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Sample records for microrna precursors based

  1. Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm

    Directory of Open Access Journals (Sweden)

    Wu Chi-Yeh

    2010-01-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are short non-coding RNA molecules, which play an important role in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs over the years. Recently, ab initio approaches have attracted more attention because they do not depend on homology information and provide broader applications than comparative approaches. Kernel based classifiers such as support vector machine (SVM are extensively adopted in these ab initio approaches due to the prediction performance they achieved. On the other hand, logic based classifiers such as decision tree, of which the constructed model is interpretable, have attracted less attention. Results This article reports the design of a predictor of pre-miRNAs with a novel kernel based classifier named the generalized Gaussian density estimator (G2DE based classifier. The G2DE is a kernel based algorithm designed to provide interpretability by utilizing a few but representative kernels for constructing the classification model. The performance of the proposed predictor has been evaluated with 692 human pre-miRNAs and has been compared with two kernel based and two logic based classifiers. The experimental results show that the proposed predictor is capable of achieving prediction performance comparable to those delivered by the prevailing kernel based classification algorithms, while providing the user with an overall picture of the distribution of the data set. Conclusion Software predictors that identify pre-miRNAs in genomic sequences have been exploited by biologists to facilitate molecular biology research in recent years. The G2DE employed in this study can deliver prediction accuracy comparable with the state-of-the-art kernel based machine learning algorithms. Furthermore, biologists can obtain valuable insights about the different characteristics of the sequences of pre-miRNAs with the models generated by the G

  2. The miR-10 microRNA precursor family

    DEFF Research Database (Denmark)

    Tehler, Disa; Høyland-Kroghsbo, Nina Molin; Lund, Anders H

    2011-01-01

    The miR-10 microRNA precursor family encodes a group of short non-coding RNAs involved in gene regulation. The miR-10 family is highly conserved and has sparked the interest of many research groups because of the genomic localization in the vicinity of, coexpression with and regulation of the Hox...... gene developmental regulators. Here, we review the current knowledge of the evolution, physiological function and involvement in cancer of this family of microRNAs....

  3. Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits.

    Science.gov (United States)

    Hazra, Anjan; Dasgupta, Nirjhar; Sengupta, Chandan; Das, Sauren

    2017-07-06

    Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program.

  4. Undesired small RNAs originate from an artificial microRNA precursor in transgenic petunia (Petunia hybrida.

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    Yulong Guo

    Full Text Available Although artificial microRNA (amiRNA technology has been used frequently in gene silencing in plants, little research has been devoted to investigating the accuracy of amiRNA precursor processing. In this work, amiRNAchs1 (amiRchs1, based on the Arabidopsis miR319a precursor, was expressed in order to suppress the expression of CHS genes in petunia. The transgenic plants showed the CHS gene-silencing phenotype. A modified 5' RACE technique was used to map small-RNA-directed cleavage sites and to detect processing intermediates of the amiRchs1 precursor. The results showed that the target CHS mRNAs were cut at the expected sites and that the amiRchs1 precursor was processed from loop to base. The accumulation of small RNAs in amiRchs1 transgenic petunia petals was analyzed using the deep-sequencing technique. The results showed that, alongside the accumulation of the desired artificial microRNAs, additional small RNAs that originated from other regions of the amiRNA precursor were also accumulated at high frequency. Some of these had previously been found to be accumulated at low frequency in the products of ath-miR319a precursor processing and some of them were accompanied by 3'-tailing variant. Potential targets of the undesired small RNAs were discovered in petunia and other Solanaceae plants. The findings draw attention to the potential occurrence of undesired target silencing induced by such additional small RNAs when amiRNA technology is used. No appreciable production of secondary small RNAs occurred, despite the fact that amiRchs1 was designed to have perfect complementarity to its CHS-J target. This confirmed that perfect pairing between an amiRNA and its targets is not the trigger for secondary small RNA production. In conjunction with the observation that amiRNAs with perfect complementarity to their target genes show high efficiency and specificity in gene silencing, this finding has an important bearing on future applications of ami

  5. Undesired small RNAs originate from an artificial microRNA precursor in transgenic petunia (Petunia hybrida).

    Science.gov (United States)

    Guo, Yulong; Han, Yao; Ma, Jing; Wang, Huiping; Sang, Xianchun; Li, Mingyang

    2014-01-01

    Although artificial microRNA (amiRNA) technology has been used frequently in gene silencing in plants, little research has been devoted to investigating the accuracy of amiRNA precursor processing. In this work, amiRNAchs1 (amiRchs1), based on the Arabidopsis miR319a precursor, was expressed in order to suppress the expression of CHS genes in petunia. The transgenic plants showed the CHS gene-silencing phenotype. A modified 5' RACE technique was used to map small-RNA-directed cleavage sites and to detect processing intermediates of the amiRchs1 precursor. The results showed that the target CHS mRNAs were cut at the expected sites and that the amiRchs1 precursor was processed from loop to base. The accumulation of small RNAs in amiRchs1 transgenic petunia petals was analyzed using the deep-sequencing technique. The results showed that, alongside the accumulation of the desired artificial microRNAs, additional small RNAs that originated from other regions of the amiRNA precursor were also accumulated at high frequency. Some of these had previously been found to be accumulated at low frequency in the products of ath-miR319a precursor processing and some of them were accompanied by 3'-tailing variant. Potential targets of the undesired small RNAs were discovered in petunia and other Solanaceae plants. The findings draw attention to the potential occurrence of undesired target silencing induced by such additional small RNAs when amiRNA technology is used. No appreciable production of secondary small RNAs occurred, despite the fact that amiRchs1 was designed to have perfect complementarity to its CHS-J target. This confirmed that perfect pairing between an amiRNA and its targets is not the trigger for secondary small RNA production. In conjunction with the observation that amiRNAs with perfect complementarity to their target genes show high efficiency and specificity in gene silencing, this finding has an important bearing on future applications of amiRNAs in gene

  6. TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms

    OpenAIRE

    Kim, Boseon; Ha, Minju; Loeff, Luuk; Chang, Hyeshik; Simanshu, Dhirendra K; Li, Sisi; Fareh, Mohamed; Patel, Dinshaw J; Joo, Chirlmin; Kim, V Narry

    2015-01-01

    Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the overhang of a pre-miRNA is the key structural element that is recognized by TUT7 and its paralogues, TUT4 (ZCCHC11) and TUT2 (GLD2/PAPD4). For group II...

  7. TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms.

    Science.gov (United States)

    Kim, Boseon; Ha, Minju; Loeff, Luuk; Chang, Hyeshik; Simanshu, Dhirendra K; Li, Sisi; Fareh, Mohamed; Patel, Dinshaw J; Joo, Chirlmin; Kim, V Narry

    2015-07-02

    Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the overhang of a pre-miRNA is the key structural element that is recognized by TUT7 and its paralogues, TUT4 (ZCCHC11) and TUT2 (GLD2/PAPD4). For group II pre-miRNAs, which have a 1-nt 3' overhang, TUT7 restores the canonical end structure (2-nt 3' overhang) through mono-uridylation, thereby promoting miRNA biogenesis. For pre-miRNAs where the 3' end is further recessed into the stem (as in 3' trimmed pre-miRNAs), TUT7 generates an oligo-U tail that leads to degradation. In contrast to Lin28-stimulated oligo-uridylation, which is processive, a distributive mode is employed by TUT7 for both mono- and oligo-uridylation in the absence of Lin28. The overhang length dictates the frequency (but not duration) of the TUT7-RNA interaction, thus explaining how TUT7 differentiates pre-miRNA species with different overhangs. Our study reveals dual roles and mechanisms of uridylation in repair and removal of defective pre-miRNAs. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.

  8. Poly(A-Specific Ribonuclease Mediates 3′-End Trimming of Argonaute2-Cleaved Precursor MicroRNAs

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    Mayuko Yoda

    2013-11-01

    Full Text Available MicroRNAs (miRNAs are typically generated as ∼22-nucleotide double-stranded RNAs via the processing of precursor hairpins by the ribonuclease III enzyme Dicer, after which they are loaded into Argonaute (Ago proteins to form an RNA-induced silencing complex (RISC. However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, occurs independently of Dicer and instead requires cleavage of the 3′ arm of the pre-miR-451 precursor hairpin by Ago2. The 3′ end of the Ago2-cleaved pre-miR-451 intermediate is then trimmed to the mature length by an unknown nuclease. Here, using a classical chromatographic approach, we identified poly(A-specific ribonuclease (PARN as the enzyme responsible for the 3′–5′ exonucleolytic trimming of Ago2-cleaved pre-miR-451. Surprisingly, our data show that trimming of Ago2-cleaved precursor miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than the mature length. Our findings define the maturation step in the miRNA biogenesis pathway that depends on Ago2-mediated cleavage.

  9. Estrogen Repression of MicroRNAs Is Associated with High Guanine Content in the Terminal Loop Sequences of Their Precursors

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    Amit Cohen

    2017-08-01

    Full Text Available Widespread microRNA (miRNA repression is a phenomenon observed in mammals after exposure to cigarette smoke and in many types of cancer. A comprehensive reduction in miRNA expression after treatment with the hormone estrogen has also previously been described. Here, we reveal a conserved association of miRNA downregulation after estrogen exposure in zebrafish, mouse, and human breast cancer cell line, with a high guanine content in the terminal loop sequences of their precursors, and offer a possible link between estrogen-related miRNA-adducts formation and carcinogenesis. We also show common gene expression patterns shared by breast cancer tumors and estrogen-treated zebrafish, suggesting that this organism can be used as a powerful model system for the study of human breast cancer.

  10. MicroRNA-125b-1 and BLID upregulation resulting from a novel IGH translocation in childhood B-Cell precursor acute lymphoblastic leukemia.

    Science.gov (United States)

    Tassano, Elisa; Acquila, Maura; Tavella, Elisa; Micalizzi, Concetta; Panarello, Claudio; Morerio, Cristina

    2010-08-01

    Chromosomal translocations involving the immunoglobulin heavy chain (IGH) locus are common abnormalities in mature B-cell neoplasms. Recent findings have also revealed their significant role in B-cell precursor acute lymphoblastic leukemia. As a rule, IGH translocations generate transcriptional activation of the oncogene localized in the proximity of the breakpoint. In this study, we describe a pediatric case of B-cell precursor acute lymphoblastic leukemia showing microRNA-125b-1 (MIR125B1) and BLID gene overexpression, resulting from a novel t(11;14)(q24.1;q32) translocation involving IGH. This is the first report describing the upregulation of a microRNA due to its juxtaposition to protein-coding gene regulatory elements and the overexpression of two neighboring genes as a consequence of transcriptional enhancers localized in the vicinity of the IGH gene.

  11. Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing

    KAUST Repository

    Iwata, Yuji

    2013-08-05

    Efficient and precise microRNA (miRNA) biogenesis in Arabidopsis is mediated by the RNaseIII-family enzyme DICER-LIKE 1 (DCL1), double-stranded RNA-binding protein HYPONASTIC LEAVES 1 and the zinc-finger (ZnF) domain-containing protein SERRATE (SE). In the present study, we examined primary miRNA precursor (pri-miRNA) processing by highly purified recombinant DCL1 and SE proteins and found that SE is integral to pri-miRNA processing by DCL1. SE stimulates DCL1 cleavage of the pri-miRNA in an ionic strength-dependent manner. SE uses its N-terminal domain to bind to RNA and requires both N-terminal and ZnF domains to bind to DCL1. However, when DCL1 is bound to RNA, the interaction with the ZnF domain of SE becomes indispensible and stimulates the activity of DCL1 without requiring SE binding to RNA. Our results suggest that the interactions among SE, DCL1 and RNA are a potential point for regulating pri-miRNA processing. 2013 The Author(s) 2013.

  12. Correlation between sequence conservation and structural thermodynamics of microRNA precursors from human, mouse, and chicken genomes

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    Wang Shengqi

    2010-10-01

    Full Text Available Abstract Background Previous studies have shown that microRNA precursors (pre-miRNAs have considerably more stable secondary structures than other native RNAs (tRNA, rRNA, and mRNA and artificial RNA sequences. However, pre-miRNAs with ultra stable secondary structures have not been investigated. It is not known if there is a tendency in pre-miRNA sequences towards or against ultra stable structures? Furthermore, the relationship between the structural thermodynamic stability of pre-miRNA and their evolution remains unclear. Results We investigated the correlation between pre-miRNA sequence conservation and structural stability as measured by adjusted minimum folding free energies in pre-miRNAs isolated from human, mouse, and chicken. The analysis revealed that conserved and non-conserved pre-miRNA sequences had structures with similar average stabilities. However, the relatively ultra stable and unstable pre-miRNAs were more likely to be non-conserved than pre-miRNAs with moderate stability. Non-conserved pre-miRNAs had more G+C than A+U nucleotides, while conserved pre-miRNAs contained more A+U nucleotides. Notably, the U content of conserved pre-miRNAs was especially higher than that of non-conserved pre-miRNAs. Further investigations showed that conserved and non-conserved pre-miRNAs exhibited different structural element features, even though they had comparable levels of stability. Conclusions We proposed that there is a correlation between structural thermodynamic stability and sequence conservation for pre-miRNAs from human, mouse, and chicken genomes. Our analyses suggested that pre-miRNAs with relatively ultra stable or unstable structures were less favoured by natural selection than those with moderately stable structures. Comparison of nucleotide compositions between non-conserved and conserved pre-miRNAs indicated the importance of U nucleotides in the pre-miRNA evolutionary process. Several characteristic structural elements were

  13. In-vivo quantification of primary microRNA processing by Drosha with a luciferase based system

    International Nuclear Information System (INIS)

    Allegra, Danilo; Mertens, Daniel

    2011-01-01

    Research highlights: → Posttranscriptional regulation of miRNA processing is difficult to quantify. → Our in-vivo processing assay can quantify Drosha cleavage in live cells. → It is based on luciferase reporters fused with pri-miRNAs. → The assay validates the processing defect caused by a mutation in pri-16-1. → It is a sensitive method to quantify pri-miRNA cleavage by Drosha in live cells. -- Abstract: The RNAse III Drosha is responsible for the first step of microRNA maturation, the cleavage of primary miRNA to produce the precursor miRNA. Processing by Drosha is finely regulated and influences the amount of mature microRNA in a cell. We describe in the present work a method to quantify Drosha processing activity in-vivo, which is applicable to any microRNA. With respect to other methods for measuring Drosha activity, our system is faster and scalable, can be used with any cellular system and does not require cell sorting or use of radioactive isotopes. This system is useful to study regulation of Drosha activity in physiological and pathological conditions.

