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https://www.readbyqxmd.com/read/28936869/ratiometric-fluorescence-sensor-for-the-microrna-determination-by-catalyzed-hairpin-assembly
#1
Yi Liu, Tian Shen, Jing Li, Hang Gong, Chunyan Chen, Xiaoming Chen, Changqun Cai
A novel catalyzed hairpin assembly-based turn-on ratiometric fluorescence biosensor was constructed for the determination of microRNA-122 (miRNA-122) by using 2-aminopurine (2-AP) and thioflavin T (ThT) as detection signal sources. Hairpin DNA sequence (H1) includes the complementary strands of miRNA-122 and G-quadruplex-forming sequence. When miRNA-122 was presented, hybridization occurred between miRNA-122 and part of H1, causing a double-stranded DNA and a G-quadruplex formed. The formed double-stranded DNA significantly decreased the fluorescence intensity of 2-AP...
September 22, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28934507/a-comprehensive-cell-specific-microrna-catalogue-of-human-peripheral-blood
#2
Simonas Juzenas, Geetha Venkatesh, Matthias Hübenthal, Marc P Hoeppner, Zhipei Gracie Du, Maren Paulsen, Philip Rosenstiel, Philipp Senger, Martin Hofmann-Apitius, Andreas Keller, Limas Kupcinskas, Andre Franke, Georg Hemmrich-Stanisak
With this study, we provide a comprehensive reference dataset of detailed miRNA expression profiles from seven types of human peripheral blood cells (NK cells, B lymphocytes, cytotoxic T lymphocytes, T helper cells, monocytes, neutrophils and erythrocytes), serum, exosomes and whole blood. The peripheral blood cells from buffy coats were typed and sorted using FACS/MACS. The overall dataset was generated from 450 small RNA libraries using high-throughput sequencing. By employing a comprehensive bioinformatics and statistical analysis, we show that 3' trimming modifications as well as composition of 3' added non-templated nucleotides are distributed in a lineage-specific manner-the closer the hematopoietic progenitors are, the higher their similarities in sequence variation of the 3' end...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934506/clip-seq-analysis-of-multi-mapped-reads-discovers-novel-functional-rna-regulatory-sites-in-the-human-transcriptome
#3
Zijun Zhang, Yi Xing
Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933597/microrna-1297-inhibits-the-growth-and-metastasis-of-colorectal-cancer-by-suppressing-cyclin-d2-expression
#4
Yanan Wang, Jinfang Xue, Haoyu Kuang, Xiaojun Zhou, Liya Liao, Fang Yin
microRNAs (miR) can potentially be used for categorizing the various subtypes of colorectal cancer (CRC) and predicting a patient's response to treatment with traditional anti-CRC therapies. We investigated how miR-1297 and its potential target molecule cyclin D2 (CCND2) might affect the progression of CRC. Thirty-two pairs of CRC specimens and corresponding samples of para-tumor tissue were collected and examined for their levels of miR-1297 and CCND2 expression. We also examined miR-1297 and CCND2 expression in cultured SW480 cells...
September 21, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28932769/microrna-expression-in-a-phosphaturic-mesenchymal-tumour
#5
Darrell Green, Irina Mohorianu, Isabelle Piec, Jeremy Turner, Clare Beadsmoore, Andoni Toms, Richard Ball, John Nolan, Iain McNamara, Tamas Dalmay, William D Fraser
Phosphaturic mesenchymal tumours are a heterogeneous set of bone and soft tissue neoplasms that can cause a number of paraneoplastic syndromes such as tumour induced osteomalacia. The term phosphaturic comes from the common finding that these tumours secrete high levels of fibroblast growth factor 23 which causes renal phosphate wasting leading to hypophosphatemia. Phosphaturic mesenchymal tumours are rare and diagnosis is difficult. A very active 68 year old male presented with bone pain and muscle weakness...
