• Title, Summary, Keyword: DICER

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Biocomputational Characterization and Evolutionary Analysis of Bubaline Dicer1 Enzyme

  • Singh, Jasdeep;Mukhopadhyay, Chandra Sekhar;Arora, Jaspreet Singh;Kaur, Simarjeet
    • Asian-Australasian Journal of Animal Sciences
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    • v.28 no.6
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    • pp.876-887
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    • 2015
  • Dicer, an ribonuclease type III type endonuclease, is the key enzyme involved in biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs), and thus plays a critical role in RNA interference through post transcriptional regulation of gene expression. This enzyme has not been well studied in the Indian water buffalo, an important species known for disease resistance and high milk production. In this study, the primary coding sequence (5,778 bp) of bubaline dicer (GenBank: AB969677.1) was determined and the bubaline Dicer1 biocomputationally characterized to determine the phylogenetic signature among higher eukaryotes. The evolutionary tree revealed that all the transcript variants of Dicer1 belonging to a specific species were within the same node and the sequences belonging to primates, rodents and lagomorphs, avians and reptiles formed independent clusters. The bubaline dicer1 is closely related to that of cattle and other ruminants and significantly divergent from dicer of lower species such as tapeworm, sea urchin and fruit fly. Evolutionary divergence analysis conducted using MEGA6 software indicated that dicer has undergone purifying selection over the time. Seventeen divergent sequences, representing each of the families/taxa were selected to study the specific regions of positive vis-$\grave{a}$-vis negative selection using different models like single likelihood ancestor counting, fixed effects likelihood, and random effects likelihood of Datamonkey server. Comparative analysis of the domain structure revealed that Dicer1 is conserved across mammalian species while variation both in terms of length of Dicer enzyme and presence or absence of domain is evident in the lower organisms.

A COMPARATIVE STUDY ON THE SHEAR BOND STRENGTH OF DICOR AND G-CERA PORCELAIN LAMINATE VENEER (DICOR와 G-CERA PORCELAIN LAMINATE VENEER의 전단결합강도에 관한 비교연구)

  • Cho Mi-Sook;Yang Jae-Ho;Lee Sun-Hyung
    • The Journal of Korean Academy of Prosthodontics
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    • v.29 no.3
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    • pp.33-41
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    • 1991
  • Cermic has been widely used because of its excellent esthetics and strength. The recently introduced castable ceramic system is regarded as the more esthetic and biocompatible restorative material. The purpose of this study was to compare the shear bond strength of Dicer & G-Cera porcelain laminate veneer according to the type of cement and surface treatment and to observe the surface of bonding failure with SEM. Total forty disks(3.5mm $diam.\times2.0mm$ thickness) were prepared. Forty extracted human maxillary central incisor teeth were stored in saline solution. Ten teeth were bonded to Dicer specimen with Dicer ZPC cement and ten teeth were bonded with Dicer resin cement. Ten silicoated G-Cera specimen and ten non-silicoated G-Cera specimen were bonded to teeth with G-Cera resin cement. Bonded units were mounted in a plastic tube with hard stone and stored in a humidor at $37^{\circ}C$ for 24 hours. Shear bond strength was measured by Instron Universal Testing Machine (Model 1125) and all the specimen were observed with SEM(JEOL, JSM-T2000)and modes of failure were recorded. The obtained results were as follows: 1. The mean shear bond strength of Dicer bonded with Dicer resin cement was 11.62 MPa and that bonded with Dicor ZPC cement was 0.88 MPa : Shear bond strength of Dicer bonded with Dicer resin cement was significantly increased(P<0.05). 2. The mean shear bond strength of silicoated G-Cera was 13.10 MPa and that of non silicoated G-Cera was 10.93 MPa : Shear bond strength of silicoated G-Cera was not significantly increased (P>0.05). 3. Shear bond strength of Dicer and G-Cera porcelain laminate veneer was not significantly different (P>0.05). 4. In observation of bond failure with SEM, Dicer bonded with Dicer ZPC cement exhibited adhesive failure. Dicer bonded with Dicer resin cement and silicoated and non silicoated G-Cera exhibited cohesive failure.

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Identification of Differentially Expressed Genes in the Dicer 1 Knock-down Mouse Embryos using Microarray

  • Lee, Jae-Dal;Cui, Xiang-Shun
    • Reproductive and Developmental Biology
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    • v.32 no.4
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    • pp.229-235
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    • 2008
  • Silencing of Dicer1 by siRNA did not inhibit development up to the blastocyst stage, but decreased expression of selected transcription factors, including Oct-4, Sox2 and Nanog, suggesting that Dicer1 gene expression is associated with differentiation processes at the blastocyst stage (Cui et al., 2007). In order to get insights into genes which may be linked with microRNA system, we compared gene expression profiles in Gapdh and Dicer1 siRNA-microinjected blastocysts using the Applied Biosystem microarray technology. Our data showed that 397 and 737 out of 16354 genes were up- and down-regulated, respectively, following siRNA microinjection (p<0.05), including 24 up- and 28 down-regulated transcription factors. Identification of genes that are preferentially expressed at particular Dicer1 knock down embryos provides insights into the complex gene regulatory networks that drive differentiation processes in embryos at blastocyst stage.

