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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/28531200/discovery-of-micrornas-during-early-spermatogenesis-in-chicken
#1
Lu Xu, Qixin Guo, Guobin Chang, Lingling Qiu, Xiangping Liu, Yulin Bi, Yu Zhang, Hongzhi Wang, Wei Lu, Lichen Ren, Ying Chen, Yang Zhang, Qi Xu, Guohong Chen
Spermatogenesis is a complex process that involves many elements. However, until now, little is known at the molecular level about spermatogenesis in poultry. Here we investigated microRNAs and their target genes that may be involved in germ cell development and spermatogonial in chicken. We used next-generation sequencing to analyze miRNA expression profiles in three types of germline cells: primordial germ cells (PGCs), spermatogonial stem cells (SSCs), and spermatogonia (Sp) during early stage of spermatogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28529949/microrna-expression-varies-according-to-glucose-tolerance-measurement-platform-and-biological-source
#2
S Dias, S Hemmings, C Muller, J Louw, C Pheiffer
Dysregulated microRNA (miRNA) expression is observed during type 2 diabetes (T2D), although the consistency of miRNA expression across measurement platform and biological source is uncertain. Here we report miRNA profiling in the whole blood and serum of South African women with different levels of glucose tolerance, using next generation sequencing (NGS) and quantitative real time PCR (qRT-PCR). Whole blood-derived miRNAs from women with newly diagnosed T2D (n = 4), impaired glucose tolerance (IGT) (n = 4), and normal glucose tolerance (NGT) (n = 4) were subjected to NGS, whereafter transcript levels of selected miRNAs were quantified in the whole blood and serum of these women using qRT-PCR...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28506408/genetics-of-medullary-thyroid-cancer-an-overview
#3
REVIEW
Giacomo Accardo, Giovanni Conzo, Daniela Esposito, Claudio Gambardella, Marco Mazzella, Filomena Castaldo, Carlo Di Donna, Andrea Polistena, Nicola Avenia, Vittorio Colantuoni, Dario Giugliano, Daniela Pasquali
Medullary thyroid carcinoma (MTC) represents 3-5% of thyroid cancers. 75% is sporadic and 25% is the dominant component of the hereditary multiple endocrine neoplasia (MEN) type 2 syndromes. Three different subtypes of MEN2, such as MEN2A, MEN2B, and Familial MTC (FMTC) have been defined, based on presence or absence of hyperparathyroidism, pheocromocytoma and characteristic clinical features. Mutations of the RET proto-oncogene are implicated in the pathogenesis of MTC, but there are many other mutational patterns involved...
May 2017: International Journal of Surgery
https://www.readbyqxmd.com/read/28498330/specific-microrna-pattern-in-colon-tissue-of-young-children-with-eosinophilic-colitis
#4
Zoltán Kiss, Nóra Judit Béres, Erna Sziksz, Bálint Tél, Katalin Borka, András Arató, Attila J Szabó, Gábor Veres
Eosinophilic colitis (EC) is a common cause of haematochezia in infants and young children. The exact pathomechanism is not understood, and the diagnosis is challenging. The role of microRNAs as key class of regulators of mRNA expression and translation in patients with EC has not been explored. Therefore, the aim of the present study was to explore the miRNA profile in EC with respect to eosinophilic inflammation. Patients enrolled in the study (n = 10) had persistent rectal bleeding, and did not respond to elimination dietary treatment...
