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miRNA prediction

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https://www.readbyqxmd.com/read/28231299/exploration-of-inhibitory-mechanisms-of-curcumin-in-lung-cancer-metastasis-using-a-mirna-transcription-factor-target-gene-network
#1
De-Min Jiao, Li Yan, Li-Shan Wang, Hui-Zhen Hu, Xia-Li Tang, Jun Chen, Jian Wang, You Li, Qing-Yong Chen
The present study was aimed to unravel the inhibitory mechanisms of curcumin for lung cancer metastasis via constructing a miRNA-transcription factor (TF)-target gene network. Differentially expressed miRNAs between human high-metastatic non-small cell lung cancer 95D cells treated with and without curcumin were identified using a TaqMan human miRNA array followed by real-time PCR, out of which, the top 6 miRNAs (miR-302b-3p, miR-335-5p, miR-338-3p, miR-34c-5p, miR-29c-3p and miR-34a-35p) with more verified target genes and TFs than other miRNAs as confirmed by a literature review were selected for further analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28229962/overexpression-of-hsa-mir-939-follows-by-ngfr-down-regulation-and-apoptosis-reduction
#2
Fahimeh Hosseini Aghdaei, Bahram M Soltani, Sadat Dokanehiifard, Seyed Javad Mowla, Masoud Soleimani
Neurotrophin receptors play a crucial role in neuronal survival, differentiation and regeneration. Nerve growth factor receptor (NGFR) or P75(NTR) is a neurotrophin receptor that is involved in many pathological conditions including cancers. Genetic factors that are involved in regulation of neurotrophin receptors are under intense investigation. MiRNAs are novel regulators of signalling pathways that are candidates for regulation of neurotrophin receptors. Computational programs predicted that NGFR gene is a bona fide target for hsa-miR- 939...
March 2017: Journal of Biosciences
https://www.readbyqxmd.com/read/28228760/perturbed-microrna-expression-by-mycobacterium-tuberculosis-promotes-macrophage-polarization-leading-to-pro-survival-foam-cell
#3
Pankaj Kumar Ahluwalia, Rajan Kumar Pandey, Prabodh Kumar Sehajpal, Vijay Kumar Prajapati
Tuberculosis (TB) is one of the prevalent causes of death worldwide, with 95% of these deaths occurring in developing countries, like India. The causative agent, Mycobacterium tuberculosis (MTb) has the tenacious ability to circumvent the host's immune system for its own advantage. Macrophages are one of the phagocytic cells that are central to immunity against MTb. These are highly plastic cells dependent on the milieu and can showcase M1/M2 polarization. M1 macrophages are bactericidal in action, but M2 macrophages are anti-inflammatory in their immune response...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28225779/combined-small-rna-and-degradome-sequencing-reveals-complex-microrna-regulation-of-catechin-biosynthesis-in-tea-camellia-sinensis
#4
Ping Sun, Chunzhen Cheng, Yuling Lin, Qiufang Zhu, Jinke Lin, Zhongxiong Lai
MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5'cDNA ends (RLM-RACE) were applied...
2017: PloS One
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#5
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28223695/the-mirnaome-of-catharanthus-roseus-identification-expression-analysis-and-potential-roles-of-micrornas-in-regulation-of-terpenoid-indole-alkaloid-biosynthesis
#6
Ethan M Shen, Sanjay K Singh, Jayadri S Ghosh, Barunava Patra, Priyanka Paul, Ling Yuan, Sitakanta Pattanaik
MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA)...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28222782/identification-of-mirna-mrna-crosstalk-in-cd4-t-cells-during-hiv-1-infection-by-integrating-transcriptome-analyses
#7
Qibin Liao, Jin Wang, Zenglin Pei, Jianqing Xu, Xiaoyan Zhang
BACKGROUND: HIV-1-infected long-term nonprogressors (LTNPs) are characterized by infection with HIV-1 more than 7-10 years, but keeping high CD4(+) T cell counts and low viral load in the absence of antiretroviral treatment, while loss of CD4(+) T cells and high viral load were observed in the most of HIV-1-infected individuals with chronic progressors (CPs) However, the mechanisms of different clinical outcomes in HIV-1 infection needs to be further resolved. METHODS: To identify microRNAs (miRNAs) and their target genes related to distinct clinical outcomes in HIV-1 infection, we performed the integrative transcriptome analyses in two series GSE24022 and GSE6740 by GEO2R, R, TargetScan, miRDB, and Cytoscape softwares...