December 2017: Bone Reports
https://www.readbyqxmd.com/read/28931848/integrated-analysis-of-microrna-and-mrna-expression-profiles-during-the-sex-differentiation-sensitive-period-in-oriental-river-prawn-macrobrachium-nipponense
#6
Shubo Jin, Hongtuo Fu, Shengming Sun, Sufei Jiang, Yiwei Xiong, Yongsheng Gong, Hui Qiao, Wenyi Zhang, Yan Wu
Male oriental river prawns (Macrobrachium nipponense) grow faster than females, and therefore, reach larger sizes by harvest time. Histological observations have indicated that the sex-differentiation sensitive period (which includes the formation of the androgenic gland, the testis, and the ovary) is from post-larvae (PL) developmental stage for M. nipponense. In this study, we prepared four microRNA (miRNA) and mRNA libraries using samples collected from sex-differentiation sensitive period (PL7 to PL16) to perform RNA-sequencing for identifying sex-related candidate miRNAs, genes, and metabolic pathways...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28927254/integrated-analysis-of-microrna-and-mrna-expression-in-peripheral-blood-leukocytes-of-warmblood-horses-before-and-after-exercise
#7
Hang-Ah Kim, Myung-Chul Kim, Na-Yon Kim, Doug-Young Ryu, Hong-Seok Lee, Yongbaek Kim
Exercise capacity is a valuable trait in horses, and it has been used as one of their selection criteria. Although exercise affects molecular homeostasis and adaptation in horses, the mechanisms underlying these effects are not fully understood. This study was carried out to identify changes in the blood profiles of microRNAs (miRNAs) and mRNAs induced by exercise in horse leukocytes. Total RNAs isolated from the peripheral blood leukocytes of four Warmblood horses before and after exercise were subjected to next-generation sequencing (NGS) and microarray analyses to determine the miRNA and mRNA expression profiles, respectively...
September 20, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/28925390/alterations-of-micrornas-throughout-the-malignant-evolution-of-cutaneous-squamous-cell-carcinoma-the-role-of-mir-497-in-epithelial-to-mesenchymal-transition-of-keratinocytes
#8
A Mizrahi, A Barzilai, D Gur-Wahnon, I Z Ben-Dov, S Glassberg, T Meningher, E Elharar, M Masalha, J Jacob-Hirsch, H Tabibian-Keissar, I Barshack, J Roszik, R Leibowitz-Amit, Y Sidi, D Avni
Skin carcinogenesis is known to be a multi-step process with several stages along its malignant evolution. We hypothesized that transformation of normal epidermis to cutaneous squamous cell carcinoma (cSCC) is causally linked to alterations in microRNAs (miRNA) expression. For this end we decided to evaluate their alterations in the pathologic states ending in cSCC. Total RNA was extracted from formalin fixed paraffin embedded biopsies of five stages along the malignant evolution of keratinocytes towards cSCC: Normal epidermis, solar elastosis, actinic keratosis KIN1-2, advanced actinic keratosis KIN3 and well-differentiated cSCC...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28923913/variations-in-microrna-25-expression-influence-the-severity-of-diabetic-kidney-disease
#9
Yunshuang Liu, Hongzhi Li, Jieting Liu, Pengfei Han, Xuefeng Li, He Bai, Chunlei Zhang, Xuelian Sun, Yanjie Teng, Yufei Zhang, Xiaohuan Yuan, Yanhui Chu, Binghai Zhao
Diabetic nephropathy is characterized by persistent albuminuria, progressive decline in GFR, and secondary hypertension. MicroRNAs are dysregulated in diabetic nephropathy, but identification of the specific microRNAs involved remains incomplete. Here, we show that the peripheral blood from patients with diabetes and the kidneys of animals with type 1 or 2 diabetes have low levels of microRNA-25 (miR-25) compared with those of their nondiabetic counterparts. Furthermore, treatment with high glucose decreased the expression of miR-25 in cultured kidney cells...
September 18, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28922562/association-between-polymorphisms-in-microrna-target-sites-and-survival-in-early-stage-non-small-cell-lung-cancer
#10
Seung Soo Yoo, Mi Jeong Hong, Jang Hyuck Lee, Jin Eun Choi, Shin Yup Lee, Jaehee Lee, Seung Ick Cha, Chang Ho Kim, Yangki Seok, Eungbae Lee, Sukki Cho, Sanghoon Jheon, Jae Yong Park
A high-throughput mapping method of RNA-RNA interactions by crosslinking, ligation, and sequencing of hybrids (CLASH) can not only provide information about canonical but also non-canonical interactions. We evaluated the associations between variants in microRNA target sites using CLASH data and survival outcomes of 782 early-stage non-small cell lung cancer (NSCLC) patients who underwent curative surgical resection. Among the 100 variants studied, two variants showed significant association with survival outcomes...
