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MicroRNA sequencing

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https://www.readbyqxmd.com/read/28643872/circulating-microrna-as-candidates-for-early-embryonic-viability-in-cattle
#1
K G Pohler, J A Green, L A Moley, S Gunewardena, W T Hung, R R Payton, X Hong, L K Christenson, T W Geary, M F Smith
Blood-borne extracellular vesicles (i.e. exosomes and microvesicles) carrying microRNAs (miRNAs) could make excellent biomarkers of disease and different physiologic states, including pregnancy status. We tested the hypothesis that circulating extracellular vesicle-derived miRNAs might differentiate the pregnancy status of cows that had maintained pregnancy to Day 30 from non-pregnant cows or from those that exhibited embryonic mortality between Days 17-30 of gestation. Cows were randomly assigned for artificial insemination with fertile semen (n= 36) or dead semen (n = 8; control group) on Day 0 (day of estrus)...
June 23, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28643865/characterization-and-biological-function-of-milk-derived-mirnas
#2
Regina Golan-Gerstl, Yaffa Elbaum Shiff, Vardit Lavi-Moshayoff, Daniel Schecter Dena Leshkowitz, Shimon Reif
SCOPE: Breastfeeding is associated with reduced risk of infection, immune mediated disorders, obesity and even cancer. Recently it was found that breast milk contains a variety of microRNAs (miRNAs) in the skim and fat layer that can be transferred to infants, and appear to play important roles in those biological functions. METHODS AND RESULTS: This study applied Next Generation Sequencing and quantitative real time PCR analysis to determine the miRNA expression profile of the skim and fat fraction of human, goat, and bovine milk as well as infant formulas...
June 23, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28641313/evaluation-of-serum-microrna-biomarkers-for-gastric-cancer-based-on-blood-and-tissue-pools-profiling-the-importance-of-mir-21-and-mir-331
#3
Marek Sierzega, Marcin Kaczor, Piotr Kolodziejczyk, Jan Kulig, Marek Sanak, Piotr Richter
BACKGROUND: High stability and disease-specific disarrangements suggest that microRNA molecules (miRNAs) present in body fluids are ideally suited for diagnostic applications, including gastric cancer (GC). However, the actual source of circulating miRNA biomarkers in GC has not been adequately evaluated, particularly in the Western populations that have some distinct characteristics compared with Asian patients. METHODS: Twenty treatment-naive patients with GC along with 20 cancer-free controls were recruited...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28640911/evolution-of-microrna-in-primates
#4
Jennifer C McCreight, Sean E Schneider, Damien B Wilburn, Willie J Swanson
MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution across the primate lineage is largely uncharacterized. A particular miRNA can have one to thousands of messenger RNA targets, establishing the potential for a small change in sequence or overall miRNA structure to have profound phenotypic effects. However, the majority of non-human primate miRNA is predicted solely by homology to the human genome and lacks experimental validation. In the present study, we sequenced thirteen species representing a wide range of the primate phylogeny...
2017: PloS One
https://www.readbyqxmd.com/read/28639887/microrna-138-enhances-trail-induced-apoptosis-through-interferon-stimulated-gene-15-downregulation-in-hepatocellular-carcinoma-cells
#5
Chaohui Zuo, Xinyi Sheng, Zhuo Liu, Min Ma, Shuhan Xiong, Hongyu Deng, Sha Li, Darong Yang, Xiaohong Wang, Hua Xiao, Hu Quan, Man Xia
Hepatocellular carcinoma is a leading cause of cancer-related mortality worldwide. TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) is a potential target for cancer therapy. However, many cancer cells are resistant to TRAIL-induced apoptosis and its mechanism is not well understood. In this study, to identify potential therapeutic targets for TRAIL-resistant cancer cells, we compared the expression levels of interferon-stimulated gene 15 in TRAIL-sensitive and TRAIL-resistant hepatocellular carcinoma cell lines...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28639503/markers-of-disease-and-steroid-responsiveness-in-paediatric-idiopathic-nephrotic-syndrome-whole-transcriptome-sequencing-of-peripheral-blood-mononuclear-cells
#6
Hee Gyung Kang, Heewon Seo, Jae Hyun Lim, Jong Il Kim, Kyoung Hee Han, Hye Won Park, Ja Wook Koo, Kee Hyuck Kim, Ju Han Kim, Hae Il Cheong, Il-Soo Ha
Objective To identify markers of disease and steroid responsiveness in paediatric idiopathic nephrotic syndrome. Methods Whole-transcriptome sequencing was performed of peripheral blood mononuclear cells (PBMCs) from patients with NS. Differentially expressed genes (DEGs) were identified in patients with active NS vs those in remission, and those with steroid-sensitive NS (SSNS) vs steroid-resistant NS (SRNS). Results A total of 1065 DEGs were identified in patients with NS ( n = 10) vs those in remission ( n = 9)...