Development of a New Duplex Real-Time Polymerase Chain Reaction Assay for Detection of Dicer in G. gallus

  • Ji, Xiaolin;Wang, Qi;Gao, Yulong;Wang, Yongqiang;Qin, Liting;Qi, Xiaole;Gao, Honglei;Wang, Xiaomei
    • Journal of Microbiology and Biotechnology
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    • v.23 no.5
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    • pp.630-636
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    • 2013
  • Recently, there has been a growing body of evidence showing that cellular microRNAs (miRNAs) are involved in virus-host interactions. Numerous studies have focused on analyses of the expression profiles of cellular miRNAs, but the expression patterns of Dicer, which is responsible for the generation of miRNAs, have only rarely been explored in Gallus gallus. We developed a duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay for the relative quantification of the mRNAs of Dicer and ${\beta}$-actin in G. gallus. To apply this method, the expression of Dicer in avian cells after infection with avian leukosis virus subgroup J (ALV-J) was detected using our established duplex real-time RT-PCR. The duplex real-time RT-PCR assay is sufficiently sensitive, specific, accurate, reproducible, and cost-effective for the detection of Dicer in G. gallus. Furthermore, this study, for the first time, demonstrated that ALV-J can induce differential expression of Dicer mRNA in the ALV-J-infected cells.

Association between the DICER rs1057035 Polymorphism and Cancer Risk: Evidence from a Meta-analysis of 1,2675 Individuals

  • Yu, Yan-Yan;Kuang, Dan;Yin, Xiao-Xv
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.1
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    • pp.119-124
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    • 2015
  • Background: DICER, one of the microRNA (miRNA) biogenesis proteins, is involved in the maturation of miRNAs and is implicated in cancer development and progression. The results from previous epidemiological studies on associations between DICER rs1057035 polymorphism and cancer risk were inconsistent. Thereforewe performed this meta-analysis to summarize possible associations. Materials and Methods: We searched all relevant articles on associations between DICER rs1057035 polymorphism and cancer risk from PubMed, EMBASE, Chinese Biomedical Literature and Chinese National Knowledge Infrastructure until August 2014. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess any associations. Heterogeneity tests, sensitivity analyses and publication bias assessments were also performed in this meta-analysis. All analyses were conducted using STATA software. Results: Seven case-control studies, including 4,875 cancer cases and 7,800 controls were included in the meta-analysis. Overall, the results indicated that the C allele of DICER rs1057035 polymorphism was significantly associated with decreased cancer risk in allelic comparison, heterozygote and dominant genetic models (C vs T: OR=0.88, 95%CI 0.81-0.95, p=0.002; TC vs TT: OR=0.85, 95%CI 0.77-0.93, p=0.001; CC/TC vs TT: OR=0.86, 95%CI 0.78-0.94, p=0.001). In the subgroup analysis by ethnicity, a significantly decreased cancer risk was found in Asian but not Caucasian populations. Conclusions: The present meta-analysis suggests that the C allele of the DICER rs1057035 polymorphism probably decreases cancer risk. However, this association may be Asian-specific and the results should be treated with caution. Further well-designed studies based on larger sample sizes and group of populations are needed to validate these findings.

Structural Characterization of pre-miRNA 155

  • Kim, Won-Je;Shin, JiYeon;Bang, Kyeongmi;Song, Hyun Kyu;Kim, Nak-Kyoon
    • Journal of the Korean Magnetic Resonance Society
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    • v.20 no.2
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    • pp.46-49
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    • 2016
  • MiRNA-155, upregulated in various cancers, is one of the miRNAs that suppress apoptosis of human cancer. Thus, inhibition of the maturation of miRNA-155 could be an effective way to induce apoptotic cancer cell death. The apical stem-loop of the pre-miRNA-155 has been known as a Dicer biding site for RNA cleavage. Here, to understand the molecular basis of the tertiary interaction between pre-miRNA-155 with Dicer, we characterize the structure of the apical stem-loop of pre-miRNA-155 using NMR spectroscopy. The RNA has a stem-bulge-stem-loop-stem structure, which is consist of G-C Watson-Crick and G-U Wobble base pairs. The assignments of imino- protons were further confirmed by 2D $^{15}N-^1H$ HSQC NMR spectrum. The NMR parameters obtained in this study can be further used to investigate the tertiary interaction between pre-miRNA-155 and other biomolecules such as protein, nucleic acids, or small chemicals which might be used to control the apoptosis of cancer.

CLINICAL STUDY ON THE CASTABLE GLASS CERAMIC(DICOR) CROWNS(I) (Dicor Crown의 적용분포 및 파절에 관한 임상적 연구(I))

  • Yang, Jae-Ho
    • The Journal of Korean Academy of Prosthodontics
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    • v.28 no.1
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    • pp.217-224
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    • 1990
  • Author examined clinical procedure, clinical application and clinical failure of castable glass ceramic (Dicor) crowns which were made at the Dept. of Prosthodontics, Seoul National University Hospital during 19 months from Jan. 1988 to July, 1989(Observation period:19 months). The author obtained the following results. 1. A total of 86 crowns were constructed ; Most of them has been set on maxillary central incisors(53 cases, 62%):maxillary lateral incisors(20 cases, 23%):maxillary canines(6 cases, 7%):others(7 cases, 8%) 2. Dicer could be used as a lamiate veneer for discolored tooth. 3. During the examination period(1-19 months), there was no fracture case. 4. Dicer could be applied on the maxillary anterior tooth with minimal occlusal force.