  14. Cryopreservation of GABAergic Neuronal Precursors for Cell-Based Therapy.

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    Daniel Rodríguez-Martínez

    Full Text Available Cryopreservation protocols are essential for stem cells storage in order to apply them in the clinic. Here we describe a new standardized cryopreservation protocol for GABAergic neural precursors derived from the medial glanglionic eminence (MGE, a promising source of GABAergic neuronal progenitors for cell therapy against interneuron-related pathologies. We used 10% Me2SO as cryoprotectant and assessed the effects of cell culture amplification and cellular organization, as in toto explants, neurospheres, or individualized cells, on post-thaw cell viability and retrieval. We confirmed that in toto cryopreservation of MGE explants is an optimal preservation system to keep intact the interneuron precursor properties for cell transplantation, together with a high cell viability (>80% and yield (>70%. Post-thaw proliferation and self-renewal of the cryopreserved precursors were tested in vitro. In addition, their migration capacity, acquisition of mature neuronal morphology, and potency to differentiate into multiple interneuron subtypes were also confirmed in vivo after transplantation. The results show that the cryopreserved precursor features remained intact and were similar to those immediately transplanted after their dissection from the MGE. We hope this protocol will facilitate the generation of biobanks to obtain a permanent and reliable source of GABAergic precursors for clinical application in cell-based therapies against interneuronopathies.

  15. Nanotechnology-Based Detection of Novel microRNAs for Early Diagnosis of Prostate Cancer

    Science.gov (United States)

    2017-08-01

    AWARD NUMBER: W81XWH-15-1-0157 TITLE: Nanotechnology -Based Detection of Novel microRNAs for Early Diagnosis of Prostate Cancer PRINCIPAL...TITLE AND SUBTITLE Nanotechnology -Based Detection of Novel microRNAs for Early Diagnosis of Prostate Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER...identify novel differentially expressed miRNAs in the body fluids (blood, urine, etc.) for an early detection of PCa. Advances in nanotechnology and

  16. Network-based ranking methods for prediction of novel disease associated microRNAs.

    Science.gov (United States)

    Le, Duc-Hau

    2015-10-01

    Many studies have shown roles of microRNAs on human disease and a number of computational methods have been proposed to predict such associations by ranking candidate microRNAs according to their relevance to a disease. Among them, machine learning-based methods usually have a limitation in specifying non-disease microRNAs as negative training samples. Meanwhile, network-based methods are becoming dominant since they well exploit a "disease module" principle in microRNA functional similarity networks. Of which, random walk with restart (RWR) algorithm-based method is currently state-of-the-art. The use of this algorithm was inspired from its success in predicting disease gene because the "disease module" principle also exists in protein interaction networks. Besides, many algorithms designed for webpage ranking have been successfully applied in ranking disease candidate genes because web networks share topological properties with protein interaction networks. However, these algorithms have not yet been utilized for disease microRNA prediction. We constructed microRNA functional similarity networks based on shared targets of microRNAs, and then we integrated them with a microRNA functional synergistic network, which was recently identified. After analyzing topological properties of these networks, in addition to RWR, we assessed the performance of (i) PRINCE (PRIoritizatioN and Complex Elucidation), which was proposed for disease gene prediction; (ii) PageRank with Priors (PRP) and K-Step Markov (KSM), which were used for studying web networks; and (iii) a neighborhood-based algorithm. Analyses on topological properties showed that all microRNA functional similarity networks are small-worldness and scale-free. The performance of each algorithm was assessed based on average AUC values on 35 disease phenotypes and average rankings of newly discovered disease microRNAs. As a result, the performance on the integrated network was better than that on individual ones. In

  17. Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing

    KAUST Repository

    Iwata, Yuji; Takahashi, Masateru; Fedoroff, Nina V.; Hamdan, Samir

    2013-01-01

    ). In the present study, we examined primary miRNA precursor (pri-miRNA) processing by highly purified recombinant DCL1 and SE proteins and found that SE is integral to pri-miRNA processing by DCL1. SE stimulates DCL1 cleavage of the pri-miRNA in an ionic strength

  18. Fission-Based Electric Propulsion for Interstellar Precursor Missions

    International Nuclear Information System (INIS)

    HOUTS, MICHAEL G.; LENARD, ROGER X.; LIPINSKI, RONALD J.; PATTON, BRUCE; POSTON, DAVID; WRIGHT, STEVEN A.

    1999-01-01

    This paper reviews the technology options for a fission-based electric propulsion system for interstellar precursor missions. To achieve a total ΔV of more than 100 km/s in less than a decade of thrusting with an electric propulsion system of 10,000s Isp requires a specific mass for the power system of less than 35 kg/kWe. Three possible configurations are described: (1) a UZrH-fueled,NaK-cooled reactor with a steam Rankine conversion system,(2) a UN-fueled gas-cooled reactor with a recuperated Brayton conversion system, and (3) a UN-fueled heat pipe-cooled reactor with a recuperated Brayton conversion system. All three of these systems have the potential to meet the specific mass requirements for interstellar precursor missions in the near term. Advanced versions of a fission-based electric propulsion system might travel as much as several light years in 200 years

  19. Molecular Beacon-Based MicroRNA Imaging During Neurogenesis.

    Science.gov (United States)

    Lee, Jonghwan; Kim, Soonhag

    2016-01-01

    The fluorescence monitoring system for examining endogenous microRNA (miRNA) activity in cellular level provides crucial information on not only understanding a critical role of miRNA involving a variety of biological processes, but also evaluating miRNA expression patterns in a noninvasive manner. In this protocol, we report the details of a new procedure for a molecular beacon-based miRNA monitoring system, which includes the illustration scheme for miRNA detection strategy, exogenous miRNA detection, and measurement of endogenous miRNA expression level during neurogenesis. The fluorescence signal of miR-124a beacon quenched by BHQ2 was gradually recovered as increasing concentration of the miR-124a in tube. The functional work of miR-124a beacon was examined in intracellular environment, allowing for the internalization of the miR-124a beacon by lipofectamine, which resulted in activated fluorescent signals of the miR-124a beacon in the HeLa cells after the addition of synthetic miR-124a. The endogenous miR-124a expression level was detected by miR-124a beacon system during neurogenesis, showing brighter fluorescence intensity in cytoplasmic area of P19 cells after induction of neuronal differentiation by retinoic acid. The molecular beacon based-miRNA detection technique could be applicable to the simultaneous visualization of a variety of miRNA expression patterns using different fluorescence dyes. For the study of examining endogenous miRNA expression level using miRNA-beacon system, if cellular differentiation step is already prepared, transfection step of miR-124a beacon into P19 cells, and acquisition of activated fluorescence signal measured by confocal microscope can be conducted approximately within 6 h.

  20. A polymorphism in the microRNA-30e precursor associated with major depressive disorder risk and P300 waveform.

    Science.gov (United States)

    Xu, Yong; Liu, Haiying; Li, Fei; Sun, Ning; Ren, Yan; Liu, Zhifen; Cao, Xiaohua; Wang, Yanfang; Liu, Pozi; Zhang, Kerang

    2010-12-01

    Growing evidence shows that the etiological causes and pathological processes underlying major depressive disorder (MDD) and schizophrenia (SCZ) overlap. Our previous study revealed a strong association between the polymorphism ss178077483 in the miRNA-30e precursor (pre-miR-30e) and the risk of SCZ. We thus hypothesized that this SCZ risk allele at the pre-miR-30e gene also confers risk of MDD. To explore the relationship between miR-30e ss178077483 and MDD, we conducted an association analyses in 1088 MDD patients and 1102 control subjects from the Han Chinese population. We also determined the effects of miR-30e ss178077483 on the development of P300 event-related potential components induced by an auditory odd-ball task. We detected a statistically significant positive association between miR-30e ss178077483 and MDD (allelic P=0.0287; genotypic P=0.0275). Moreover, the P300 latency was associated with miR-30e ss178077483 genotypes and the individuals with the C/T genotype have a longer P300 latency than those carrying the C/C genotype (P=0.009). Larger numbers of subjects and different ethnic groups would confirm and strengthen these preliminary findings. To our knowledge, this is the first evidence to suggest that miRNA polymorphisms may play an important role in MDD susceptibility. These findings also imply that certain miRNAs may be involved in the etiology of MDD. Copyright © 2010 Elsevier B.V. All rights reserved.

  1. Discovery of precursor and mature microRNAs and their putative gene targets using high-throughput sequencing in pineapple (Ananas comosus var. comosus).

    Science.gov (United States)

    Yusuf, Noor Hydayaty Md; Ong, Wen Dee; Redwan, Raimi Mohamed; Latip, Mariam Abd; Kumar, S Vijay

    2015-10-15

    MicroRNAs (miRNAs) are a class of small, endogenous non-coding RNAs that negatively regulate gene expression, resulting in the silencing of target mRNA transcripts through mRNA cleavage or translational inhibition. MiRNAs play significant roles in various biological and physiological processes in plants. However, the miRNA-mediated gene regulatory network in pineapple, the model tropical non-climacteric fruit, remains largely unexplored. Here, we report a complete list of pineapple mature miRNAs obtained from high-throughput small RNA sequencing and precursor miRNAs (pre-miRNAs) obtained from ESTs. Two small RNA libraries were constructed from pineapple fruits and leaves, respectively, using Illumina's Solexa technology. Sequence similarity analysis using miRBase revealed 579,179 reads homologous to 153 miRNAs from 41 miRNA families. In addition, a pineapple fruit transcriptome library consisting of approximately 30,000 EST contigs constructed using Solexa sequencing was used for the discovery of pre-miRNAs. In all, four pre-miRNAs were identified (MIR156, MIR399, MIR444 and MIR2673). Furthermore, the same pineapple transcriptome was used to dissect the function of the miRNAs in pineapple by predicting their putative targets in conjunction with their regulatory networks. In total, 23 metabolic pathways were found to be regulated by miRNAs in pineapple. The use of high-throughput sequencing in pineapples to unveil the presence of miRNAs and their regulatory pathways provides insight into the repertoire of miRNA regulation used exclusively in this non-climacteric model plant. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss).

    Science.gov (United States)

    Yang, Liandong; He, Shunping

    2014-01-01

    MicroRNAs (miRNAs) participate in various vitally biological processes via controlling target genes activity and thousands of miRNAs have been identified in many species to date, including 18,698 known animal miRNA in miRBase. However, there are only limited studies reported in rainbow trout (Oncorhynchus mykiss) especially via the computational-based approaches. In present study, we systematically investigated the miRNAs in rainbow trout using a well-developed comparative genome-based homologue search. A total of 196 potential miRNAs, belonging to 124 miRNA families, were identified, most of which were firstly reported in rainbow trout. The length of miRNAs ranged from 17 to 24 nt with an average of 20 nt while the length of their precursors varied from 47 to 152 nt with an average of 85 nt. The identified miRNAs were not evenly distributed in each miRNA family, with only one member per family for a majority, and multiple members were also identified for several families. Nucleotide U was dominant in the pre-miRNAs with a percentage of 30.04%. The rainbow trout pre-miRNAs had relatively high negative minimal folding free energy (MFE) and adjusted MFE (AMFE). Not only the mature miRNAs but their precursor sequences are conserved among the living organisms. About 2466 O. mykiss genes were predicted as potential targets for 189 miRNAs. Gene Ontology (GO) analysis showed that nearly 2093, 2107, and 2081 target genes are involved in cellular component, molecular function, and biological processes respectively. KEGG pathway enrichment analysis illuminated that these miRNAs targets might regulate 105 metabolic pathways, including those of purine metabolism, nitrogen metabolism, and oxidative phosphorylation. This study has provided an update on rainbow trout miRNAs and their targets, which represents a foundation for future studies. © 2013.