May 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28497038/epigenetics-and-vascular-diseases-influence-of-non-coding-rnas-and-their-clinical-implications
#5
REVIEW
Leonardo Elia, Manuela Quintavalle
Epigenetics refers to heritable mechanisms able to modulate gene expression that do not involve alteration of the genomic DNA sequence. Classically, mechanisms such as DNA methylation and histone modifications were part of this classification. Today, this field of study has been expanded and includes also the large class of non-coding RNAs (ncRNAs). Indeed, with the extraordinary possibilities introduced by the next-generation sequencing approaches, our knowledge of the mammalian transcriptome has greatly improved...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28487235/transcriptome-wide-analysis-of-micrornas-in-branchiostoma-belcheri-upon-vibrio-parahemolyticus-infection
#6
Ping Jin, Lianjie Sun, Caiyun Lv, Fei Ma
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that participate in diverse biological processes via regulating expressions of target genes at post-transcriptional level. Amphioxus, as modern survivor of an ancient chordate lineage, is a model organism for comparative genomics study. However, miRNAs involved in regulating immune responses in Branchiostoma belcheri are largely unclear. Here, we systematically investigated the microRNAs (miRNAs) involved in regulating immune responses in the cephalochordate amphioxus (Branchiostoma belcheri) through next-generation deep sequencing of amphioxus samples infected with Vibrio parahemolyticus...
May 6, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28486694/differential-microrna-expression-in-cultured-palatal-fibroblasts-from-infants-with-cleft-palate-and-controls
#7
Christian Schoen, Jeffrey C Glennon, Shaghayegh Abghari, Marjon Bloemen, Armaz Aschrafi, Carine E L Carels, Johannes W Von den Hoff
Background: The role of microRNAs (miRNAs) in animal models of palatogenesis has been shown, but only limited research has been carried out in humans. To date, no miRNA expression study on tissues or cells from cleft palate patients has been published. We compared miRNA expression in palatal fibroblasts from cleft palate patients and age-matched controls. Material and Methods: Cultured palatal fibroblasts from 10 non-syndromic cleft lip and palate patients (nsCLP; mean age: 18 ± 2 months), 5 non-syndromic cleft palate only patients (nsCPO; mean age: 17 ± 2 months), and 10 controls (mean age: 24 ± 5 months) were analysed with next-generation small RNA sequencing...
May 9, 2017: European Journal of Orthodontics
https://www.readbyqxmd.com/read/28486552/identification-of-novel-mirnas-and-mirna-expression-profiling-in-embryogenic-tissues-of-picea-balfouriana-treated-by-6-benzylaminopurine
#8
Qingfen Li, Cheng Deng, Yan Xia, Lisheng Kong, Hanguo Zhang, Shougong Zhang, Junhui Wang
Here, we compared miRNA expression profiles in embryonic cell cultures of the conifer Picea balfouriana following application of the synthetic cytokinin 6-benzylaminopurine (6-BAP). We used next-generation sequencing to analyze three libraries of small RNAs from the treated embryogenic cell cultures and generated 24,000,000 raw reads from each of the libraries. Over 70 differentially regulated micro RNA (miRNA) families (≥2 fold change in expression) were identified between pairs of treatments. A quantitative analysis showed that miR3633 and miR1026 were upregulated in tissues with the highest embryogenic ability...
2017: PloS One
https://www.readbyqxmd.com/read/28485684/circular-rna-new-member-of-noncoding-rna-with-novel-functions
#9
Kuei-Yang Hsiao, H Sunny Sun, Shaw-Jenq Tsai
A growing body of evidence indicates that circular RNAs are not simply a side product of splicing but a new class of noncoding RNAs in higher eukaryotes. The progression for the studies of circular RNAs is accelerated by combination of several advanced technologies such as next generation sequencing, gene silencing (small interfering RNAs) and editing (CRISPR/Cas9). More and more studies showed that dysregulated expression of circular RNAs plays critical roles during the development of several human diseases...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28484274/monocytic-microrna-profile-associated-with-coronary-collateral-artery-function-in-chronic-total-occlusion-patients
#10
Nazanin Hakimzadeh, Joëlle Elias, Gilbert W M Wijntjens, Ruud Theunissen, Angela van Weert, Martijn W Smulders, Nynke van den Akker, Perry D Moerland, Hein J Verberne, Loes P Hoebers, Jose P S Henriques, Anja M van der Laan, Mustafa Ilhan, Mark Post, Sebastiaan C A M Bekkers, Jan J Piek