February 21, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28219439/rnas-competing-for-micrornas-mutually-influence-their-fluctuations-in-a-highly-non-linear-microrna-dependent-manner-in-single-cells
#8
Carla Bosia, Francesco Sgrò, Laura Conti, Carlo Baldassi, Davide Brusa, Federica Cavallo, Ferdinando Di Cunto, Emilia Turco, Andrea Pagnani, Riccardo Zecchina
BACKGROUND: Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other's expression levels. Theoretical predictions suggest that not only the mean expression levels of targets but also the fluctuations around the means are coupled through miRNAs. This may result in striking effects on a broad range of cellular processes, such as cell differentiation and proliferation...
February 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28219342/effects-of-exposure-to-streptococcus-iniae-on-microrna-expression-in-the-head-kidney-of-genetically-improved-farmed-tilapia-oreochromis-niloticus
#9
Jun Qiang, Fanyi Tao, Jie He, Lanyi Sun, Pao Xu, Wenjin Bao
BACKGROUND: Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219339/deep-illumina-sequencing-reveals-conserved-and-novel-micrornas-in-grass-carp-in-response-to-grass-carp-reovirus-infection
#10
Libo He, Aidi Zhang, Pengfei Chu, Yongming Li, Rong Huang, Lanjie Liao, Zuoyan Zhu, Yaping Wang
BACKGROUND: The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic symptoms is still unknown. MicroRNAs (miRNAs) are key regulators involved in various biological processes. The aim of this study was to identify conserved and novel miRNAs in grass carp in response to GCRV infection, as well as attempt to reveal the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28215993/microrna-profiling-analysis-revealed-different-cellular-senescence-mechanisms-in-human-mesenchymal-stem-cells-derived-from-different-origin
#11
Xianhui Meng, Mengying Xue, Peng Xu, Feihu Hu, Bo Sun, Zhongdang Xiao
Mesenchymal stem cells (MSCs) from human umbilical cord (UC) and cord blood (CB) share many common properties and exhibit promising clinical potential. Cellular senescence, which induces the loss of stem cells characters and disrupts their therapeutic functions, has been demonstrated to be under the regulation of microRNAs (miRNAs). In this study, we compared the miRNA profiles in early and late passage UCMSCs and CBMSCs based on deep sequencing. 224 and 170 miRNAs were significantly altered in UCMSCs and CBMSCs respectively...
February 12, 2017: Genomics
https://www.readbyqxmd.com/read/28215541/evaluation-of-a-combinational-use-of-serum-micrornas-as-biomarkers-for-liver-diseases
#12
Ping Xu, Anliang Guo, Junchi Xu, Jianer Yao, Hui Chen, Fengping Wang, Chuanwu Zhu
Circulating microRNAs (miRNA) have been widely recognized as a novel noninvasive biomarker in a variety of physiological and pathological conditions. In order to assess the sensitivity and reliability of potential miRNAs as diagnostic markers for liver disease related to viral infection, alcohol abuse, or chemical exposure, we collected serum samples from 326 participants and evaluated the single and combination diagnostic values of three serum miRNAs (miR-122, miR-125b, miR-192) compared with a conventional marker ALT...
February 16, 2017: Clinics and Research in Hepatology and Gastroenterology
https://www.readbyqxmd.com/read/28214897/mir-125b-regulates-the-osteogenic-differentiation-of-human-mesenchymal-stem-cells-by-targeting-bmpr1b
#13
Huaqing Wang, Zhao Xie, Tianyong Hou, Zhiqiang Li, Ke Huang, Jicheng Gong, Wei Zhou, Kanglai Tang, Jianzhong Xu, Shiwu Dong
BACKGROUND/AIMS: Osteogenic differentiation of mesenchymal stem cells (MSCs) plays a crucial role in bone regeneration and bone reparation. This complex process is regulated precisely and firmly by specific factors. Recent studies have demonstrated that miR-125b regulates osteogenic differentiation, but little is known about the molecular mechanisms of this regulation. Furthermore, how miR-125b regulates the osteogenic differentiation of MSCs still needs elucidation. METHODS: In the present study, human bone marrow-derived mesenchymal stem cells (hBMSCs) were isolated and induced to osteoblasts with miR-125b inhibition or overexpression...
January 31, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28213571/mir-146a-b-a-family-with-shared-seeds-and-different-roots
#14
Mark Paterson, Alison J Kriegel
MicroRNAs are small, non-coding, RNAs known for their powerful modulation of molecular processes, making them a major focus for studying pathological mechanisms. The human miR-146 family of microRNAs consists of two member genes - MIR146A and MIR146B These two miRNAs are located on different chromosomes and exhibit differential regulation in many cases. However, they are nearly identical in sequence and share a seed sequence, thus they are predicted to target the same set of genes. A large proportion of the miR-146 literature focuses on its role in regulating the innate immune response in the context of various pathologies by modulating two widely studied target genes in the toll-like receptor signaling cascade...
