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miRNA analysis

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https://www.readbyqxmd.com/read/29792949/srnaome-and-transcriptome-analysis-provide-insight-into-chilling-response-of-cowpea-pods
#1
Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu Gao
Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pod's nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29790900/gscalite-a-web-server-for-gene-set-cancer-analysis
#2
Chun-Jie Liu, Fei-Fei Hu, Mengxuan Xia, Leng Han, Qiong Zhang, An-Yuan Guo
Summary: The availability of cancer genomic data makes it possible to analyze genes related to cancer. Cancer is usually the result of a set of genes and the signal of a single gene could be covered by background noise. Here, we present a web server named Gene Set Cancer Analysis (GSCALite) to analyze a set of genes in cancers with the following functional modules. (i) Differential expression in tumor vs normal, and the survival analysis; (ii) Genomic variations and their survival analysis; (iii) Gene expression associated cancer pathway activity; (iv) miRNA regulatory network for genes; (v) Drug sensitivity for genes; (vi) Normal tissue expression and eQTL for genes...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29789629/non-coding-rnas-in-various-stages-of-liver-disease-leading-to-hepatocellular-carcinoma-differential-expression-of-mirnas-pirnas-lncrnas-circrnas-and-sno-mt-rnas
#3
Srinivas V Koduru, Ashley N Leberfinger, Yuka I Kawasawa, Milind Mahajan, Niraj J Gusani, Arun J Sanyal, Dino J Ravnic
Hepatocellular carcinoma (HCC) was the fifth leading cause of cancer death in men and eighth leading cause of death in women in the United States in 2017. In our study, we sought to identify sncRNAs in various stages of development of HCC. We obtained publicly available small RNA-seq data derived from patients with cirrhosis (n = 14), low-grade dysplastic nodules (LGDN, n = 9), high grade dysplastic nodules (HGDN, n = 6), early hepatocellular carcinoma (eHCC, n = 6), and advanced hepatocellular carcinoma (HCC, n = 20), along with healthy liver tissue samples (n = 9)...
May 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29788742/mir-483-is-down-regulated-in-gastric-cancer-and-suppresses-cell-proliferation-invasion-and-protein-o-glcnacylation-by-targeting-ogt
#4
F Y Yu, C Y Zhou, Y B Liu, B Wang, L Mao, Y Li
MicroRNAs (miRNAs) are involved in the gastric carcinogenesis and progression. Here, we confirmed that miR-483 was frequently decreased in gastric cancer patients. The expression levels of miR-483 were negatively correlated with tumor stage, node metastasis and stromal invasion. Log-rank tests demonstrated that low expression of miR-483 was strongly correlated with poor overall survival in patients with gastric cancer. Moreover, ectopic expression of miR-483 remarkably suppressed gastric cancer cell proliferation by enhancing cell apoptosis and significantly inhibited the invasion of gastric cancer cells, while low expression of miR-483 exhibited the opposite effect...
March 14, 2018: Neoplasma
https://www.readbyqxmd.com/read/29788729/three-novel-micrornas-based-on-microrna-signatures-for-gastric-mucosa-associated-lymphoid-tissue-lymphoma
#5
Y Zhang, A Liu, M E, L Quan, Y Qu, A Gu
This study aimed to identify novel microRNAs (miRNAs) that play crucial regulatory roles in the pathogenesis of mucosa-associated lymphoid tissue (MALT) lymphoma by retrieving and analyzing the miRNA expression profile GSE23877. Differentially expressed miRNAs between gastric MALT lymphoma samples and human tonsil tissue samples as well as their target genes were identified. The transcriptional regulatory relationships between miRNAs and target genes were analyzed, and the regulatory network between them was constructed...
March 14, 2018: Neoplasma
https://www.readbyqxmd.com/read/29787577/analysis-of-micrornas-in-familial-mediterranean-fever
#6
Gil Amarilyo, Nir Pillar, Ilan Ben-Zvi, Daphna Weissglas-Volkov, Jonatan Zalcman, Liora Harel, Avi Livneh, Noam Shomron
OBJECTIVES: Although Familial Mediterranean fever (FMF) is categorized as autosomal recessive, frequent exceptions to this model exist and therefore we aimed to search epigenetic modifications in this disease. METHODS: Ten M694V homozygous FMF patients (the most severe phenotype) were recruited for this study. Patients with inflammatory flare were excluded. Total RNA was extracted from peripheral blood, and microRNA expression profiled using NanoString nCounter technology...
2018: PloS One
https://www.readbyqxmd.com/read/29786812/the-microrna-expression-profile-in-rat-lung-tissue-early-after-burn-injury
#7
Donghai Zhang, Yang Chang, Shaofang Han, Longlong Yang, Quan Hu, Yonghui Yu, Lingying Liu, Jiake Chai
BACKGROUND: Severe burn causes acute lung injury in many victims, but the related mechanisms have been barely investigated. microRNAs (miRNAs) important regulators in numerous physiological and pathophysiological process. However, the roles of miRNAs in burn lung injury are untested. METHODS: Six healthy male Sprague-Dawley rats were randomly assigned into burn and sham groups. Lung injury was evaluated by hematoxylin and eosin (HE) staining at 24 h after injury...