June 2017: Journal of International Medical Research
https://www.readbyqxmd.com/read/28638836/detecting-the-candidate-gender-determinants-by-bioinformatic-prediction-of-mirnas-and-their-targets-from-transcriptome-sequences-of-the-male-and-female-flowers-in-salix-suchowensis
#7
Suyun Wei, Ning Ye, Tongming Yin
MicroRNAs (miRNAs) belong to a class of small, noncoding, and endogenous single-stranded RNAs that negatively regulate gene expression at the posttranscriptional level. Potential miRNAs can be identified based on sequence homology since miRNAs are highly conserved in plants. In this study, we aligned the expressed sequence tags derived from flower buds of male and female S. suchowensis to miRNAs in the miRBase, which enable us to identify 34 potential miRNAs from flower buds of the alternate sexes. Among them, 11 were from the female and 23 were from the male...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28638346/micrornas-in-muscle-characterizing-the-powerlifter-phenotype
#8
Randall F D'Souza, Thomas Bjørnsen, Nina Zeng, Kirsten M M Aasen, Truls Raastad, David Cameron-Smith, Cameron J Mitchell
Powerlifters are the epitome of muscular adaptation and are able to generate extreme forces. The molecular mechanisms underpinning the significant capacity for force generation and hypertrophy are not fully elucidated. MicroRNAs (miRs) are short non-coding RNA sequences that control gene expression via promotion of transcript breakdown and/or translational inhibition. Differences in basal miR expression may partially account for phenotypic differences in muscle mass and function between powerlifters and untrained age-matched controls...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28637930/towards-a-consistent-quantitative-evaluation-of-microrna-evolution
#9
Ali M Yazbeck, Kifah R Tout, Peter F Stadler, Jana Hertel
The miRBase currently reports more than 25,000 microRNAs in several hundred genomes that belong to more than 1000 families of homologous sequences. Quantitative investigations of miRNA gene evolution requires the construction of data sets that are consistent in their coverage and include those genomes that are of interest in a given study. Given the size and structure of data, this can be achieved only with the help of a fully automatic pipeline that improves the available seed alignments, extends the set of available sequences by homology search, and reliably identifies true positive homology search results...
June 5, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28637929/systematic-prediction-of-the-impacts-of-mutations-in-microrna-seed-sequences
#10
Anindya Bhattacharya, Yan Cui
MicroRNAs are a class of small non-coding RNAs that are involved in many important biological processes and the dysfunction of microRNA has been associated with many diseases. The seed region of a microRNA is of crucial importance to its target recognition. Mutations in microRNA seed regions may disrupt the binding of microRNAs to their original target genes and make them bind to new target genes. Here we use a knowledge-based computational method to systematically predict the functional effects of all the possible single nucleotide mutations in human microRNA seed regions...