An expansive collateral artery network is correlated with improved survival in case of adverse cardiac episodes. We aimed to identify cellular microRNAs (miRNA; miR) important for collateral artery growth. Chronic total occlusion (CTO) patients (n = 26) were dichotomized using pressure-derived collateral flow index (CFIp) measurements; high collateral capacity (CFIp > 0.39; n = 14) and low collateral (CFIp < 0.39; n = 12) capacity. MiRNA profiling via next generation sequencing from various monocyte phenotypes (freshly isolated monocytes, monocytes cultured without stimulant, or stimulation with lipopolysaccharide, interleukin 4, transforming growth factor beta-1, or interferon gamma) revealed significantly different miRNA expression patterns between high versus low collateral capacity patients...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28483594/differences-in-the-microrna-profiles-of-subcutaneous-adipose-derived-stem-cells-and-omental-adipose-derived-stem-cells
#11
Feihu Hu, Peng Xu, Bo Sun, Zhongdang Xiao
Adipose-derived stem cells (ASCs) isolated from subcutaneous (SC) and omentum (O) share similar characteristics, but the differences in their microRNA profiles are mostly unknown. In this study, besides significant differences in cell morphology and the differentiation ability of the two types of ASCs, the microRNA expression profiles of the cell lines were determined using SOLiD next-generation sequencing. The in-depth analysis found that miR-214, miR-222, miR-181a, miR-26a and miR-23/27/24 clusters and miR-375 act as "markers" to distinguish the different fat deposit-derived ASCs...
May 5, 2017: Gene
https://www.readbyqxmd.com/read/28472764/comparative-analysis-of-diagnostic-performance-feasibility-and-cost-of-different-test-methods-for-thyroid-nodules-with-indeterminate-cytology
#12
Salvatore Sciacchitano, Luca Lavra, Alessandra Ulivieri, Fiorenza Magi, Gian Paolo De Francesco, Carlo Bellotti, Leila B Salehi, Maria Trovato, Carlo Drago, Armando Bartolazzi
Since it is impossible to recognize malignancy at fine needle aspiration (FNA) cytology in indeterminate thyroid nodules, surgery is recommended for all of them. However, cancer rate at final histology is <30%. Many different test-methods have been proposed to increase diagnostic accuracy in such lesions, including Galectin-3-ICC (GAL-3-ICC), BRAF mutation analysis (BRAF), Gene Expression Classifier (GEC) alone and GEC+BRAF, mutation/fusion (M/F) panel, alone, M/F panel+miRNA GEC, and M/F panel by next generation sequencing (NGS), FDG-PET/CT, MIBI-Scan and TSHR mRNA blood assay...
April 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28469141/serum-micrornas-reflect-injury-severity-in-a-large-animal-model-of-thoracic-spinal-cord-injury
#13
Seth Tigchelaar, Femke Streijger, Sunita Sinha, Stephane Flibotte, Neda Manouchehri, Kitty So, Katelyn Shortt, Elena Okon, Michael A Rizzuto, Ivana Malenica, Amanda Courtright-Lim, Andrew Eisen, Kendall Van Keuren-Jensen, Corey Nislow, Brian K Kwon
Therapeutic development for spinal cord injury is hindered by the difficulty in conducting clinical trials, which to date have relied solely on functional outcome measures for patient enrollment, stratification, and evaluation. Biological biomarkers that accurately classify injury severity and predict neurologic outcome would represent a paradigm shift in the way spinal cord injury clinical trials could be conducted. MicroRNAs have emerged as attractive biomarker candidates due to their stability in biological fluids, their phylogenetic similarities, and their tissue specificity...
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28460582/comprehensive-analysis-of-circulating-microrna-specific-to-the-liver-heart-and-skeletal-muscle-of-cynomolgus-monkeys
#14
Takuma Iguchi, Noriyo Niino, Satoshi Tamai, Ken Sakurai, Kazuhiko Mori
Circulating microRNAs (miRNAs) could represent sensitive and specific biomarkers for tissue injury. However, their utility as biomarkers in nonclinical toxicological studies using nonhuman primates is limited by a lack of information on their organ specificity and circulating levels under resting condition of the animals. Herein, liver, heart, and skeletal muscle-specific expression patterns of miRNAs were determined in 27 tissues/organs from male and female monkeys (n =2/sex) by next-generation sequencing (NGS) analysis...
