit CRC cell proliferation. Yet, the mechanisms involved are not completely understood. Here we investigate whether NaBt regulates miR-203 to inhibit CRC growth and explore the promising target gene of miR-203 in CRC cells...
October 24, 2016: Cellular Physiology and Biochemistry
Na Li, Yunhuan Yan, Angke Zhang, Jiming Gao, Chong Zhang, Xue Wang, Gaopeng Hou, Gaiping Zhang, Jinbu Jia, En-Min Zhou, Shuqi Xiao
Many viruses encode microRNAs (miRNAs) that are small non-coding single-stranded RNAs which play critical roles in virus-host interactions. Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically impactful viruses in the swine industry. The present study sought to determine whether PRRSV encodes miRNAs that could regulate PRRSV replication. Four viral small RNAs (vsRNAs) were mapped to the stem-loop structures in the ORF1a, ORF1b and GP2a regions of the PRRSV genome by bioinformatics prediction and experimental verification...
October 17, 2016: Oncotarget
Anna Chung-Kwan Tse, Jing-Woei Li, Simon Yuan Wang, Ting-Fung Chan, Keng Po Lai, Rudolf Shiu-Sun Wu
Hypoxia is a global environmental concern and poses a significant threat to aquatic ecosystems, including the sustainability of natural fish populations. The deleterious effects of hypoxia on fish reproductive fitness, as mediated by disruption of sex hormones and gene expression along the Brain-Pituitary-Gonad axis, have been well documented. Recently, we further demonstrated that the observed disruption of steroidogenesis in the ovary of marine medaka Oryzias melastigma is mediated through microRNAs (miRNAs)...
October 8, 2016: Aquatic Toxicology
Rongsheng Zhu, Zhanguo Zhang, Yang Li, Zhenbang Hu, Dawei Xin, Zhaoming Qi, Qingshan Chen
Previous studies have confirmed that there are many differences between animal and plant microRNAs (miRNAs), and that numerical features based on sequence and structure can be used to predict the function of individual miRNAs. However, there is little research regarding numerical differences between animal and plant miRNAs, and whether a single numerical feature or combination of features could be used to distinguish animal and plant miRNAs or not. Therefore, in current study we aimed to discover numerical features that could be used to accomplish this...
2016: PloS One
Nina Holland
Environmental research and public health in the 21st century face serious challenges such as increased air pollution and global warming, widespread use of potentially harmful chemicals including pesticides, plasticizers, and other endocrine disruptors, and radical changes in nutrition and lifestyle typical of modern societies. In particular, exposure to environmental and occupational toxicants may contribute to the occurrence of adverse birth outcomes, neurodevelopmental deficits, and increased risk of cancer and other multifactorial diseases such as diabetes and asthma...
October 21, 2016: Reviews on Environmental Health
Yongsheng Bai, Lizhong Ding, Steve Baker, Jenny M Bai, Ethan Rath, Feng Jiang, Jianghong Wu, Hui Jiang, Gary Stuart
BACKGROUND: MicroRNAs (miRNA) are short nucleotides that interact with their target genes through 3' untranslated regions (UTRs). The Cancer Genome Atlas (TCGA) harbors an increasing amount of cancer genome data for both tumor and normal samples. However, there are few visualization tools focusing on concurrently displaying important relationships and attributes between miRNAs and mRNAs of both cancer tumor and normal samples. Moreover, a deep investigation of miRNA-mRNA target and biological relationships across multiple cancer types by integrating web-based analysis has not been thoroughly conducted...
October 6, 2016: BMC Bioinformatics
Hiroko Mataki, Naohiko Seki, Keiko Mizuno, Nijiro Nohata, Kazuto Kamikawaji, Tomohiro Kumamoto, Keiichi Koshizuka, Yusuke Goto, Hiromasa Inoue
Patients with lung adenocarcinoma may benefit from recently developed molecular targeted therapies. However, analogous advanced treatments are not available for patients with lung squamous cell carcinoma (lung SCC). The survival rate of patients with the advanced stage of lung SCC remains poor. Exploration of novel lung SCC oncogenic pathways might lead to new treatment protocols for the disease. Based on this concept, we have identified microRNA- (miRNA) mediated oncogenic pathways in lung SCC. It is well known that miR-145-5p (the guide strand) functions as a tumor suppressor in several types of cancer...
September 27, 2016: Oncotarget
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