  3. Development and blind clinical validation of a microRNA based predictor of response to treatment with R-CHO(E)P in DLBCL

    DEFF Research Database (Denmark)

    Knudsen, Steen; Hother, Christoffer; Grønbæk, Kirsten

    2015-01-01

    MicroRNAs (miRNA) are a group of short noncoding RNAs that regulate gene expression at the posttranscriptional level. It has been shown that microRNAs are independent predictors of outcome in patients with diffuse large B-cell lymphoma (DLBCL) treated with the drug combination R-CHOP. Based on th...

  4. Isolation of microRNA targets using biotinylated synthetic microRNAs

    DEFF Research Database (Denmark)

    Ørom, Ulf Andersson; Lund, Anders H

    2007-01-01

    MicroRNAs are small regulatory RNAs found in multicellular organisms where they post-transcriptionally regulate gene expression. In animals, microRNAs bind mRNAs via incomplete base pairings making the identification of microRNA targets inherently difficult. Here, we present a detailed method...... for experimental identification of microRNA targets based on affinity purification of tagged microRNAs associated with their targets. Udgivelsesdato: 2007-Oct...

  5. A novel method of predicting microRNA-disease associations based on microRNA, disease, gene and environment factor networks.

    Science.gov (United States)

    Peng, Wei; Lan, Wei; Zhong, Jiancheng; Wang, Jianxin; Pan, Yi

    2017-07-15

    MicroRNAs have been reported to have close relationship with diseases due to their deregulation of the expression of target mRNAs. Detecting disease-related microRNAs is helpful for disease therapies. With the development of high throughput experimental techniques, a large number of microRNAs have been sequenced. However, it is still a big challenge to identify which microRNAs are related to diseases. Recently, researchers are interesting in combining multiple-biological information to identify the associations between microRNAs and diseases. In this work, we have proposed a novel method to predict the microRNA-disease associations based on four biological properties. They are microRNA, disease, gene and environment factor. Compared with previous methods, our method makes predictions not only by using the prior knowledge of associations among microRNAs, disease, environment factors and genes, but also by using the internal relationship among these biological properties. We constructed four biological networks based on the similarity of microRNAs, diseases, environment factors and genes, respectively. Then random walking was implemented on the four networks unequally. In the walking course, the associations can be inferred from the neighbors in the same networks. Meanwhile the association information can be transferred from one network to another. The results of experiment showed that our method achieved better prediction performance than other existing state-of-the-art methods. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection.

    Science.gov (United States)

    Winata, Patrick; Williams, Marissa; McGowan, Eileen; Nassif, Najah; van Zandwijk, Nico; Reid, Glen

    2017-11-17

    MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

  7. Biofluid-based microRNA Biomarkers for Parkinsons Disease: an Overview and Update

    Directory of Open Access Journals (Sweden)

    Sapana Shinde

    2015-02-01

    Full Text Available Parkinson's disease (PD is a highly debilitating motor disorder and is the second most common neurodegenerative disease after Alzheimer's disease. Its current method of diagnosis mainly relies on subjective clinical rating scales in the presence of clinical motor features. Early detection of PD is a known challenge as neuronal cell death may range from 50% to 80% when a patient is first diagnosed with PD. Therefore, there is an urgent need to identify and develop biomarkers for early detection of this progressive disease. This mini review focuses on the recent developments of biofluid-based microRNAs (miRNAs as molecular biomarkers for PD. A comprehensive list of miRNA biomarkers found in blood, plasma, serum, and cerebral spinal fluid is presented. Challenges and future perspectives of using these PD-related molecular biomarkers in a “real-world” clinical setting are also discussed.

  8. Ratiometric FRET-based detection of DNA and micro-RNA in solution

    International Nuclear Information System (INIS)

    Matveeva, Evgenia G.; Gryczynski, Zygmunt; Stewart, Donald R.; Gryczynski, Ignacy

    2009-01-01

    A ratiometric method for detecting DNA oligomers in bulk solution based on Foerster resonance energy transfer (FRET) is described. The two fluorescence signals (green and red), originating from Cy3 (donor, green) and Cy5 (acceptor, red) labels, are simultaneously detected from the pre-hybridized Cy3oligomerY:Cy5oligomerX system. The ratio of red to green intensities is sensitive to the presence of the single-stranded complimentary oligomer, which replaces single-stranded Cy3oligomerY in the donor:acceptor complex and perturbs the FRET. The detection scheme is generally applicable to the detection of DNA and RNA, and particularly micro-RNA. The proposed method is applicable to various double-stranded various lengths targets (manipulation of the sample preparation conditions, such as temperature, incubation time, denaturizing agent, may be needed).

  9. Isolation of Exosome-Like Nanoparticles and Analysis of MicroRNAs Derived from Coconut Water Based on Small RNA High-Throughput Sequencing.

    Science.gov (United States)

    Zhao, Zhehao; Yu, Siran; Li, Min; Gui, Xin; Li, Ping

    2018-03-21

    In this study, the presence of microRNAs in coconut water was identified by real-time polymerase chain reaction (PCR) based on the results of high-throughput small RNA sequencing. In addition, the differences in microRNA content between immature and mature coconut water were compared. A total of 47 known microRNAs belonging to 25 families and 14 new microRNAs were identified in coconut endosperm. Through analysis using a target gene prediction software, potential microRNA target genes were identified in the human genome. Real-time PCR showed that the level of most microRNAs was higher in mature coconut water than in immature coconut water. Then, exosome-like nanoparticles were isolated from coconut water. After ultracentrifugation, some particle structures were seen in coconut water samples using 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate fluorescence staining. Subsequent scanning electron microscopy observation and dynamic light scattering analysis also revealed some exosome-like nanoparticles in coconut water, and the mean diameters of the particles detected by the two methods were 13.16 and 59.72 nm, respectively. In conclusion, there are extracellular microRNAs in coconut water, and their levels are higher in mature coconut water than in immature coconut water. Some exosome-like nanoparticles were isolated from coconut water, and the diameter of these particles was smaller than that of animal-derived exosomes.

  10. Biosensor-based microRNA detection: techniques, design, performance, and challenges.

    Science.gov (United States)

    Johnson, Blake N; Mutharasan, Raj

    2014-04-07

    The current state of biosensor-based techniques for amplification-free microRNA (miRNA) detection is critically reviewed. Comparison with non-sensor and amplification-based molecular techniques (MTs), such as polymerase-based methods, is made in terms of transduction mechanism, associated protocol, and sensitivity. Challenges associated with miRNA hybridization thermodynamics which affect assay selectivity and amplification bias are briefly discussed. Electrochemical, electromechanical, and optical classes of miRNA biosensors are reviewed in terms of transduction mechanism, limit of detection (LOD), time-to-results (TTR), multiplexing potential, and measurement robustness. Current trends suggest that biosensor-based techniques (BTs) for miRNA assay will complement MTs due to the advantages of amplification-free detection, LOD being femtomolar (fM)-attomolar (aM), short TTR, multiplexing capability, and minimal sample preparation requirement. Areas of future importance in miRNA BT development are presented which include focus on achieving high measurement confidence and multiplexing capabilities.

  11. Relative importance and interactions of furan precursors in sterilised, vegetable-based food systems.

    Science.gov (United States)

    Palmers, Stijn; Grauwet, Tara; Buvé, Carolien; Vanratingen, Koen; Kebede, Biniam T; Goos, Peter; Hendrickx, Marc E; Van Loey, Ann

    2016-01-01

    Mitigation strategies aimed at an intervention in the reaction pathways for furan formation (e.g., by adjusting precursor concentrations) might offer an additional route for furan reduction in sterilised, vegetable-based foods, without adverse effects on other food safety or quality attributes. As a first step towards product reformulation, the aim of the present study was to determine the relative importance and interactions of possible furan precursors in these types of foods. Based on an I-optimal experimental design, potato purée (naturally low in furan precursors) was spiked with known amounts of sugars, ascorbic acid, olive oil and β-carotene, and subjected to a thermal sterilisation. Significant correlations were observed between furan concentrations after thermal treatment and starting concentrations of ascorbic acid and monosaccharides (i.e., fructose and glucose). Ascorbic acid had a clear furan-reducing effect as an antioxidant by protecting (polyunsaturated) fatty acids against oxidative degradation. Fructose and glucose were the main precursors, which can most probably be attributed to their high, but realistic, concentrations in the product. The contributions of fatty acids and β-carotene were strongly dependent on redox interactions with other food constituents. In the same potato purées, only low concentrations (0-2 ng g(-1) purée) of 2-methylfuran were detected, indicating that the direct importance of the spiked food constituents as a precursor for methylfuran formation was rather small. Based on the results of this study, reducing the amount of monosaccharides or adjusting the redox conditions of the matrix are suggested as two possible approaches for furan mitigation on the product side.

  12. Paper-Based MicroRNA Expression Profiling from Plasma and Circulating Tumor Cells.

    Science.gov (United States)

    Leong, Sai Mun; Tan, Karen Mei-Ling; Chua, Hui Wen; Huang, Mo-Chao; Cheong, Wai Chye; Li, Mo-Huang; Tucker, Steven; Koay, Evelyn Siew-Chuan

    2017-03-01

    Molecular characterization of circulating tumor cells (CTCs) holds great promise for monitoring metastatic progression and characterizing metastatic disease. However, leukocyte and red blood cell contamination of routinely isolated CTCs makes CTC-specific molecular characterization extremely challenging. Here we report the use of a paper-based medium for efficient extraction of microRNAs (miRNAs) from limited amounts of biological samples such as rare CTCs harvested from cancer patient blood. Specifically, we devised a workflow involving the use of Flinders Technology Associates (FTA) ® Elute Card with a digital PCR-inspired "partitioning" method to extract and purify miRNAs from plasma and CTCs. We demonstrated the sensitivity of this method to detect miRNA expression from as few as 3 cancer cells spiked into human blood. Using this method, background miRNA expression was excluded from contaminating blood cells, and CTC-specific miRNA expression profiles were derived from breast and colorectal cancer patients. Plasma separated out during purification of CTCs could likewise be processed using the same paper-based method for miRNA detection, thereby maximizing the amount of patient-specific information that can be derived from a single blood draw. Overall, this paper-based extraction method enables an efficient, cost-effective workflow for maximized recovery of small RNAs from limited biological samples for downstream molecular analyses. © 2016 American Association for Clinical Chemistry.

  13. Computational prediction and experimental validation of Ciona intestinalis microRNA genes

    Directory of Open Access Journals (Sweden)

    Pasquinelli Amy E

    2007-11-01

    Full Text Available Abstract Background This study reports the first collection of validated microRNA genes in the sea squirt, Ciona intestinalis. MicroRNAs are processed from hairpin precursors to ~22 nucleotide RNAs that base pair to target mRNAs and inhibit expression. As a member of the subphylum Urochordata (Tunicata whose larval form has a notochord, the sea squirt is situated at the emergence of vertebrates, and therefore may provide information about the evolution of molecular regulators of early development. Results In this study, computational methods were used to predict 14 microRNA gene families in Ciona intestinalis. The microRNA prediction algorithm utilizes configurable microRNA sequence conservation and stem-loop specificity parameters, grouping by miRNA family, and phylogenetic conservation to the related species, Ciona savignyi. The expression for 8, out of 9 attempted, of the putative microRNAs in the adult tissue of Ciona intestinalis was validated by Northern blot analyses. Additionally, a target prediction algorithm was implemented, which identified a high confidence list of 240 potential target genes. Over half of the predicted targets can be grouped into the gene ontology categories of metabolism, transport, regulation of transcription, and cell signaling. Conclusion The computational techniques implemented in this study can be applied to other organisms and serve to increase the understanding of the origins of non-coding RNAs, embryological and cellular developmental pathways, and the mechanisms for microRNA-controlled gene regulatory networks.

  14. Optimal consistency in microRNA expression analysis using reference-gene-based normalization.

    Science.gov (United States)

    Wang, Xi; Gardiner, Erin J; Cairns, Murray J

    2015-05-01

    Normalization of high-throughput molecular expression profiles secures differential expression analysis between samples of different phenotypes or biological conditions, and facilitates comparison between experimental batches. While the same general principles apply to microRNA (miRNA) normalization, there is mounting evidence that global shifts in their expression patterns occur in specific circumstances, which pose a challenge for normalizing miRNA expression data. As an alternative to global normalization, which has the propensity to flatten large trends, normalization against constitutively expressed reference genes presents an advantage through their relative independence. Here we investigated the performance of reference-gene-based (RGB) normalization for differential miRNA expression analysis of microarray expression data, and compared the results with other normalization methods, including: quantile, variance stabilization, robust spline, simple scaling, rank invariant, and Loess regression. The comparative analyses were executed using miRNA expression in tissue samples derived from subjects with schizophrenia and non-psychiatric controls. We proposed a consistency criterion for evaluating methods by examining the overlapping of differentially expressed miRNAs detected using different partitions of the whole data. Based on this criterion, we found that RGB normalization generally outperformed global normalization methods. Thus we recommend the application of RGB normalization for miRNA expression data sets, and believe that this will yield a more consistent and useful readout of differentially expressed miRNAs, particularly in biological conditions characterized by large shifts in miRNA expression.