January 1, 2017: International Journal of Toxicology
https://www.readbyqxmd.com/read/28456960/detection-and-characterization-of-small-noncoding-rnas-in-mouse-gametes-and-embryos-prior-to-zygotic-genome-activation
#15
Jesús García-López, Eduardo Larriba, Jesús Del Mazo
Small noncoding RNAs (ncRNAs) are regulatory elements of gene expression in all cell types and tissues. An ever-increasing number of studies have implicated ncRNAs in differentiation and developmental processes. In mammals, as a consequence of fertilization, the content of ncRNAs in the zygote is mostly the result of the maternal material included on oocytes and the potential sperm-borne paternal contributions. The genetic identity program of any individual is the reprogramming of each parental contribution to the zygotic genome activation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28450057/environmental-neurotoxicant-manganese-regulates-exosome-mediated-extracellular-mirnas-in-cell-culture-model-of-parkinson-s-disease-relevance-to-%C3%AE-synuclein-misfolding-in-metal-neurotoxicity
#16
Dilshan S Harischandra, Shivani Ghaisas, Dharmin Rokad, Mostafa Zamanian, Huajun Jin, Vellareddy Anantharam, Michael Kimber, Arthi Kanthasamy, Anumantha Kanthasamy
Many chronic neurodegenerative disorders share a common pathogenic mechanism involving the aggregation and deposition of misfolded proteins. Recently, it was shown that these aggregated proteins could be transferred from one cell to another via extracellular nanovesicles called exosomes. Initially thought to be a means of cellular waste removal, exosomes have since been discovered to actively participate in cell-to-cell communication. Importantly, various inflammatory and signaling molecules, as well as small RNAs are selectively packaged in these vesicles...
April 24, 2017: Neurotoxicology
https://www.readbyqxmd.com/read/28448765/digital-assays-part-i-partitioning-statistics-and-digital-pcr
#17
Amar S Basu
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error...
April 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28439834/an-assessment-of-the-next-generation-of-animal-mirna-target-prediction-algorithms
#18
Thomas Bradley, Simon Moxon
The advent of genome-wide next-generation sequencing technologies has revolutionized the genomic and transcriptomic fields. New technologies also present an opportunity for greater discovery and understanding of post-transcriptional processes, in particular, translational inhibition of transcripts by miRBP (microRNA-RNA binding protein) complexes. Not only have novel methodologies been developed for the direct sequencing of RBP-bound RNA, but a new class of miRNA (microRNA) target prediction algorithms trained on this data has emerged...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439832/computational-and-experimental-identification-of-tissue-specific-microrna-targets
#19
Raheleh Amirkhah, Hojjat Naderi Meshkin, Ali Farazmand, John E J Rasko, Ulf Schmitz
In this chapter we discuss computational methods for the prediction of microRNA (miRNA) targets. More specifically, we consider machine learning-based approaches and explain why these methods have been relatively unsuccessful in reducing the number of false positive predictions. Further we suggest approaches designed to improve their performance by considering tissue-specific target regulation. We argue that the miRNA targetome differs depending on the tissue type and introduce a novel algorithm that predicts miRNA targets specifically for colorectal cancer...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28435243/peripheral-leukocyte-micrornas-as-novel-biomarkers-for-copd
#20
Ruiying Wang, Jianying Xu, Hu Liu, Zhiping Zhao
COPD is a multifactorial disease caused by environmental determinants as well as genetic risk factors. The prevalence and mortality of COPD continue to increase, and underdiagnosis of COPD remains a critical issue. Previous reports investigated promising microRNAs (miRNAs) to reveal the molecular mechanism for the development of COPD; however, diagnostic and therapeutic markers for COPD have not yet been found. For this study, 20 representative COPD patients were separated into four groups based on increasing severity (A, B, C, and D) and compared to six healthy controls...
2017: International Journal of Chronic Obstructive Pulmonary Disease
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