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Soybean mosaic virus Infection and Helper Component-protease Enhance Accumulation of Bean pod mottle virus-Specific siRNAs

  • Lim, Hyoun-Sub;Jang, Chan-Yong;Bae, Han-Hong;Kim, Joon-Ki;Lee, Cheol-Ho;Hong, Jin-Sung;Ju, Ho-Jong;Kim, Hong-Gi;Domier, Leslie L.
    • The Plant Pathology Journal
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    • v.27 no.4
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    • pp.315-323
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    • 2011
  • Soybean plants infected with Bean pod mottle virus (BPMV) develop acute symptoms that usually decrease in severity over time. In other plant-virus interactions, this type of symptom recovery has been associated with degradation of viral RNAs by RNA silencing, which is accompanied by the accumulation of virus-derived small interfering RNAs (siRNAs). In this study, changes in the accumulation of BPMV siRNAs were investigated in soybean plants infected with BPMV alone, or infected with both BPMV and Soybean mosaic virus (SMV) and in transgenic soybean plants expressing SMV helper component-protease (HC-Pro). In many potyviruses, HC-Pro is a potent suppressor of RNA silencing. In plants infected with BPMV alone, accumulation of siRNAs was positively correlated with symptom severity and accumulation of BPMV genomic RNAs. Plants infected with both BPMV and SMV and BPMV-infected transgenic soybean plants expressing SMV HC-Pro exhibited severe symptoms characteristic of BPMVSMV synergism, and showed enhanced accumulation of BPMV RNAs and siRNAs compared to plants infected with BPMV alone and nontransgenic plants. Likewise, SMV HC-Pro enhanced the accumulation of siRNAs produced from a silenced green fluorescent protein gene in transient expression assays, while the P19 silencing suppressor of Tomato bushy stunt virus did not. Consistent with the modes of action of HC-Pro in other systems, which have shown that HC-Pro suppresses RNA silencing by preventing the unwinding of duplex siRNAs and inhibiting siRNA methylation, these studies showed that SMV HC-Pro interfered with the activities of RNA-induced silencing complexes, but not the activities of Dicer-like enzymes in antiviral defenses.

Learning miRNA scoring models using base IUPAC code (염기의 IUPAC 코드를 이용한 miRNA Scoring Model의 학습)

  • 이화진;남진우;장병탁
    • Proceedings of the Korean Information Science Society Conference
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    • pp.775-777
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    • 2003
  • miRNA(microRNA)는 길이가 약 22nt 정도 되는 작은 ncRNA로서 유전자 작용을 조절하는데 중요한 역할을 하는 것으로 알려져 있다. 다이서(dicer)에 의해 성숙한 miRNA(mature miRNA)를 계산학적(computational)방법으로 학습하여 인간 miRNA의 구조를 예측하였다. miRNA에 관한 구체적인 기작은 아직 확실히 밝혀지지 않았기 때문에 서열 기반과 구조 기반 모두를 포함 하는 모델을 구현 하였으며 ambiguity code를 씀으로써 정보의 손실을 최소화 하도록 하였다. miRNA와 비슷한 구조를 가진 인간 EST로부터 데이터를 무작위 추출하여 실제 인간 miRNA 데이터와 비교함으로써 학습된 결과의 성능을 평가하였다.

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Estimation of Dinucleotide Step Parameters of Double Helix Structure on MicroRNA Using Genetic Algorithms (유전알고리즘을 이용한 MicroRNA 이중나선 구조의 Dinucleotide Step 파라미터 추정)

  • Nam Jin-Wu;Zhang Byoung-Tak
    • Proceedings of the Korean Information Science Society Conference
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    • pp.262-264
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    • 2005
  • MicroRNA는 약 22 nucleotide 길이로, 세포질에서 유전자의 전사 후 조절 기능을 맡는 small RNA의 한 종류이다. MiRNA는 긴 전사체인 pri-miRNA에서 Drosha에 의해 절단 되어 핵 밖으로 나가 최종 Dicer에 의해 성숙된다. 하지만, 아직까지 이 효소들이 pri-miRNA를 잘라내는 3차 구조상의 메커니즘을 이해하지 못하고 있다. 본 연구에서는 완숙한 miRNA 이중나선이 약 2 회전을 이루게 된다는 정보를 바탕으로, Drosha가 붙는 miRNA stem구조의 dinucleotide step 파라미터를 유전 알고리즘을 이용하여 추정한다. 추정된 파라미터로부터 실제 miRNA들의 3차구조를 예측할 수 있으며, 3차 구조상의 Drosha의 절단 메커니즘을 이해하는데 도움을 줄 것이다.

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