  15. Synthesis, characterization and biological assay of Salicylaldehyde Schiff base Cu(II) complexes and their precursors

    Science.gov (United States)

    Iftikhar, Bushra; Javed, Kanwal; Khan, Muhammad Saif Ullah; Akhter, Zareen; Mirza, Bushra; Mckee, Vickie

    2018-03-01

    Three new Schiff base ligands were synthesized by the reaction of Salicylaldehyde with semi-aromatic diamines, prepared by the reduction of corresponding dinitro-compounds, and were further used for the formation of complexes with Cu(II) metal ion. The structural features of the synthesized compounds were confirmed by their physical properties and infrared, electronic and NMR spectroscopic techniques. The studies revealed that the synthesized Schiff bases existed as tetradentate ligands and bonded to the metal ion through the phenolic oxygen and azomethine nitrogen. One of the dinitro precursors was also analyzed by single crystal X-ray crystallography, which showed that it crystallizes in monoclinic system with space group P2/n. The thermal behavior of the Cu(II) complexes was determined by thermogravimetric analysis (TGA) and kinetic parameters were evaluated from the data. Schiff base ligands, their precursors and metal complexes were also screened for antibacterial, antifungal, antitumor, Brine shrimp lethality, DPPH free radical scavenging and DNA damage assays. The results of these analyses indicated the substantial potential of the synthesized Schiff bases, their precursors and Cu(II) complexes in biological field as future drugs.

  16. Emerging RNA-based drugs: siRNAs, microRNAs and derivates.

    Science.gov (United States)

    Pereira, Tiago Campos; Lopes-Cendes, Iscia

    2012-09-01

    An emerging new category of therapeutic agents based on ribonucleic acid has emerged and shown very promising in vitro, animal and pre-clinical results, known as small interfering RNAs (siRNAs), microRNAs mimics (miRNA mimics) and their derivates. siRNAs are small RNA molecules that promote potent and specific silencing of mutant, exogenous or aberrant genes through a mechanism known as RNA interference. These agents have called special attention to medicine since they have been used to experimentally treat a series of neurological conditions with distinct etiologies such as prion, viral, bacterial, fungal, genetic disorders and others. siRNAs have also been tested in other scenarios such as: control of anxiety, alcohol consumption, drug-receptor blockage and inhibition of pain signaling. Although in a much earlier stage, miRNAs mimics, anti-miRs and small activating RNAs (saRNAs) also promise novel therapeutic approaches to control gene expression. In this review we intend to introduce clinicians and medical researchers to the most recent advances in the world of siRNA- and miRNA-mediated gene control, its history, applications in cells, animals and humans, delivery methods (an yet unsolved hurdle), current status and possible applications in future clinical practice.

  17. Application of TALE-Based Approach for Dissecting Functional MicroRNA-302/367 in Cellular Reprogramming.

    Science.gov (United States)

    Zhang, Zhonghui; Wu, Wen-Shu

    2018-01-01

    MicroRNAs are small 18-24 nt single-stranded noncoding RNA molecules involved in many biological processes, including stemness maintenance and cellular reprogramming. Current methods used in loss-of-function studies of microRNAs have several limitations. Here, we describe a new approach for dissecting miR-302/367 functions by transcription activator-like effectors (TALEs), which are natural effector proteins secreted by Xanthomonas and Ralstonia bacteria. Knockdown of the miR-302/367 cluster uses the Kruppel-associated box repressor domain fused with specific TALEs designed to bind the miR-302/367 cluster promoter. Knockout of the miR-302/367 cluster uses two pairs of TALE nucleases (TALENs) to delete the miR-302/367 cluster in human primary cells. Together, both TALE-based transcriptional repressor and TALENs are two promising approaches for loss-of-function studies of microRNA cluster in human primary cells.

  18. A Circulating microRNA Signature Predicts Age-Based Development of Lymphoma.

    Directory of Open Access Journals (Sweden)

    Afshin Beheshti

    Full Text Available Extensive epidemiological data have demonstrated an exponential rise in the incidence of non-Hodgkin lymphoma (NHL that is associated with increasing age. The molecular etiology of this remains largely unknown, which impacts the effectiveness of treatment for patients. We proposed that age-dependent circulating microRNA (miRNA signatures in the host influence diffuse large B cell lymphoma (DLBCL development. Our objective was to examine tumor development in an age-based DLBCL system using an inventive systems biology approach. We harnessed a novel murine model of spontaneous DLBCL initiation (Smurf2-deficient at two age groups: 3 and 15 months old. All Smurf2-deficient mice develop visible DLBCL tumor starting at 15 months of age. Total miRNA was isolated from serum, bone marrow and spleen and were collected for all age groups for Smurf2-deficient mice and age-matched wild-type C57BL/6 mice. Using systems biology techniques, we identified a list of 10 circulating miRNAs being regulated in both the spleen and bone marrow that were present in DLBCL forming mice starting at 3 months of age that were not present in the control mice. Furthermore, this miRNA signature was found to occur circulating in the blood and it strongly impacted JUN and MYC oncogenic signaling. In addition, quantification of the miRNA signature was performed via Droplet Digital PCR technology. It was discovered that a key miRNA signature circulates throughout a host prior to the formation of a tumor starting at 3 months old, which becomes further modulated by age and yielded calculation of a 'carcinogenic risk score'. This novel age-based circulating miRNA signature may potentially be leveraged as a DLBCL risk profile at a young age to predict future lymphoma development or disease progression as well as for potential innovative miRNA-based targeted therapeutic strategies in lymphoma.

  19. Magnetic bead-based hybridization assay for electrochemical detection of microRNA

    Czech Academy of Sciences Publication Activity Database

    Bartošík, Martin; Hrstka, R.; Paleček, Emil; Vojtešek, B.

    2014-01-01

    Roč. 813, FEB2014 (2014), s. 35-40 ISSN 0003-2670 R&D Projects: GA ČR(CZ) GBP206/12/G151; GA ČR(CZ) GA13-00956S Institutional support: RVO:68081707 Keywords : MicroRNA * Electrochemistry * Mercury electrodes Subject RIV: BO - Biophysics Impact factor: 4.513, year: 2014

  20. Stability of Circulating Blood-Based MicroRNAs - Pre-Analytic Methodological Considerations

    DEFF Research Database (Denmark)

    Glinge, Charlotte; Clauss, Sebastian; Boddum, Kim

    2017-01-01

    BACKGROUND AND AIM: The potential of microRNAs (miRNA) as non-invasive diagnostic, prognostic, and predictive biomarkers, as well as therapeutic targets, has recently been recognized. Previous studies have highlighted the importance of consistency in the methodology used, but to our knowledge, no...

  1. Quantum dot-based molecular beacon to monitor intracellular microRNAs.

    Science.gov (United States)

    Lee, Jonghwan; Moon, Sung Ung; Lee, Yong Seung; Ali, Bahy A; Al-Khedhairy, Abdulaziz A; Ali, Daoud; Ahmed, Javed; Al Salem, Abdullah M; Kim, Soonhag

    2015-06-02

    Fluorescence monitoring of endogenous microRNA (miRNA or miR) activity related to neuronal development using nano-sized materials provides crucial information on miRNA expression patterns in a noninvasive manner. In this study, we report a new method to monitor intracellular miRNA124a using quantum dot-based molecular beacon (R9-QD-miR124a beacon). The R9-QD-miR124a beacon was constructed using QDs and two probes, miR124a-targeting oligomer and arginine rich cell-penetrating peptide (R9 peptide). The miR124a-targeting oligomer contains a miR124a binging sequence and a black hole quencher 1 (BHQ1). In the absence of target miR124a, the R9-QD-miR124a beacon forms a partial duplex beacon and remained in quenched state because the BHQ1 quenches the fluorescence signal of the R9-QD-miR124a beacon. The binding of miR124a to the miR124a binding sequence of the miR124a-targeting oligomer triggered the separation of the BHQ1 quencher and subsequent signal-on of a red fluorescence signal. Moreover, enhanced cellular uptake was achieved by conjugation with the R9 peptide, which resulted in increased fluorescent signal of the R9-QD-miR124a beacons in P19 cells during neurogenesis due to the endogenous expression of miR124a.

  2. Theragnosis-based combined cancer therapy using doxorubicin-conjugated microRNA-221 molecular beacon.

    Science.gov (United States)

    Lee, Jonghwan; Choi, Kyung-Ju; Moon, Sung Ung; Kim, Soonhag

    2016-01-01

    Recently, microRNA (miRNA or miR) has emerged as a new cancer biomarker because of its high expression level in various cancer types and its role in the control of tumor suppressor genes. In cancer studies, molecular imaging and treatment based on target cancer markers have been combined to facilitate simultaneous cancer diagnosis and therapy. In this study, for combined therapy with diagnosis of cancer, we developed a doxorubicin-conjugated miR-221 molecular beacon (miR-221 DOXO MB) in a single platform composed of three different nucleotides: miR-221 binding sequence, black hole quencher 1 (BHQ1), and doxorubicin binding site. Imaging of endogenous miR-221 was achieved by specific hybridization between miR-221 and the miR-221 binding site in miR-221 DOXO MB. The presence of miR-221 triggered detachment of the quencher oligo and subsequent activation of a fluorescent signal of miR-221 DOXO MB. Simultaneous cancer therapy in C6 astrocytoma cells and nude mice was achieved by inhibition of miRNA-221 function that downregulates tumor suppressor genes. The detection of miR-221 expression and inhibition of miR-221 function by miR-221 DOXO MB provide the feasibility as a cancer theragnostic probe. Furthermore, a cytotoxic effect was induced by unloading of doxorubicin intercalated into miR-221 DOXO MB inside cells. Loss of miR-221 function and cytotoxicity induced by the miR-221 DOXO MB provides combined therapeutic efficacy against cancers. This method could be used as a new theragnostic probe with enhanced therapy to detect and inhibit many cancer-related miRNAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Quantum Dot-Based Molecular Beacon to Monitor Intracellular MicroRNAs

    Directory of Open Access Journals (Sweden)

    Jonghwan Lee

    2015-06-01

    Full Text Available Fluorescence monitoring of endogenous microRNA (miRNA or miR activity related to neuronal development using nano-sized materials provides crucial information on miRNA expression patterns in a noninvasive manner. In this study, we report a new method to monitor intracellular miRNA124a using quantum dot-based molecular beacon (R9-QD-miR124a beacon. The R9-QD-miR124a beacon was constructed using QDs and two probes, miR124a-targeting oligomer and arginine rich cell-penetrating peptide (R9 peptide. The miR124a-targeting oligomer contains a miR124a binging sequence and a black hole quencher 1 (BHQ1. In the absence of target miR124a, the R9-QD-miR124a beacon forms a partial duplex beacon and remained in quenched state because the BHQ1 quenches the fluorescence signal of the R9-QD-miR124a beacon. The binding of miR124a to the miR124a binding sequence of the miR124a-targeting oligomer triggered the separation of the BHQ1 quencher and subsequent signal-on of a red fluorescence signal. Moreover, enhanced cellular uptake was achieved by conjugation with the R9 peptide, which resulted in increased fluorescent signal of the R9-QD-miR124a beacons in P19 cells during neurogenesis due to the endogenous expression of miR124a.

  4. Sulfonic-based precursors (SAPs for silica mesostructures: Advances in synthesis and applications

    Directory of Open Access Journals (Sweden)

    Sadegh Rostamnia*

    2016-01-01

    Full Text Available Sulfonic acid-based precursors (SAP play an important role in tailoring mesoporous silica’s and convert them to a solid acid catalyst with a Bronsted-type nature. These kinds of solid acids contribute to sustainable and green chemistry by their heterogeneous, recyclable, and high efficiency features. Therefore, knowing the properties and reactivity of SAPs can guide us to manufacture a sulfonated mesostructures compatible with reaction type and conditions. In the present review, some of the important SAPs, their reactivity and mechanism of functionalization are discussed.