May 2018: Ulusal Travma Ve Acil Cerrahi Dergisi, Turkish Journal of Trauma & Emergency Surgery: TJTES
https://www.readbyqxmd.com/read/29786747/microrna-137-dysregulation-predisposes-to-osteoporotic-fracture-by-impeding-alp-activity-and-expression-via-suppression-of-leucine-rich-repeat-containing-g-protein-coupled-receptor-4-expression
#8
Xiangjun Liu, Xiaohui Xu
Osteoporosis is defined as a loss of bone mass and deterioration of its architecture resulting in bone weakness, which becomes prone to fracture. The objective of this study was to investigate the molecular mechanism by which miR-137 can reduce the risk of fracture in patients with osteoporosis. An online miRNA database and a luciferase reporter assay system were used to confirm that leucine-rich repeat-containing G-protein-coupled receptor 4 (LGR4) was the target of miR-137. Real-time PCR and western blot analysis were used to study miR-137 mRNA, the expression of LGR4 mRNA and protein among different groups or cells transfected with a scrambled miRNA control, miR-137 mimic, LGR4 siRNA and miR-137 inhibitor...
May 17, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786687/genome-wide-analysis-of-circular-rnas-in-bovine-cumulus-cells-treated-with-bmp15-and-gdf9
#9
Yao Fu, Hao Jiang, Jian-Bo Liu, Xu-Lei Sun, Zhe Zhang, Sheng Li, Yan Gao, Bao Yuan, Jia-Bao Zhang
Circular RNAs (circRNAs) are important members of the non-coding RNA family, and those relating to animal physiologies have been widely studied in recent years. This study aimed to explore the roles of circRNAs in the regulation of follicular development. We constructed four bovine cumulus cell cDNA libraries, including a negative control group (NC) and groups treated with BMP15, GDF9 and BMP15 + GDF9, and we sequenced the libraries on the Illumina HiSeq Xten platform. We identified 1706 circRNAs and screened for differential circRNA expression...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29785036/a-novel-microrna-signature-predicts-survival-in-liver-hepatocellular-carcinoma-after-hepatectomy
#10
Qiang Fu, Fan Yang, Tengxiao Xiang, Guoli Huai, Xingxing Yang, Liang Wei, Hongji Yang, Shaoping Deng
Liver hepatocellular carcinoma (LIHC) is the most common type of primary liver cancer. In the current study, genome-wide miRNA-Seq and mRNA profiles in 318 LIHC patients derived from The Cancer Genome Atlas (TCGA) were analysed to identify miRNA-based signatures for LIHC prognosis with survival analysis and a semi-supervised principal components (SPC) method. A seven-miRNA signature was confirmed for overall survival (OS) prediction by comparing miRNA profiles in paired primary tumour and solid tumour normal tissues...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29785014/3-utr-shortening-represses-tumor-suppressor-genes-in-trans-by-disrupting-cerna-crosstalk
#11
Hyun Jung Park, Ping Ji, Soyeon Kim, Zheng Xia, Benjamin Rodriguez, Lei Li, Jianzhong Su, Kaifu Chen, Chioniso P Masamha, David Baillat, Camila R Fontes-Garfias, Ann-Bin Shyu, Joel R Neilson, Eric J Wagner, Wei Li
Widespread mRNA 3' UTR shortening through alternative polyadenylation 1 promotes tumor growth in vivo 2 . A prevailing hypothesis is that it induces proto-oncogene expression in cis through escaping microRNA-mediated repression. Here we report a surprising enrichment of 3'UTR shortening among transcripts that are predicted to act as competing-endogenous RNAs (ceRNAs) for tumor-suppressor genes. Our model-based analysis of the trans effect of 3' UTR shortening (MAT3UTR) reveals a significant role in altering ceRNA expression...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29784986/a-workflow-for-the-integrative-transcriptomic-description-of-molecular-pathology-and-the-suggestion-of-normalizing-compounds-exemplified-by-parkinson-s-disease
#12
Mohamed Hamed, Yvonne Gladbach, Steffen Möller, Sarah Fischer, Mathias Ernst, Stephan Struckmann, Alexander Storch, Georg Fuellen
The volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and regulatory RNA, proteomics) emerged in order to identify biomarkers for early diagnosis and prognosis of complex diseases and therefore facilitating the development of novel treatment approaches...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784930/comparative-mrna-and-mirna-expression-in-european-mouflon-ovis-musimon-and-sheep-ovis-aries-provides-novel-insights-into-the-genetic-mechanisms-for-female-reproductive-success
#13
Ji Yang, Xin Li, Yin-Hong Cao, Kisun Pokharel, Xiao-Ju Hu, Ze-Hui Chen, Song-Song Xu, Jaana Peippo, Mervi Honkatukia, Juha Kantanen, Meng-Hua Li
Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis musimon) and performed an mRNA-miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep...