May 18, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28637758/genome-wide-analysis-of-eighteen-epstein-barr-viruses-isolated-from-primary-nasopharyngeal-carcinoma-biopsies
#11
Chaofeng Tu, Zhaoyang Zeng, Peng Qi, Xiayu Li, Zhengyuan Yu, Can Guo, Fang Xiong, Bo Xiang, Ming Zhou, Zhaojian Gong, Qianjin Liao, Jianjun Yu, Yi He, Wenling Zhang, Xiaoling Li, Yong Li, Guiyuan Li, Wei Xiong
Epstein-Barr virus (EBV) is a ubiquitous gamma-herpesvirus that is highly prevalent in almost all human populations, and is associated with many human cancers such as nasopharyngeal carcinoma (NPC), Hodgkin's disease, and gastric carcinoma. However, in these EBV-associated cancers, only NPC exhibits remarkable ethnic and geographic distribution. We hypothesized that EBV genomic variations might contribute to the pathogenesis of different human cancers in different geographic areas. In this study, we collected 18 NPC biopsies from the Hunan Province in Southern China and de novo assembled 18 NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated as HN1 to HN18...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637221/digital-direct-detection-of-micrornas-using-single-molecule-arrays
#12
Limor Cohen, Mark R Hartman, Aaron Amardey-Wellington, David R Walt
MicroRNAs (miRNAs) are involved in many biological pathways, and detecting miRNAs accurately is critical for diagnosing a variety of diseases including cancer. However, most current methods for miRNA detection require lengthy sample preparation and amplification steps that can bias the results. In addition, lack of specificity and reproducibility give rise to various challenges in detection of circulating miRNAs in biological samples. In this work, we applied the Single Molecule Array (Simoa) technique to develop an ultra-sensitive sandwich assay for direct detection of multiple miRNAs without pre-amplification...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28635129/micrornas-involved-in-auxin-signalling-modulate-male-sterility-under-high-temperature-stress-in-cotton-gossypium-hirsutum
#13
Yuanhao Ding, Yizan Ma, Nian Liu, Jiao Xu, Qin Hu, Yaoyao Li, Yuanlong Wu, Sai Xie, Longfu Zhu, Ling Min, Xianlong Zhang
Male sterility caused by long-term high temperature (HT) stress occurs widely in crops. MicroRNAs (miRNAs), a class of endogenous non-coding small RNAs, play an important role in the plant response to various abiotic stresses. To dissect the working principle of miRNAs in male sterility under HT stress in cotton, a total of 112 known miRNAs, 270 novel miRNAs and 347 target genes were identified from anthers of HT-insensitive (84021) and HT-sensitive (H05) cotton cultivars under normal temperature (NT) and HT conditions through small RNA and degradome sequencing...
June 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28633390/investigating-microrna-mediated-regulation-of-the-nascent-nuclear-transcripts-in-plants-a-bioinformatics-workflow
#14
Dongliang Yu, Zhonghai Tang, Chaogang Shao, Xiaoxia Ma, Taihe Xiang, Zhihong Fan, Huizhong Wang, Yijun Meng
Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs...
June 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28632727/post-translational-regulation-contributes-to-the-loss-of-lkb1-expression-through-sirt1-deacetylase-in-osteosarcomas
#15
Nadège Presneau, Laure Alice Duhamel, Hongtao Ye, Roberto Tirabosco, Adrienne M Flanagan, Malihe Eskandarpour
BACKGROUND: The most prevalent form of bone cancer is osteosarcoma (OS), which is associated with poor prognosis in case of metastases formation. Mice harbouring liver kinase B1 (LKB1(+/-)) develop osteoblastoma-like tumours. Therefore, we asked whether loss of LKB1 gene has a role in the pathogenesis of human OS. METHODS: Osteosarcomas (n=259) were screened for LKB1 and sirtuin 1 (SIRT1) protein expression using immunohistochemistry and western blot. Those cases were also screened for LKB1 genetic alterations by next-generation sequencing, Sanger sequencing, restriction fragment length polymorphism and fluorescence in situ hybridisation approaches...
June 20, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28631889/microrna-containing-extracellular-vesicles-released-from-endothelial-colony-forming-cells-modulate-angiogenesis-during-ischaemic-retinopathy
#16
Margaret Dellett, Eoin D Brown, Jasenka Guduric-Fuchs, Anna O'Connor, Alan W Stitt, Reinhold J Medina, David A Simpson
Endothelial colony-forming cells (ECFCs) are a defined subtype of endothelial progenitors that modulate vascular repair and promote perfusion in ischaemic tissues. Their paracrine activity on resident vasculature is ill-defined, but mediated, at least in part, by the transfer of extracellular vesicles (EVs). To evaluate the potential of isolated EVs to provide an alternative to cell-based therapies, we first performed a physical and molecular characterization of those released by ECFCs. Their effects upon endothelial cells in vitro and angiogenesis in vivo in a model of proliferative retinopathy were assessed...