  5. Systematic validation of predicted microRNAs for cyclin D1

    International Nuclear Information System (INIS)

    Jiang, Qiong; Feng, Ming-Guang; Mo, Yin-Yuan

    2009-01-01

    MicroRNAs are the endogenous small non-coding RNA molecules capable of silencing protein coding genes at the posttranscriptional level. Based on computer-aided predictions, a single microRNA could have over a hundred of targets. On the other hand, a single protein-coding gene could be targeted by many potential microRNAs. However, only a relatively small number of these predicted microRNA/mRNA interactions are experimentally validated, and no systematic validation has been carried out using a reporter system. In this study, we used luciferease reporter assays to validate microRNAs that can silence cyclin D1 (CCND1) because CCND1 is a well known proto-oncogene implicated in a variety of types of cancers. We chose miRanda (http://www.microRNA.org) as a primary prediction method. We then cloned 51 of 58 predicted microRNA precursors into pCDH-CMV-MCS-EF1-copGFP and tested for their effect on the luciferase reporter carrying the 3'-untranslated region (UTR) of CCND1 gene. Real-time PCR revealed the 45 of 51 cloned microRNA precursors expressed a relatively high level of the exogenous microRNAs which were used in our validation experiments. By an arbitrary cutoff of 35% reduction, we identified 7 microRNAs that were able to suppress Luc-CCND1-UTR activity. Among them, 4 of them were previously validated targets and the rest 3 microRNAs were validated to be positive in this study. Of interest, we found that miR-503 not only suppressed the luciferase activity, but also suppressed the endogenous CCND1 both at protein and mRNA levels. Furthermore, we showed that miR-503 was able to reduce S phase cell populations and caused cell growth inhibition, suggesting that miR-503 may be a putative tumor suppressor. This study provides a more comprehensive picture of microRNA/CCND1 interactions and it further demonstrates the importance of experimental target validation

  6. A novel vector-based method for exclusive overexpression of star-form microRNAs.

    Directory of Open Access Journals (Sweden)

    Bo Qu

    Full Text Available The roles of microRNAs (miRNAs as important regulators of gene expression have been studied intensively. Although most of these investigations have involved the highly expressed form of the two mature miRNA species, increasing evidence points to essential roles for star-form microRNAs (miRNA*, which are usually expressed at much lower levels. Owing to the nature of miRNA biogenesis, it is challenging to use plasmids containing miRNA coding sequences for gain-of-function experiments concerning the roles of microRNA* species. Synthetic microRNA mimics could introduce specific miRNA* species into cells, but this transient overexpression system has many shortcomings. Here, we report that specific miRNA* species can be overexpressed by introducing artificially designed stem-loop sequences into short hairpin RNA (shRNA overexpression vectors. By our prototypic plasmid, designed to overexpress hsa-miR-146b-3p, we successfully expressed high levels of hsa-miR-146b-3p without detectable change of hsa-miR-146b-5p. Functional analysis involving luciferase reporter assays showed that, like natural miRNAs, the overexpressed hsa-miR-146b-3p inhibited target gene expression by 3'UTR seed pairing. Our demonstration that this method could overexpress two other miRNAs suggests that the approach should be broadly applicable. Our novel strategy opens the way for exclusively stable overexpression of miRNA* species and analyzing their unique functions both in vitro and in vivo.

  7. Differently-catalyzed silica-based precursors as functional additives for the epoxy-based hybrid materials

    Czech Academy of Sciences Publication Activity Database

    Perchacz, Magdalena; Beneš, Hynek; Zhigunov, Alexander; Serkis, Magdalena; Pavlova, Ewa

    2016-01-01

    Roč. 99, 2 September (2016), s. 434-446 ISSN 0032-3861 R&D Projects: GA ČR(CZ) GA14-05146S; GA MŠk(CZ) LO1507 Institutional support: RVO:61389013 Keywords : epoxy-silica hybrid material * solvent-free sol-gel process * silica-based precursor Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.684, year: 2016

  8. Signal-on electrochemiluminescence biosensor for microRNA-319a detection based on two-stage isothermal strand-displacement polymerase reaction.

    Science.gov (United States)

    Wang, Minghui; Zhou, Yunlei; Yin, Huanshun; Jiang, Wenjing; Wang, Haiyan; Ai, Shiyun

    2018-06-01

    MicroRNAs play crucial role in regulating gene expression in organism, thus it is very necessary to exploit an efficient method for the sensitive and specific detection of microRNA. Herein, a signal-on electrochemiluminescence biosensor was fabricated for microRNA-319a detection based on two-stage isothermal strand-displacement polymerase reaction (ISDPR). In the presence of target microRNA, amounts of trigger DNA could be generated by the first ISDPR. Then, the trigger DNA and the primer hybridized simultaneously with the hairpin probe to open the stem of the probe, and then the ECL signal will be emitted. In the presence of phi29 DNA polymerase and dNTPs, the trigger DNA could be displaced to initiate a new cycle which was the second ISDPR. Due to the two-stage amplification, this method presented excellent detection sensitivity with a low detection limit of 0.14 fM. Moreover, the applicability of the developed method was demonstrated by detecting the change of microRNA-319a content in the leaves of rice seedlings after the rice seeds were incubated with chemical mutagen of ethyl methanesulfonate. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Synthesis of encapsulated pigments based on Fe, Co and Si by route of polymeric precursors

    International Nuclear Information System (INIS)

    Macedo, D.S.S.M.; Macedo Neto, O.C.; Paskocimas, C.A.; Varela, M.L.N.

    2012-01-01

    The objective is to apply the polymeric precursor method to obtain encapsulated pigments, the basis of oxides of iron and cobalt deposited on silica. The method has advantages such as reduction of time and reproducibility in the conventional methods, and also improves optical properties, thermal stability and morphology. The synthesis was based on the dissolution of the citric acid (complexing agent), addition of oxides of iron and cobalt (ions chromophores) polymerization of ethylene glycol and silica coating. The mixture was pre-calcined to form the precursor powder was analyzed by TG and DTA. Was then split, and calcined at different temperatures (700 ° C - 900 ° C) and analyzed by BET, DRX, MEV and UV-Visible. The pigments were stable thermally, with surface area ranging between 3,09 and 7,65 m² / g, formation of crystalline phases of cobalt ferrite (CoFe 2 O 4 ) and Cristobalite (SiO 2 ) and agglomerates of particles slightly rounded. (author)

  10. Intermediate obtained from photoionization, serving as precursor for the synthesis of Schiff’s base

    Directory of Open Access Journals (Sweden)

    R. Sanjeev

    2014-05-01

    Full Text Available In this article, we have introduced an intermediate benzyl carbocation (formed as a result of photoionization which serves as precursor for the synthesis of Schiff’s base. Lifetimes of many carbocations were determined from our laboratory. During the determination of the lifetimes, our endeavor was to obtain a carbocation with high selectivity, s = knu/kH2O. The selectivity is the ratio of the rate constant of the reaction of carbocation with an externally added nucleophile, (nu, aniline to that of the rate constant of the water. Our intention was to obtain a carbocation with high selectivity, so that one can pave a path for the synthesis of Schiff’s base by the reaction of the carbocation intermediate with aniline. DOI: http://dx.doi.org/10.4314/bcse.v28i2.13

  11. Formation of Micro and Mesoporous Amorphous Silica-Based Materials from Single Source Precursors

    Directory of Open Access Journals (Sweden)

    Mohd Nazri Mohd Sokri

    2016-03-01

    Full Text Available Polysilazanes functionalized with alkoxy groups were designed and synthesized as single source precursors for fabrication of micro and mesoporous amorphous silica-based materials. The pyrolytic behaviors during the polymer to ceramic conversion were studied by the simultaneous thermogravimetry-mass spectrometry (TG-MS analysis. The porosity of the resulting ceramics was characterized by the N2 adsorption/desorption isotherm measurements. The Fourier transform infrared spectroscopy (FT-IR and Raman spectroscopic analyses as well as elemental composition analysis were performed on the polymer-derived amorphous silica-based materials, and the role of the alkoxy group as a sacrificial template for the micro and mesopore formations was discussed from a viewpoint to establish novel micro and mesoporous structure controlling technologies through the polymer-derived ceramics (PDCs route.

  12. Effect of Chemical Prevention Drugs-based MicroRNAs and Their Target Genes 
on Tumor Inhibition

    Directory of Open Access Journals (Sweden)

    Yanhui JIANG

    2015-04-01

    Full Text Available Chemopreventive drugs including natural chemopreventive drugs and synthetic chemopreventive drugs, it not only can prevent cancer, can also play a role in tumor treatment. MicroRNAs (miRNAs is a kind of short chains of non-coding RNA, regulating the expression of many genes through the way of degradation of mRNA or inhibitting mRNA translation. In recent years, more and more studies have shown that chemopreventive drugs through influence the expression of miRNAs and their target genes play a role in the prevention and treatment in a variety of tumors, and chemopreventive drugs on the experimental study of miRNAs and their target genes in tumor have demonstrated a good safety and efficacy. Effect on chemopreventive drugs-based microRNAs and their target genes into cancer cells will be expected as a new starting point for cancer research. The thesis expounds and analyzes between the natural chemopreventive drugs and synthetic chemopreventive drugs and miRNAs and their target genes in tumor research progress.

  13. An integrated one-chip-sensor system for microRNA quantitative analysis based on digital droplet polymerase chain reaction

    Science.gov (United States)

    Tsukuda, Masahiko; Wiederkehr, Rodrigo Sergio; Cai, Qing; Majeed, Bivragh; Fiorini, Paolo; Stakenborg, Tim; Matsuno, Toshinobu

    2016-04-01

    A silicon microfluidic chip was developed for microRNA (miRNA) quantitative analysis. It performs sequentially reverse transcription and polymerase chain reaction in a digital droplet format. Individual processes take place on different cavities, and reagent and sample mixing is carried out on a chip, prior to entering each compartment. The droplets are generated on a T-junction channel before the polymerase chain reaction step. Also, a miniaturized fluorescence detector was developed, based on an optical pick-up head of digital versatile disc (DVD) and a micro-photomultiplier tube. The chip integrated in the detection system was tested using synthetic miRNA with known concentrations, ranging from 300 to 3,000 templates/µL. Results proved the functionality of the system.

  14. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

    Science.gov (United States)

    Hackenberg, Michael; Rodríguez-Ezpeleta, Naiara; Aransay, Ana M.

    2011-01-01

    We present a new version of miRanalyzer, a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features. Alignments are now based on the ultrafast short-read aligner Bowtie (granting also colour space support, allowing mismatches and improving speed) and 31 genomes, including 6 plant genomes, can now be analysed (previous version contained only 7). Differences between plant and animal microRNAs have been taken into account for the prediction models and differential expression of both, known and predicted microRNAs, between two conditions can be calculated. Additionally, consensus sequences of predicted mature and precursor microRNAs can be obtained from multiple samples, which increases the reliability of the predicted microRNAs. Finally, a stand-alone version of the miRanalyzer that is based on a local and easily customized database is also available; this allows the user to have more control on certain parameters as well as to use specific data such as unpublished assemblies or other libraries that are not available in the web server. miRanalyzer is available at http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php. PMID:21515631

  15. A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources.

    Directory of Open Access Journals (Sweden)

    Jun-Zhi Wen

    Full Text Available MicroRNAs (miRNAs are important regulators of many cellular processes and exist in a wide range of eukaryotes. High-throughput sequencing is a mainstream method of miRNA identification through which it is possible to obtain the complete small RNA profile of an organism. Currently, most approaches to miRNA identification rely on a reference genome for the prediction of hairpin structures. However, many species of economic and phylogenetic importance are non-model organisms without complete genome sequences, and this limits miRNA discovery. Here, to overcome this limitation, we have developed a contig-based miRNA identification strategy. We applied this method to a triploid species of edible banana (GCTCV-119, Musa spp. AAA group and identified 180 pre-miRNAs and 314 mature miRNAs, which is three times more than those were predicted by the available dataset-based methods (represented by EST+GSS. Based on the recently published miRNA data set of Musa acuminate, the recall rate and precision of our strategy are estimated to be 70.6% and 92.2%, respectively, significantly better than those of EST+GSS-based strategy (10.2% and 50.0%, respectively. Our novel, efficient and cost-effective strategy facilitates the study of the functional and evolutionary role of miRNAs, as well as miRNA-based molecular breeding, in non-model species of economic or evolutionary interest.

  16. Effects of Chemical Curing Temperature and Time on the Properties of Liquefied Wood based As-cured Precursors and Carbon Fibers

    Directory of Open Access Journals (Sweden)

    Junbo Shang

    2015-09-01

    Full Text Available Liquefied wood based as-cured precursors and carbon fibers prepared by different chemical curing processes were carried out to investigate the effects of curing temperature and time on the thermostability and microstructure of liquefied wood based precursors, the tensile strength of carbon fibers as well. The primary fibers can be converted into precursors with high performance by directly heating at target curing temperature. With the temperature and duration increasing, the numbers of methylene bonds in precursors increased, resulting in the enhancement of cross-linkages among molecular chains and then the improvement of thermostability of precursors. Carbon fibers prepared from as-cured precursors (curing temperature 95 oC, curing time 3h had the minimum value of the average interlayer spacing (d002, it also showed the highest tensile strength, almost 800 MPa, which can be classified as fibers of general grade.

  17. A collagen-based scaffold delivering exogenous microrna-29B to modulate extracellular matrix remodeling.

    Science.gov (United States)

    Monaghan, Michael; Browne, Shane; Schenke-Layland, Katja; Pandit, Abhay

    2014-04-01

    Directing appropriate extracellular matrix remodeling is a key aim of regenerative medicine strategies. Thus, antifibrotic interfering RNA (RNAi) therapy with exogenous microRNA (miR)-29B was proposed as a method to modulate extracellular matrix remodeling following cutaneous injury. It was hypothesized that delivery of miR-29B from a collagen scaffold will efficiently modulate the extracellular matrix remodeling response and reduce maladaptive remodeling such as aggressive deposition of collagen type I after injury. The release of RNA from the scaffold was assessed and its ability to silence collagen type I and collagen type III expression was evaluated in vitro. When primary fibroblasts were cultured with scaffolds doped with miR-29B, reduced levels of collagen type I and collagen type III mRNA expression were observed for up to 2 weeks of culture. When the scaffolds were applied to full thickness wounds in vivo, reduced wound contraction, improved collagen type III/I ratios and a significantly higher matrix metalloproteinase (MMP)-8: tissue inhibitor of metalloproteinase (TIMP)-1 ratio were detected when the scaffolds were functionalized with miR-29B. Furthermore, these effects were significantly influenced by the dose of miR-29B in the collagen scaffold (0.5 versus 5 μg). This study shows a potential of combining exogenous miRs with collagen scaffolds to improve extracellular matrix remodeling following injury.