September 18, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28919164/integrated-analysis-of-microrna-and-gene-expression-profiles-reveals-a-functional-regulatory-module-associated-with-liver-fibrosis
#11
Wei Chen, Wenshan Zhao, Aiting Yang, Anjian Xu, Huan Wang, Min Cong, Tianhui Liu, Ping Wang, Hong You
BACKGROUND: Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation have important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. METHODS: The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28918518/micro-rna-profiling-of-exosomes-from-marrow-derived-mesenchymal-stromal-cells-in-patients-with-acute-myeloid-leukemia-implications-in-leukemogenesis
#12
Juliana Barrera-Ramirez, Jessie R Lavoie, Harinad B Maganti, William L Stanford, Caryn Ito, Mitchell Sabloff, Marjorie Brand, Michael Rosu-Myles, Yevgeniya Le, David S Allan
Gene regulatory networks in AML may be influenced by microRNAs (miRs) contained in exosomes derived from bone marrow mesenchymal stromal cells (MSCs). We sequenced miRs from exosomes isolated from marrow-derived MSCs from patients with AML (n = 3) and from healthy controls (n = 3; not age-matched). Known targets of mIRs that were significantly different in AML-derived MSC exosomes compared to controls were identified. Of the five candidate miRs identified by differential packaging in exosomes, only miR-26a-5p and miR-101-3p were significantly increased in AML-derived samples while miR-23b-5p, miR-339-3p and miR-425-5p were significantly decreased...
September 16, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/28918159/identification-of-circular-rna-in-the-bombyx-mori-silk-gland
#13
Huaiyan Gan, Tieshan Feng, Yuqian Wu, Chun Liu, Qingyou Xia, Tingcai Cheng
Bombyx mori is an economically important holometabolous lepidopteran insect. In B. mori endogenous noncoding RNAs such as microRNAs (miRNAs) and Piwi-interacting RNAs play crucial biological functions in metamorphosis and sex determination. In addition, circular RNAs (circRNAs) have been recently identified as noncoding RNAs in most common model organisms and show potential as gene regulators. However, to date, there have been few studies on the circRNAs present in the B. mori genome conducted to date. Here, we identified 3916 circRNAs by deep circular transcriptome sequencing using the silk gland of B...
September 14, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28918015/a-microrna124-target-sequence-restores-astrocyte-specificity-of-gfaabc1d-driven-transgene-expression-in-aav-mediated-gene-transfer
#14
Grit Taschenberger, Julia Tereshchenko, Sebastian Kügler
Experimentally restricting transgene expression exclusively to astrocytes has proven difficult. Using adeno-associated-virus-mediated gene transfer, we assessed two commonly used glial fibrillary acidic protein promoters: the full-length version gfa2 (2,210-bp human glial fibrillary acidic protein [GFAP] promoter) and the truncated variant gfaABC1D (681-bp GFAP promoter). The capacity to drive efficient, but also cell-type specific, expression of the EGFP in astrocytes was tested both in vitro in rat primary cortical cultures as well as in vivo in the rat striatum...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28916650/differential-expression-of-mirnas-in-the-respiratory-tree-of-the-sea-cucumber-apostichopus-japonicus-under-hypoxia-stress
#15
Da Huo, Lina Sun, Xiaoni Li, Xiaoshang Ru, Shilin Liu, Libin Zhang, Lili Xing, Hongsheng Yang
Sea cucumber, an important economic species, has encountered high mortality since 2013 in northern China because of seasonal environmental stress such as hypoxia, high temperature, and low salinity. MicroRNAs (miRNAs) are important in regulating gene expression in marine organisms in response to environmental change. In the present study, high-throughput sequencing was used to investigate alterations in miRNA expression in the sea cucumber under different levels of dissolved oxygen (DO). Nine small RNA libraries were constructed from the sea cucumber respiratory trees...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28916343/the-role-of-a-new-class-of-long-noncoding-rnas-transcribed-from-ultraconserved-regions-in-cancer
#16
REVIEW
Daniela Terracciano, Sara Terreri, Filomena de Nigris, Valerio Costa, George A Calin, Amelia Cimmino
Ultraconserved regions (UCRs) represent a relatively new class of non-coding genomic sequences highly conserved between human, rat and mouse genomes. These regions can reside within exons of protein-coding genes, despite the vast majority of them localizes within introns or intergenic regions. Several studies have undoubtedly demonstrated that most of these regions are actively transcribed in normal cells/tissues, where they contribute to regulate many cellular processes. Interestingly, these non-coding RNAs exhibit aberrant expression levels in human cancer cells and their expression profiles have been used as prognostic factors in human malignancies, as well as to unambiguously distinguish among distinct cancer types...