June 20, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28630098/comparative-micrornaome-analysis-of-the-testis-and-ovary-of-the-chinese-giant-salamander
#17
Rui Chen, Jian Du, Lin Ma, Li-Qing Wang, Sheng-Song Xie, Chang-Ming Yang, Xian-Yong Lan, Chuan-Ying Pan, Wu-Zi Dong
MicroRNAs (miRNAs) are 18-24 nucleotides non-coding RNAs that regulate gene expression by post-transcriptional suppression of mRNA. The Chinese giant salamander (CGS, Andrias davidianus), which is an endangered species, has become one of important models of animal evolution; however, no miRNA studies on this species have been conducted. In this study, two small RNA libraries of CGS ovary and testis were constructed using deep sequencing technology. A bioinformatics pipeline was developed to distinguish miRNA sequences from other classes of small RNAs represented in the sequencing data...
June 19, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28628609/a-multidimensional-integration-analysis-reveals-potential-bridging-targets-in-the-process-of-colorectal-cancer-liver-metastasis
#18
Bo Gao, Tian Yu, Dongbo Xue, Boshi Sun, Qin Shao, Hani Choudhry, Victoria Marcus, Jiannis Ragoussis, Yuguo Zhang, Weihui Zhang, Zu-Hua Gao
Approximately 9% of cancer-related deaths are caused by colorectal cancer. Liver metastasis is a major factor for the high colorectal cancer mortality rate. However, the molecular mechanism underlying colorectal cancer liver metastasis remains unclear. Using a global and multidimensional integration approach, we studied sequencing data, protein-protein interactions, and regulation of transcription factor and non-coding RNAs in primary tumor samples and liver metastasis samples to unveil the potential bridging molecules and the regulators that functionally link different stages of colorectal cancer liver metastasis...
2017: PloS One
https://www.readbyqxmd.com/read/28627677/integrated-analysis-of-the-potential-roles-of-mirna%C3%A2-mrna-networks-in-triple-negative-breast-cancer
#19
Huiru Zhu, Meiyu Dai, Xiaoli Chen, Xiang Chen, Shini Qin, Shengming Dai
Triple negative breast cancer (TNBC) is a type of breast cancer where the tumor cells are negative for the estrogen, progesterone and human epidermal growth factor 2 receptors. To date, expression profiling of microRNA (miRNA/miR) and mRNA sequences have been widely applied for the diagnosis of TNBC. In the present study, an integrated analysis of miRNA‑mRNA profiling arrays was performed. A total of five dysregulated miRNAs in patients with TNBC were identified, including upregulated miR‑558 expression and downregulated miR‑320d‑1, miR‑548v, miR‑99a and miR‑21 expression...
June 9, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28627609/microrna-149-contributes-to-scarless-wound-healing-by-attenuating-inflammatory-response
#20
Hongxin Lang, Feng Zhao, Tao Zhang, Xiaoyu Liu, Zhe Wang, Rui Wang, Ping Shi, Xining Pang
A fibrotic or pathological scar is an undesired consequence of skin wound healing and may trigger a series of problems. An attenuated inflammatory response is a significant characteristic of fetal skin wound healing, which can contribute to the scarless healing of fetal skin. According to deep sequencing data, microRNA‑149 (miR‑149) expression was increased in mid-gestational compared with that in late‑gestational fetal skin keratinocytes. It was demonstrated that overexpression of miR‑149 in HaCaT cells can downregulate the expression of pro‑inflammatory cytokines interleukin (IL)‑1α, IL‑1β, and IL‑6 at basal levels and in inflammatory conditions...
June 15, 2017: Molecular Medicine Reports
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