  18. Web-based tools for microRNAs involved in human cancer.

    Science.gov (United States)

    Mar-Aguilar, Fermín; Rodríguez-Padilla, Cristina; Reséndez-Pérez, Diana

    2016-06-01

    MicroRNAs (miRNAs/miRs) are a family of small, endogenous and evolutionarily-conserved non-coding RNAs that are involved in the regulation of several cellular and functional processes. miRNAs can act as oncogenes or tumor suppressors in all types of cancer, and could be used as prognostic and diagnostic biomarkers. Databases and computational algorithms are behind the majority of the research performed on miRNAs. These tools assemble and curate the relevant information on miRNAs and present it in a user-friendly manner. The current review presents 14 online databases that address every aspect of miRNA cancer research. Certain databases focus on miRNAs and a particular type of cancer, while others analyze the behavior of miRNAs in different malignancies at the same time. Additional databases allow researchers to search for mutations in miRNAs or their targets, and to review the naming history of a particular miRNA. All these databases are open-access, and are a valuable tool for those researchers working with these molecules, particularly those who lack access to an advanced computational infrastructure.

  19. DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.

    Science.gov (United States)

    Yang, Jian-Hua; Qu, Liang-Hu

    2012-01-01

    Recent advances in high-throughput deep-sequencing technology have produced large numbers of short and long RNA sequences and enabled the detection and profiling of known and novel microRNAs (miRNAs) and other noncoding RNAs (ncRNAs) at unprecedented sensitivity and depth. In this chapter, we describe the use of deepBase, a database that we have developed to integrate all public deep-sequencing data and to facilitate the comprehensive annotation and discovery of miRNAs and other ncRNAs from these data. deepBase provides an integrative, interactive, and versatile web graphical interface to evaluate miRBase-annotated miRNA genes and other known ncRNAs, explores the expression patterns of miRNAs and other ncRNAs, and discovers novel miRNAs and other ncRNAs from deep-sequencing data. deepBase also provides a deepView genome browser to comparatively analyze these data at multiple levels. deepBase is available at http://deepbase.sysu.edu.cn/.

  20. Redefining high-risk patients with stage II colon cancer by risk index and microRNA-21: results from a population-based cohort

    DEFF Research Database (Denmark)

    Hansen, T F; Kjær-Frifeldt, S; Christensen, R D

    2014-01-01

    Background:The aim of the present study was to analyse the prognostic value of microRNA-21 (miRNA-21) in patients with stage II colon cancer aiming at a risk index for this group of patients.Methods:A population-based cohort of 554 patients was included. MicroRNA-21 was analysed by qPCR based.......001). The overall survival (OS) index identified three different subgroups (Pcolon cancer. Furthermore...... on tumour tissue. An index was created using the coefficients obtained from a collective multiple Cox regression. The entire procedure was cross-validated (10-fold). The performance of the index was quantified by time-dependent receiver operating characteristics curves.Results:High miRNA-21 expression...

  1. Selection of events at Ukrainian NPPs using the algorithm based on accident precursor method

    International Nuclear Information System (INIS)

    Vorontsov, D.V.; Lyigots'kij, O.Yi.; Serafin, R.Yi.; Tkachova, L.M.

    2012-01-01

    The paper describes a general approach to the first stage of research and development on analysis of Ukrainian NPP operation events from 1 January 2000 to 31 December 2010 using the accident precursor approach. Groups of potentially important events formed after their selection and classification are provided

  2. Cancer Exosomes Perform Cell-Independent MicroRNA Biogenesis and Promote Tumorigenesis

    Science.gov (United States)

    Melo, Sonia A.; Sugimoto, Hikaru; O’Connell, Joyce T.; Kato, Noritoshi; Villanueva, Alberto; Vidal, August; Qiu, Le; Vitkin, Edward; Perelman, Lev T.; Melo, Carlos A.; Lucci, Anthony; Ivan, Cristina; Calin, George A.; Kalluri, Raghu

    2014-01-01

    SUMMARY Exosomes are secreted by all cell types and contain proteins and nucleic acids. Here, we report that breast cancer associated exosomes contain microRNAs (miRNAs) associated with the RISC Loading Complex (RLC) and display cell-independent capacity to process precursor microRNAs (pre-miRNAs) into mature miRNAs. Pre-miRNAs, along with Dicer, AGO2, and TRBP, are present in exosomes of cancer cells. CD43 mediates the accumulation of Dicer specifically in cancer exosomes. Cancer exosomes mediate an efficient and rapid silencing of mRNAs to reprogram the target cell transcriptome. Exosomes derived from cells and sera of patients with breast cancer instigate non-tumorigenic epithelial cells to form tumors in a Dicer-dependent manner. These findings offer opportunities for the development of exosomes based biomarkers and therapies. PMID:25446899

  3. Using an Internet-Based Breast Cancer Risk Assessment Tool to Improve Social-Cognitive Precursors of Physical Activity.

    Science.gov (United States)

    Fowler, Stephanie L; Klein, William M P; Ball, Linda; McGuire, Jaclyn; Colditz, Graham A; Waters, Erika A

    2017-08-01

    Internet-based cancer risk assessment tools might serve as a strategy for translating epidemiological risk prediction research into public health practice. Understanding how such tools affect key social-cognitive precursors of behavior change is crucial for leveraging their potential into effective interventions. To test the effects of a publicly available, Internet-based, breast cancer risk assessment tool on social-cognitive precursors of physical activity. Women (N = 132) aged 40-78 with no personal cancer history indicated their perceived risk of breast cancer and were randomly assigned to receive personalized ( www.yourdiseaserisk.wustl.edu ) or nonpersonalized breast cancer risk information. Immediately thereafter, breast cancer risk perceptions and physical activity-related behavioral intentions, self-efficacy, and response efficacy were assessed. Personalized information elicited higher intentions, self-efficacy, and response efficacy than nonpersonalized information, P values Internet-based risk assessment tools can produce beneficial effects on important social-cognitive precursors of behavior change, but lingering skepticism, possibly due to defensive processing, needs to be addressed before the effects can be maximized.

  4. Polymerase-free measurement of microRNA-122 with single base specificity using single molecule arrays: Detection of drug-induced liver injury.

    Directory of Open Access Journals (Sweden)

    David M Rissin

    Full Text Available We have developed a single probe method for detecting microRNA from human serum using single molecule arrays, with sequence specificity down to a single base, and without the use of amplification by polymerases. An abasic peptide nucleic acid (PNA probe-containing a reactive amine instead of a nucleotide at a specific position in the sequence-for detecting a microRNA was conjugated to superparamagnetic beads. These beads were incubated with a sample containing microRNA, a biotinylated reactive nucleobase-containing an aldehyde group-that was complementary to the missing base in the probe sequence, and a reducing agent. When a target molecule with an exact match in sequence hybridized to the capture probe, the reactive nucleobase was covalently attached to the backbone of the probe by a dynamic covalent chemical reaction. Single molecules of the biotin-labeled probe were then labeled with streptavidin-β-galactosidase (SβG, the beads were resuspended in a fluorogenic enzyme substrate, loaded into an array of femtoliter wells, and sealed with oil. The array was imaged fluorescently to determine which beads were associated with single enzymes, and the average number of enzymes per bead was determined. The assay had a limit of detection of 500 fM, approximately 500 times more sensitive than a corresponding analog bead-based assay, with target specificity down to a single base mis-match. This assay was used to measure microRNA-122 (miR-122-an established biomarker of liver toxicity-extracted from the serum of patients who had acute liver injury due to acetaminophen, and control healthy patients. All patients with liver injury had higher levels of miR-122 in their serum compared to controls, and the concentrations measured correlated well with those determined using RT-qPCR. This approach allows rapid quantification of circulating microRNA with single-based specificity and a limit of quantification suitable for clinical use.

  5. Annotation of novel neuropeptide precursors in the migratory locust based on transcript screening of a public EST database and mass spectrometry

    Directory of Open Access Journals (Sweden)

    De Loof Arnold

    2006-08-01

    Full Text Available Abstract Background For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, have been far less studied. The migratory locust Locusta migratoria, a heterometabolous insect, is one of the most infamous agricultural pests. They undergo a well-known and profound phase transition from the relatively harmless solitary form to a ferocious gregarious form. The underlying regulatory mechanisms of this phase transition are not fully understood, but it is undoubtedly that neuropeptides are involved. However, neuropeptide research in locusts is hampered by the absence of genomic information. Results Recently, EST (Expressed Sequence Tag databases from Locusta migratoria were constructed. Using bioinformatical tools, we searched these EST databases specifically for neuropeptide precursors. Based on known locust neuropeptide sequences, we confirmed the sequence of several previously identified neuropeptide precursors (i.e. pacifastin-related peptides, which consolidated our method. In addition, we found two novel neuroparsin precursors and annotated the hitherto unknown tachykinin precursor. Besides one of the known tachykinin peptides, this EST contained an additional tachykinin-like sequence. Using neuropeptide precursors from Drosophila melanogaster as a query, we succeeded in annotating the Locusta neuropeptide F, allatostatin-C and ecdysis-triggering hormone precursor, which until now had not been identified in locusts or in any other heterometabolous insect. For the tachykinin precursor, the ecdysis-triggering hormone precursor and the allatostatin-C precursor, translation of the predicted neuropeptides in neural tissues was confirmed with mass spectrometric techniques. Conclusion In this study we describe the annotation of 6 novel neuropeptide precursors and the neuropeptides they encode from the

  6. Microarray-based approach identifies microRNAs and their target functional patterns in polycystic kidney disease

    Directory of Open Access Journals (Sweden)

    Boehn Susanne NE

    2008-12-01

    Full Text Available Abstract Background MicroRNAs (miRNAs play key roles in mammalian gene expression and several cellular processes, including differentiation, development, apoptosis and cancer pathomechanisms. Recently the biological importance of primary cilia has been recognized in a number of human genetic diseases. Numerous disorders are related to cilia dysfunction, including polycystic kidney disease (PKD. Although involvement of certain genes and transcriptional networks in PKD development has been shown, not much is known how they are regulated molecularly. Results Given the emerging role of miRNAs in gene expression, we explored the possibilities of miRNA-based regulations in PKD. Here, we analyzed the simultaneous expression changes of miRNAs and mRNAs by microarrays. 935 genes, classified into 24 functional categories, were differentially regulated between PKD and control animals. In parallel, 30 miRNAs were differentially regulated in PKD rats: our results suggest that several miRNAs might be involved in regulating genetic switches in PKD. Furthermore, we describe some newly detected miRNAs, miR-31 and miR-217, in the kidney which have not been reported previously. We determine functionally related gene sets, or pathways to reveal the functional correlation between differentially expressed mRNAs and miRNAs. Conclusion We find that the functional patterns of predicted miRNA targets and differentially expressed mRNAs are similar. Our results suggest an important role of miRNAs in specific pathways underlying PKD.

  7. Alkoxide-based precursors for direct drawing of metal oxide micro- and nanofibres

    Energy Technology Data Exchange (ETDEWEB)

    Taette, Tanel; Hussainov, Medhat; Paalo, Madis; Part, Marko; Talviste, Rasmus; Kiisk, Valter; Maendar, Hugo; Pohako, Kaija; Reivelt, Kaido; Lohmus, Ants [Institute of Physics, University of Tartu, Riia 142, Tartu 51014 (Estonia); Pehk, Tonis [National Institute of Chemical and Biological Physics, Akadeemia tee 23, Tallinn 12618 (Estonia); Natali, Marco [ICIS-CNR, Corso Stati Uniti 4, Padova 35127 (Italy); Gurauskis, Jonas [Instituto de Ciencia de Materiales de Aragon C.S.I.C., University of Zaragoza Fac. De Ciencias, c/Pedro Cerbuna 12, Zaragoza 50009 (Spain); Maeeorg, Uno, E-mail: tanelt@fi.tartu.ee [Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411 (Estonia)

    2011-06-15

    The invention of electrospinning has solved the problem of producing micro- and nanoscaled metal oxide fibres in bulk quantities. However, until now no methods have been available for preparing a single nanofibre of a metal oxide. In this work, the direct drawing method was successfully applied to produce metal oxide (SnO{sub 2}, TiO{sub 2}, ZrO{sub 2}, HfO{sub 2} and CeO{sub 2}) fibres with a high aspect ratio (up to 10 000) and a diameter as small as 200 nm. The sol-gel processing includes consumption of precursors obtained from alkoxides by aqueous or non-aqueous polymerization. Shear thinning of the precursors enables pulling a material into a fibre. This rheological behaviour can be explained by sliding of particles owing to external forces. Transmission (propagation) of light along microscaled fibres and their excellent surface morphology suggest that metal oxide nanofibres can be directly drawn from sol precursors for use in integrated photonic systems.