May 21, 2018: Heredity
https://www.readbyqxmd.com/read/29784358/short-probe-based-duplex-specific-nuclease-signal-amplification-strategy-enables-imaging-of-endogenous-micrornas-in-living-cells-with-ultrahigh-specificity
#14
Yingjun Ma, Jun Chen, Danping Chen, Yuzhi Xu, Li Zhang, Zong Dai, Xiaoyong Zou
Specific nucleic acids amplification at a constant and mild temperature is important for imaging assay of endogenous microRNAs (miRNAs) in living cells. Duplex-specific nuclease (DSN) is attractive in one-step isothermal assay of miRNA; however, its intrinsic limitations of low amplification specificity and high reaction temperature greatly restrict the application scope. Herein, we present a short-probe-based DSN signal amplification (spDSNSA) strategy enabling analysis of miRNAs at body temperature with significantly high specificity...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29783973/erythrocyte-microrna-sequencing-reveals-differential-expression-in-relapsing-remitting-multiple-sclerosis
#15
Kira Groen, Vicki E Maltby, Rodney A Lea, Katherine A Sanders, J Lynn Fink, Rodney J Scott, Lotti Tajouri, Jeannette Lechner-Scott
BACKGROUND: There is a paucity of knowledge concerning erythrocytes in the aetiology of Multiple Sclerosis (MS) despite their potential to contribute to disease through impaired antioxidant capacity and altered haemorheological features. Several studies have identified an abundance of erythrocyte miRNAs and variable profiles associated with disease states, such as sickle cell disease and malaria. The aim of this study was to compare the erythrocyte miRNA profile of relapsing-remitting MS (RRMS) patients to healthy sex- and age-matched controls...
May 21, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29783093/a-direct-plasma-mirna-assay-for-early-detection-and-histological-classification-of-lung-cancer
#16
Qixin Leng, Yue Wang, Feng Jiang
Cell-free microRNAs in plasma provide circulating biomarkers for lung cancer. Most techniques for analysis of miRNAs require a large plasma volume to purify a sufficient RNA yield followed by complicated downstream processing. Small differences in the multiple procedures often cause large analytical variations and poor diagnostic values of the plasma biomarkers. Here we investigate whether directly quantifying plasma miRNAs without RNA purification could diagnose lung cancer. FirePlex assay was directly applied to 20 μl plasma of 56 lung cancer patients and 28 cancer free controls for quantifying 11 lung tumor-associated miRNAs...
May 17, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29782494/ubiquitin-dependent-proteolysis-of-cxcl7-leads-to-posterior-longitudinal-ligament-ossification
#17
Michiyo Tsuru, Atsushi Ono, Hideaki Umeyama, Masahiro Takeuchi, Kensei Nagata
Ossification of the posterior longitudinal ligament (OPLL), a spinal ligament, reduces the range of motion in limbs. No treatment is currently available for OPLL, which is why therapies are urgently needed. OPLL occurs in obesity, is more common in men, and has an onset after 40 years of age. The mechanisms underlying OPLL remain unclear. In this study, we performed a serum proteomic analysis in both OPLL patients and healthy subjects to identify factors potentially involved in the development of OPLL, and found reduced levels of a protein that might underlie the pathology of OPLL...
2018: PloS One
https://www.readbyqxmd.com/read/29782194/five-common-functional-polymorphisms-in-micrornas-and-susceptibility-to-breast-cancer-an-updated-meta-analysis
#18
Jie Wu, Yusi Wang, Lihua Shang, Lichun Qi, Mowei Song
AIMS: microRNAs (miRNA) play a key role in the pathogenesis of breast cancer (BC) as regulators of tumor-associated genes, and understanding their polymorphisms is critical to the control of breast carcinogenesis. Thus, the present study explored the association between five common functional polymorphisms in miRNAs (i.e., miRNA-196a2C>T, rs11614913; miRNA-146aG>C, rs2910164; miRNA-423C>A, rs6505162; miRNA-608G>C, rs4919510; miRNA-27aC>T, rs895819) and the risk of BC. MATERIALS AND METHODS: Meta-analyses were performed on 31 studies, including 14,677 BC patients and 16,143 cancer-free controls...
May 21, 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29781987/retrospective-microrna-sequencing-complementary-dna-library-preparation-protocol-using-formalin-fixed-paraffin-embedded-rna-specimens
#19
Olivier Loudig, Christina Liu, Thomas Rohan, Iddo Z Ben-Dov
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781875/feasibility-of-microrna-profiling-in-human-inner-ear-perilymph
#20
Matthew Shew, Athanasia Warnecke, Thomas Lenarz, Heike Schmitt, Sumedha Gunewardena, Hinrich Staecker
Hearing loss is common and caused by a wide range of molecular and cellular pathologies. Current diagnosis of hearing loss depends on a combination of physiologic testing, patient history, and in some cases genetic testing. Currently, no biopsy or equivalent procedure exists to diagnose inner ear disorders. MicroRNAs (miRNA) are short ribonucleic acids that regulate a variety of cellular processes. They have been found to be reliable markers for a variety of disease processes. In particular, a variety of miRNAs that are markers for neurodegenerative disease have been identified in cerebrospinal fluid...
May 17, 2018: Neuroreport
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