February 17, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28212605/erratum-to-mirnacle-machine-learning-with-smote-and-random-forest-for-improving-selectivity-in-pre-mirna-ab-initio-prediction
#15
Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro Vasconcelos, Fabio Ribeiro Cerqueira
No abstract text is available yet for this article.
February 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28212556/urinary-cell-microrna-based-prognostic-classifier-for-non-muscle-invasive-bladder-cancer
#16
Mercedes Ingelmo-Torres, Juan José Lozano, Laura Izquierdo, Albert Carrion, Meritxell Costa, Lidia Gómez, María José Ribal, Antonio Alcaraz, Lourdes Mengual
Current prognostic tools for non-muscle invasive bladder cancer (NMIBC) do not have enough discriminative capacity to predict the risk of tumour progression. This study aimed to identify urinary cell microRNAs that may be useful as non-invasive predictive biomarkers of tumour progression in NMIBC patients. To this end, 210 urine samples from NMIBC patients were included in the study. RNA was extracted from urinary cells and expression of 8 microRNAs, previously described by our group, was analysed by quantitative PCR...
February 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28211800/upregulated-mir-483-5p-expression-as-a-prognostic-biomarker-for-esophageal-squamous-cell-carcinoma
#17
Liying Xue, Jinglong Nan, Li Dong, Cuiying Zhang, Hui Li, Rentura Na, Huijie He, Yadi Wang
BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is one of the most common cause of cancer-associated mortality. Uncovering novel molecular biomarkers that can predict ESCC development will improve personalized therapy. OBJECTIVE: The goal of the current study was to investigate the expression pattern of miR-483-5p and determine its prognostic value in ESCC. METHODS: We first analyzed miRNA-seq data obtained from the Cancer Genome Atlas (TCGA) cohort to evaluate the prognostic value of miR-483-5p in ESCC...
February 3, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28209211/comparative-expression-profile-of-micrornas-in-anopheles-anthropophagus-midgut-after-blood-feeding-and-plasmodium-infection
#18
Wenquan Liu, Zhenhua Hao, Liyang Huang, Lingzi Chen, Qimei Wei, Liya Cai, Shaohui Liang
BACKGROUND: Anopheles anthropophagus is one of the major vectors of malaria in Asia. MicroRNAs (miRNAs) play important roles in cell development and differentiation as well as in the cellular response to stress and infection. In a former study, we have investigated the global miRNA profiles in relation to sex in An. anthropophagus. However, the miRNAs contributing to the blood-feeding and infection with Plasmodium are still unknown. METHODS: High-throughput sequencing was performed to identify miRNA profiles of An...
February 16, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28207805/unraveling-the-microrna-of-caragana-korshinskii-along-a-precipitation-gradient-on-the-loess-plateau-china-using-high-throughput-sequencing
#19
Pengbo Ning, Yulu Zhou, Lifang Gao, Yingying Sun, Wenfei Zhou, Furong Liu, Zhenye Yao, Lifang Xie, Junhui Wang, Chunmei Gong
Drought remains one of the main factors that negatively affect plant growth and development. Caragana korshinskii is widely distributed on the Loess Plateau, China, where it mediates soil and water loss and helps prevent desertification. However, little is known about the stress response mechanisms of C. korshinskii in water-starved environments. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several types of biotic and abiotic stress. Here, we describe the miRNAs of wild C...
2017: PloS One
https://www.readbyqxmd.com/read/28205634/circulating-mir-155-mir-145-and-let-7c-as-diagnostic-biomarkers-of-the-coronary-artery-disease
#20
Julien Faccini, Jean-Bernard Ruidavets, Pierre Cordelier, Frédéric Martins, Jean-José Maoret, Vanina Bongard, Jean Ferrières, Jérôme Roncalli, Meyer Elbaz, Cécile Vindis
Coronary artery disease (CAD) is the most prevalent cause of mortality and morbidity worldwide and the number of individuals at risk is increasing. To better manage cardiovascular diseases, improved tools for risk prediction including the identification of novel accurate biomarkers are needed. MicroRNA (miRNA) are essential post-transcriptional modulators of gene expression leading to mRNA suppression or translational repression. Specific expression profiles of circulating miRNA have emerged as potential noninvasive diagnostic biomarkers of diseases...
February 16, 2017: Scientific Reports
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