  8. Direct nanoimprint lithography of Al2O3 using a chelated monomer-based precursor

    International Nuclear Information System (INIS)

    Ganesan, Ramakrishnan; Dinachali, Saman Safari; Lim, Su Hui; Saifullah, M S M; He, Chaobin; Low, Hong Yee; Chong, Wee Tit; Lim, Andrew H H; Yong, Jin Jie; Thian, Eng San

    2012-01-01

    Nanostructuring of Al 2 O 3 is predominantly achieved by the anodization of aluminum film and is limited to obtaining porous anodized aluminum oxide (AAO). One of the main restrictions in developing approaches for direct fabrication of various types of Al 2 O 3 patterns, such as lines, pillars, holes, etc, is the lack of a processable aluminum-containing resist. In this paper, we demonstrate a stable precursor prepared by reacting aluminum tri-sec-butoxide with 2-(methacryloyloxy)ethyl acetoacetate, a chelating monomer, which can be used for large area direct nanoimprint lithography of Al 2 O 3 . Chelation in the precursor makes it stable against hydrolysis whilst the presence of a reactive methacrylate group renders it polymerizable. The precursor was mixed with a cross-linker and their in situ thermal free-radical co-polymerization during nanoimprinting rigidly shaped the patterns, trapped the metal atoms, reduced the surface energy and strengthened the structures, thereby giving a ∼100% yield after demolding. The imprinted structures were heat-treated, leading to the loss of organics and their subsequent shrinkage. Amorphous Al 2 O 3 patterns with line-widths as small as 17 nm were obtained. Our process utilizes the advantages of sol–gel and methacrylate routes for imprinting and at the same time alleviates the disadvantages associated with both these methods. With these benefits, the chelating monomer route may be the harbinger of the universal scheme for direct nanoimprinting of metal oxides. (paper)

  9. Vanadium oxides supported on hydrotalcite-type precursors: the effect of acid-base properties on the oxidation of isopropanol

    Directory of Open Access Journals (Sweden)

    D. M. Meira

    2006-09-01

    Full Text Available Vanadium oxide supported on hydrotalcite-type precursors was studied in the oxidation of isopropanol. Hydrotalcites with different y = Mg/Al ratios were synthesized by the method of coprecipitation nitrates of Mg and Al cations with K2CO3 as precipitant. The decomposition of these hydrotalcite precursors at 450°C yielded homogeneous MgyAlOx mixed oxides that contain the Al+3 cations totally incorporated into the MgO framework. The materials were characterized by chemical analysis, BET superficial area, X-ray diffraction, temperature-programmed reduction (TPR and the reaction of isopropanol, a probe molecule used to evaluate the acid-base properties. The results of TPR showed that the reducibility of V+5 decreased with the increase in magnesium loading in catalysts. The X-ray diffraction patterns of Al-rich hydrotalcite precursors showed the presence of crystalline phases of brucite and gibbsite. It was shown that chemical composition, texture, acid-base properties of the active sites and also Mg/Al ratio strongly affect the formation of the products in the oxidation of isopropanol. The Al-rich catalysts were much more active than the Mg-rich ones, converting isopropanol mainly to propylene.

  10. Vanadium oxides supported on hydrotalcite-type precursors: the effect of acid base properties on the oxidation of isopropanol

    Energy Technology Data Exchange (ETDEWEB)

    Meira, D.M.; Cortez, G.G. [Faculdade de Engenharia Quimica de Lorena, Lorena, SP (Brazil). Dept. de Engenharia Quimica. Lab. de Catalise II]. E-mail: cortez@dequi.faenquil.br; Monteiro, W.R.; Rodrigues, J.A.J. [Instituto Nacional de Pesquisas Espaciais (INPE), Sao Jose dos Campos, SP (Brazil). Lab. Associado de Combustao e Propulsao]. E-mail: jajr@lcp.inpe.br

    2006-07-15

    Vanadium oxide supported on hydrotalcite-type precursors was studied in the oxidation of isopropanol. Hydrotalcites with different y = Mg/Al ratios were synthesized by the method of coprecipitation nitrates of Mg and Al cations with K{sub 2}CO{sub 3} as precipitant. The decomposition of these hydrotalcite precursors at 450 deg C yielded homogeneous MgyAlOx mixed oxides that contain the Al{sup +3} cations totally incorporated into the MgO framework. The materials were characterized by chemical analysis, BET superficial area, X-ray diffraction, temperature-programmed reduction (TPR) and the reaction of isopropanol, a probe molecule used to evaluate the acid-base properties. The results of TPR showed that the reducibility of V{sup +5} decreased with the increase in magnesium loading in catalysts. The X-ray diffraction patterns of Al-rich hydrotalcite precursors showed the presence of crystalline phases of brucite and gibbsite. It was shown that chemical composition, texture, acid-base properties of the active sites and also Mg/Al ratio strongly affect the formation of the products in the oxidation of isopropanol. The Al-rich catalysts were much more active than the Mg-rich ones, converting isopropanol mainly to propylene. (author)

  11. Stability of Circulating Blood-Based MicroRNAs - Pre-Analytic Methodological Considerations.

    Directory of Open Access Journals (Sweden)

    Charlotte Glinge

    Full Text Available The potential of microRNAs (miRNA as non-invasive diagnostic, prognostic, and predictive biomarkers, as well as therapeutic targets, has recently been recognized. Previous studies have highlighted the importance of consistency in the methodology used, but to our knowledge, no study has described the methodology of sample preparation and storage systematically with respect to miRNAs as blood biomarkers. The aim of this study was to investigate the stability of miRNAs in blood under various relevant clinical and research conditions: different collection tubes, storage at different temperatures, physical disturbance, as well as serial freeze-thaw cycles.Blood samples were collected from 12 healthy donors into different collection tubes containing anticoagulants, including EDTA, citrate and lithium-heparin, as well as into serum collection tubes. MiRNA stability was evaluated by measuring expression changes of miR-1, miR-21 and miR-29b at different conditions: varying processing time of whole blood (up to 72 hours (h, long-term storage (9 months at -80°C, physical disturbance (1 and 8 h, as well as in a series of freeze/thaw cycles (1 and 4 times.Different collection tubes revealed comparable concentrations of miR-1, miR-21 and miR-29b. Tubes with lithium-heparin were found unsuitable for miRNA quantification. MiRNA levels were stable for at least 24 h at room temperature in whole blood, while separated fractions did show alterations within 24 h. There were significant changes in the miR-21 and miR-29b levels after 72 h incubation of whole blood at room temperature (p<0.01 for both. Both miR-1 and miR-21 showed decreased levels after physical disturbance for 8 h in separated plasma and miR-1 in serum whole blood, while after 1 h of disturbance no changes were observed. Storage of samples at -80°C extended the miRNA stability remarkably, however, miRNA levels in long-term stored (9 months whole blood samples were significantly changed, which is in

  12. Large scale synthesis of nanostructured zirconia-based compounds from freeze-dried precursors

    International Nuclear Information System (INIS)

    Gómez, A.; Villanueva, R.; Vie, D.; Murcia-Mascaros, S.; Martínez, E.; Beltrán, A.; Sapiña, F.; Vicent, M.; Sánchez, E.

    2013-01-01

    Nanocrystalline zirconia powders have been obtained at the multigram scale by thermal decomposition of precursors resulting from the freeze-drying of aqueous acetic solutions. This technique has equally made possible to synthesize a variety of nanostructured yttria or scandia doped zirconia compositions. SEM images, as well as the analysis of the XRD patterns, show the nanoparticulated character of those solids obtained at low temperature, with typical particle size in the 10–15 nm range when prepared at 673 K. The presence of the monoclinic, the tetragonal or both phases depends on the temperature of the thermal treatment, the doping concentration and the nature of the dopant. In addition, Rietveld refinement of the XRD profiles of selected samples allows detecting the coexistence of the tetragonal and the cubic phases for high doping concentration and high thermal treatment temperatures. Raman experiments suggest the presence of both phases also at relatively low treatment temperatures. - Graphical abstract: Zr 1−x A x O 2−x/2 (A=Y, Sc; 0≤x≤0.12) solid solutions have been prepared as nanostructured powders by thermal decomposition of precursors obtained by freeze-drying, and this synthetic procedure has been scaled up to the 100 g scale. Highlights: ► Zr 1−x A x O 2−x/2 (A=Y, Sc; 0≤x≤0.12) solid solutions have been prepared as nanostructured powders. ► The synthetic method involves the thermal decomposition of precursors obtained by freeze-drying. ► The temperature of the thermal treatment controls particle sizes. ► The preparation procedure has been scaled up to the 100 g scale. ► This method is appropriate for the large-scale industrial preparation of multimetallic systems.

  13. Natural precursor based hydrothermal synthesis of sodium carbide for reactor applications

    Science.gov (United States)

    Swapna, M. S.; Saritha Devi, H. V.; Sebastian, Riya; Ambadas, G.; Sankararaman, S.

    2017-12-01

    Carbides are a class of materials with high mechanical strength and refractory nature which finds a wide range of applications in industries and nuclear reactors. The existing synthesis methods of all types of carbides have problems in terms of use of toxic chemical precursors, high-cost, etc. Sodium carbide (Na2C2) which is an alkali metal carbide is the least explored one and also that there is no report of low-cost and low-temperature synthesis of sodium carbide using the eco-friendly, easily available natural precursors. In the present work, we report a simple low-cost, non-toxic hydrothermal synthesis of refractory sodium carbide using the natural precursor—Pandanus. The formation of sodium carbide along with boron carbide is evidenced by the structural and morphological characterizations. The sample thus synthesized is subjected to field emission scanning electron microscopy (FESEM), x-ray powder diffraction (XRD), ultraviolet (UV)—visible spectroscopy, Fourier transform infrared spectroscopy (FTIR), Raman, and photoluminescent (PL) spectroscopic techniques.

  14. Thioether profragrances: parameters influencing the performance of precursor-based fragrance delivery in functional perfumery.

    Science.gov (United States)

    Maddalena, Umberto; Trachsel, Alain; Fankhauser, Peter; Berthier, Damien L; Benczédi, Daniel; Wang, Wei; Xi, Xiujuan; Shen, Youqing; Herrmann, Andreas

    2014-11-01

    A series of thioether profragrances was prepared by reaction of different sulfanylalkanoates with δ-damascone and tested for their release efficiencies in a fabric-softener and an all-purpose cleaner application. Dynamic headspace analysis on dry cotton and on a ceramic plate revealed that the performance of the different precursors depended on the structure, but also on the particular conditions encountered in different applications. Moreover, profragrances derived from other α,β-unsaturated fragrance aldehydes and ketones were synthesized analogously and evaluated using the same test protocol. Thioethers were found to be suitable precursors to release the corresponding fragrances, but neither the quantity of profragrance deposited from an aqueous environment onto the target surface, nor the amount of fragrance released after deposition could be linearly correlated to the hydrophilicity or hydrophobicity of the compounds. Different sets of compounds were found to be the best performers for different types of applications. Only one of the compounds evaluated in the present work, namely the thiolactic acid derivative of δ-damascone, efficiently released the corresponding fragrance in both of the tested applications. Profragrance development for functional perfumery thus remains a partially empirical endeavour. More knowledge (and control) of the various application conditions are required for an efficient profragrance design. Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

  15. High energy radiation precursors to the collapse of black holes binaries based on resonating plasma modes

    Science.gov (United States)

    Coppi, B.

    2018-05-01

    The presence of well organized plasma structures around binary systems of collapsed objects [1,2] (black holes and neutron stars) is proposed in which processes can develop [3] leading to high energy electromagnetic radiation emission immediately before the binary collapse. The formulated theoretical model supporting this argument shows that resonating plasma collective modes can be excited in the relevant magnetized plasma structure. Accordingly, the collapse of the binary approaches, with the loss of angular momentum by emission of gravitational waves [2], the resonance conditions with vertically standing plasma density and magnetic field oscillations are met. Then, secondary plasma modes propagating along the magnetic field are envisioned to be sustained with mode-particle interactions producing the particle populations responsible for the observable electromagnetic radiation emission. Weak evidence for a precursor to the binary collapse reported in Ref. [2], has been offered by the Agile X-γ-ray observatory [4] while the August 17 (2017) event, identified first by the LIGO-Virgo detection of gravitational waves and featuring the inferred collapse of a neutron star binary, improves the evidence of such a precursor. A new set of experimental observations is needed to reassess the presented theory.

  16. On-Particle Rolling Circle Amplification-Based Core-Satellite Magnetic Superstructures for MicroRNA Detection

    DEFF Research Database (Denmark)

    Tian, Bo; Qiu, Zhen; Ma, Jing

    2018-01-01

    -specific nuclease in the presence of target microRNA, resulting in a release of MNPs that can be quantified in an optomagnetic sensor. The proposed biosensor has a simple mix-separate-measure strategy. For let-7b detection, the proposed biosensor offers a wide linear detection range of approximately 5 orders...