September 12, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28916307/extreme-conservation-of-mirna-complements-in-opisthorchiids
#17
Vladimir Y Ovchinnikov, Viatcheslav A Mordvinov, Bastian Fromm
MicroRNAs (miRNAs) are important gene regulators that are key players in animal development and diseases. They are excreted in extracellular vesicles and because they were shown to be taken up by host cells they have been proposed as mediators of parasite-host communication, and potential biomarkers for the detection of parasitic infections from host blood. Consequently, it is crucial to precisely know the miRNA complements of medically important agents such as the liver flukes of the Opisthorchiidae. Using publicly available and new datasets we curated and reannotated the surprisingly small and variable miRNA complements previously described for Opisthorchis viverrini, O...
September 12, 2017: Parasitology International
https://www.readbyqxmd.com/read/28915579/microrna-profiling-associated-with-non-small-cell-lung-cancer-next-generation-sequencing-detection-experimental-validation-and-prognostic-value
#18
Sandra Gallach, Eloisa Jantus-Lewintre, Silvia Calabuig-Fariñas, David Montaner, Sergio Alonso, Rafael Sirera, Ana Blasco, Marta Usó, Ricardo Guijarro, Miguel Martorell, Carlos Camps
BACKGROUND: The average five-year survival for non-small cell lung cancer (NSCLC) patients is approximately 15%. Emerging evidence indicates that microRNAs (miRNAs) constitute a new class of gene regulators in humans that may play an important role in tumorigenesis. Hence, there is growing interest in studying their role as possible new biomarkers whose expression is aberrant in cancer. Therefore, in this study we identified dysregulated miRNAs by next generation sequencing (NGS) and analyzed their prognostic value...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28912250/role-of-microrna-423-5p-in-post-transcriptional-regulation-of-the-intestinal-riboflavin-transporter-3
#19
Ram Lakhan, Veedamali S Subramanian, Hamid M Said
Riboflavin (RF) is essential for normal cellular functions and health. Humans obtain RF from exogenous sources via intestinal absorption that involves a highly specific carrier-mediated process. We have recently established that the riboflavin transporter-3 (RFVT3) is vital for the normal intestinal RF uptake process, and have characterized certain aspects of its transcriptional regulation. Little is known, however, about how this transporter is regulated at the post-transcriptional level. We address this issue focusing on the role of microRNAs...
September 14, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/28912247/mir-212-mediates-counter-regulation-on-crh-expression-and-hpa-axis-activity-in-male-mice
#20
Yuxiao Tang, Xingjian Cai, Hongwei Zhang, Hui Shen, Wanyin Wang, Zhilei Shen, Wei Gu, Changquan Ling, Min Li
The mechanisms of hypothalamic-pituitary-adrenal (HPA) axis regulation have been studied persistently but still are not elucidated. Considering the emerging roles of microRNA in stress response, we conducted a microRNA microarray in mice hypothalamus to identify the potential role of microRNAs in regulating the HPA axis. In total, 41 microRNAs changed during heat stress, in which we found that miR-212 contains binding sequence with corticotropin-releasing hormone (CRH) 3'UTR according to sequence analysis. We observed that miR-212 expression in the hypothalamus was escalated by repeated heat and restraint stress...
September 14, 2017: Journal of Molecular Endocrinology
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