  17. Universal, colorimetric microRNA detection strategy based on target-catalyzed toehold-mediated strand displacement reaction

    Science.gov (United States)

    Park, Yeonkyung; Lee, Chang Yeol; Kang, Shinyoung; Kim, Hansol; Park, Ki Soo; Park, Hyun Gyu

    2018-02-01

    In this work, we developed a novel, label-free, and enzyme-free strategy for the colorimetric detection of microRNA (miRNA), which relies on a target-catalyzed toehold-mediated strand displacement (TMSD) reaction. The system employs a detection probe that specifically binds to the target miRNA and sequentially releases a catalyst strand (CS) intended to trigger the subsequent TMSD reaction. Thus, the presence of target miRNA releases the CS that mediates the formation of an active G-quadruplex DNAzyme which is initially caged and inactivated by a blocker strand. In addition, a fuel strand that is supplemented for the recycling of the CS promotes another TMSD reaction, consequently generating a large number of active G-quadruplex DNAzymes. As a result, a distinct colorimetric signal is produced by the ABTS oxidation promoted by the peroxidase mimicking activity of the released G-quadruplex DNAzymes. Based on this novel strategy, we successfully detected miR-141, a promising biomarker for human prostate cancer, with high selectivity. The diagnostic capability of this system was also demonstrated by reliably determining target miR-141 in human serum, showing its great potential towards real clinical applications. Importantly, the proposed approach is composed of separate target recognition and signal transduction modules. Thus, it could be extended to analyze different target miRNAs by simply redesigning the detection probe while keeping the same signal transduction module as a universal signal amplification unit, which was successfully demonstrated by analyzing another target miRNA, let-7d.

  18. Novel friction law for the static friction force based on local precursor slipping.

    Science.gov (United States)

    Katano, Yu; Nakano, Ken; Otsuki, Michio; Matsukawa, Hiroshi

    2014-09-10

    The sliding of a solid object on a solid substrate requires a shear force that is larger than the maximum static friction force. It is commonly believed that the maximum static friction force is proportional to the loading force and does not depend on the apparent contact area. The ratio of the maximum static friction force to the loading force is called the static friction coefficient µM, which is considered to be a constant. Here, we conduct experiments demonstrating that the static friction force of a slider on a substrate follows a novel friction law under certain conditions. The magnitude of µM decreases as the loading force increases or as the apparent contact area decreases. This behavior is caused by the slip of local precursors before the onset of bulk sliding and is consistent with recent theory. The results of this study will develop novel methods for static friction control.

  19. The formation of CuInSe{sub 2}-based thin-film solar cell absorbers from alternative low-cost precursors

    Energy Technology Data Exchange (ETDEWEB)

    Jost, S.

    2008-01-18

    This work deals with real-time investigations concerning the crystallisation process of CuInSe{sub 2}-based thin-film solar cell absorbers while annealing differently produced and composed ''low-cost'' precursors. Various types of precursors have been investigated concerning their crystallisation behaviour. Three groups of experiments have been performed: (i) Investigations concerning the crystallisation process of the quaternary chalcopyrite Cu(In,Al)Se{sub 2} and Cu(In,Al)S{sub 2}, (ii) investigations concerning the formation process of the compound semiconductor CuInSe{sub 2} from electroplated precursors, and (iii) investigations concerning the crystallisation of Cu(In,Ga)Se{sub 2} using precursors with thermally evaporated indium. A specific sample surrounding has been constructed, which enables to perform time-resolved angle-dispersive X-ray powder diffraction experiments during the annealing process of precursor samples. A thorough analysis of subsequently recorded diffraction patterns using the Rietveld method provides a detailed knowledge about the semiconductor crystallisation process while annealing. Based on these fundamental investigations, conclusions have been drawn concerning an adaptation of the precursor deposition process in order to optimise the final solar cell results. The investigations have shown, that one class of electroplated precursors shows a crystallisation behaviour identical to the one known for vacuum-deposited precursors. The investigations concerning the crystallisation process of the quaternary chalcopyrite Cu(In,Al)Se{sub 2} revealed, that the chalcopyrite forms from the ternary selenide (Al,In){sub 2}Se{sub 3} and Cu{sub 2}Se at elevated process temperatures. This result is used to explain the separation of the absorber layer into an aluminum-rich and an indium-rich chalcopyrite phase, which has been observed at processed Cu(In,Al)Se{sub 2} absorbers from several research groups. In addition, differences

  20. Nickel Oxide (NiO nanoparticles prepared by solid-state thermal decomposition of Nickel (II schiff base precursor

    Directory of Open Access Journals (Sweden)

    Aliakbar Dehno Khalaji

    2015-06-01

    Full Text Available In this paper, plate-like NiO nanoparticles were prepared by one-pot solid-state thermal decomposition of nickel (II Schiff base complex as new precursor. First, the nickel (II Schiff base precursor was prepared by solid-state grinding using nickel (II nitrate hexahydrate, Ni(NO32∙6H2O, and the Schiff base ligand N,N′-bis-(salicylidene benzene-1,4-diamine for 30 min without using any solvent, catalyst, template or surfactant. It was characterized by Fourier Transform Infrared spectroscopy (FT-IR and elemental analysis (CHN. The resultant solid was subsequently annealed in the electrical furnace at 450 °C for 3 h in air atmosphere. Nanoparticles of NiO were produced and characterized by X-ray powder diffraction (XRD at 2θ degree 0-140°, FT-IR spectroscopy, scanning electron microscopy (SEM and transmission electron microscopy (TEM. The XRD and FT-IR results showed that the product is pure and has good crystallinity with cubic structure because no characteristic peaks of impurity were observed, while the SEM and TEM results showed that the obtained product is tiny, aggregated with plate-like shape, narrow size distribution with an average size between 10-40 nm. Results show that the solid state thermal decomposition method is simple, environmentally friendly, safe and suitable for preparation of NiO nanoparticles. This method can also be used to synthesize nanoparticles of other metal oxides.

  1. Exploration of coal-based pitch precursors for ultra-high thermal conductivity graphite fibers. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Deshpande, G.V. [Amoco Performance Products, Inc., Alpharetta, GA (United States)

    1996-12-27

    Goal was to explore the utility of coal-based pitch precursors for use in ultra high thermal conductivity carbon (graphite) fibers. From graphite electrode experience, it was established that coal-based pitches tend to form more highly crystalline graphite at lower temperatures. Since the funding was limited to year 1 effort of the 3 year program, the goal was only partially achieved. The coal-base pitches can form large domain mesophase in spite of high N and O contents. The mesophase reactivity test performed on one of the variants of coal-based pitch (DO84) showed that it was not a good candidate for carbon fiber processing. Optimization of WVU`s isotropic pitch process is required to tailor the pitch for carbon fiber processing. The hetero atoms in the coal pitch need to be reduced to improve mesophase formation.

  2. HuMiTar: A sequence-based method for prediction of human microRNA targets

    Directory of Open Access Journals (Sweden)

    Chen Ke

    2008-12-01

    Full Text Available Abstract Background MicroRNAs (miRs are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to induce mRNA degradation or mRNA cleavage. The ability to perform accurate, high-throughput identification of physiologically active miR targets would enable functional characterization of individual miRs. Current target prediction methods include traditional approaches that are based on specific base-pairing rules in the miR's seed region and implementation of cross-species conservation of the target site, and machine learning (ML methods that explore patterns that contrast true and false miR-mRNA duplexes. However, in the case of the traditional methods research shows that some seed region matches that are conserved are false positives and that some of the experimentally validated target sites are not conserved. Results We present HuMiTar, a computational method for identifying common targets of miRs, which is based on a scoring function that considers base-pairing for both seed and non-seed positions for human miR-mRNA duplexes. Our design shows that certain non-seed miR nucleotides, such as 14, 18, 13, 11, and 17, are characterized by a strong bias towards formation of Watson-Crick pairing. We contrasted HuMiTar with several representative competing methods on two sets of human miR targets and a set of ten glioblastoma oncogenes. Comparison with the two best performing traditional methods, PicTar and TargetScanS, and a representative ML method that considers the non-seed positions, NBmiRTar, shows that HuMiTar predictions include majority of the predictions of the other three methods. At the same time, the proposed method is also capable of finding more true positive targets as a trade-off for an increased number of predictions. Genome-wide predictions show that the proposed method is characterized by 1.99 signal

  3. MicroRNA prediction using a fixed-order Markov model based on the secondary structure pattern.

    Directory of Open Access Journals (Sweden)

    Wei Shen

    Full Text Available Predicting miRNAs is an arduous task, due to the diversity of the precursors and complexity of enzyme processes. Although several prediction approaches have reached impressive performances, few of them could achieve a full-function recognition of mature miRNA directly from the candidate hairpins across species. Therefore, researchers continue to seek a more powerful model close to biological recognition to miRNA structure. In this report, we describe a novel miRNA prediction algorithm, known as FOMmiR, using a fixed-order Markov model based on the secondary structural pattern. For a training dataset containing 809 human pre-miRNAs and 6441 human pseudo-miRNA hairpins, the model's parameters were defined and evaluated. The results showed that FOMmiR reached 91% accuracy on the human dataset through 5-fold cross-validation. Moreover, for the independent test datasets, the FOMmiR presented an outstanding prediction in human and other species including vertebrates, Drosophila, worms and viruses, even plants, in contrast to the well-known algorithms and models. Especially, the FOMmiR was not only able to distinguish the miRNA precursors from the hairpins, but also locate the position and strand of the mature miRNA. Therefore, this study provides a new generation of miRNA prediction algorithm, which successfully realizes a full-function recognition of the mature miRNAs directly from the hairpin sequences. And it presents a new understanding of the biological recognition based on the strongest signal's location detected by FOMmiR, which might be closely associated with the enzyme cleavage mechanism during the miRNA maturation.

  4. Polymeric nanoparticle-based delivery of microRNA-199a-3p inhibits proliferation and growth of osteosarcoma cells

    Directory of Open Access Journals (Sweden)

    Zhang L

    2015-04-01

    Full Text Available Linlin Zhang,1,2,* Arun K lyer,3,4,* Xiaoqian Yang,1 Eisuke Kobayashi,1 Yuqi Guo,1,2 Henry Mankin,1 Francis J Hornicek,1 Mansoor M Amiji,3 Zhenfeng Duan1 1Sarcoma Biology Laboratory, Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA; 2Department of Pathology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China; 3Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, Massachusetts, USA; 4Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA *These authors contributed equally to this work Abstract: Our prior screening of microRNAs (miRs identified that miR-199a-3p expression is reduced in osteosarcoma cells, one of the most common types of bone tumor. miR-199a-3p exhibited functions of tumor cell growth inhibition, suggesting the potential application of miR-199a-3p as an anticancer agent. In the study reported here, we designed and developed a lipid-modified dextran-based polymeric nanoparticle platform for encapsulation of miRs, and determined the efficiency and efficacy of delivering miR-199a-3p into osteosarcoma cells. In addition, another potent miR, let-7a, which also displayed tumor suppressive ability, was selected as a candidate miR for evaluation. Fluorescence microscopy studies and real-time polymerase chain reaction results showed that dextran nanoparticles could deliver both miR-199a-3p and let-7a into osteosarcoma cell lines (KHOS and U-2OS successfully. Western blotting analysis and 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide (MTT assays demonstrated that dextran nanoparticles loaded with miRs could efficiently downregulate the expression of target proteins and effectively inhibit the growth and proliferation of osteosarcoma cells. These results demonstrate that a lipid-modified dextran-based

  5. EPR interpretation, magnetism and biological study of a Cu(II) dinuclear complex assisted by a schiff base precursor.

    Science.gov (United States)

    Das, Kuheli; Patra, Chiranjit; Sen, Chandana; Datta, Amitabha; Massera, Chiara; Garribba, Eugenio; El Fallah, Mohamed Salah; Beyene, Belete B; Hung, Chen-Hsiung; Sinha, Chittaranjan; Askun, Tulin; Celikboyun, Pinar; Escudero, Daniel; Frontera, Antonio

    2017-06-01

    A new Cu(II) dinuclear complex, Cu 2 L 2 (1) was afforded employing the potentially pentatentate Schiff base precursor H 2 L, a refluxed product of o-vanillin and diethylenetriamine in methanol. Complex 1 was systematically characterized by FTIR, UV-Vis, emission and EPR spectrometry. The single crystal X-ray diffraction analysis of 1 reveals that the copper atom exhibits a distorted square planar geometry, comprising two pairs of phenolato-O and imine-N donors from two different H 2 L ligands. The temperature dependent magnetic interpretation agrees with the existence of weak antiferromagnetic interactions between the bridging dinuclear Cu(II) ions. A considerable body of experimental evidence has been accumulated to elucidate the magneto-structural relationship in this dinuclear Cu(II) complex by DFT computation. Both the ligand and complex 1 exhibit anti-mycobacterial activity and considerable efficacy on M. tuberculosis H 37 Ra (ATCC 25177) and M. tuberculosis H 37 Rv (ATCC 25618) strains. The practical applicability of the ligand and complex 1 has been examined in living cells (African Monkey Vero Cells). The MTT assay proves the non-toxicity of the probe up to 100 mg mL -1 . A new homometallic dinuclear Cu(II) complex is afforded with a tetradentate Schiff base precursor. EPR interpretation and temperature dependent magnetic studies show that complex 1 has weak antiferromagnetic coupling and DFT computation is governed to explain the magneto-structural correlation.

  6. MicroRNA signature of the human developing pancreas

    Directory of Open Access Journals (Sweden)

    Correa-Medina Mayrin

    2010-09-01

    Full Text Available Abstract Background MicroRNAs are non-coding RNAs that regulate gene expression including differentiation and development by either inhibiting translation or inducing target degradation. The aim of this study is to determine the microRNA expression signature during human pancreatic development and to identify potential microRNA gene targets calculating correlations between the signature microRNAs and their corresponding mRNA targets, predicted by bioinformatics, in genome-wide RNA microarray study. Results The microRNA signature of human fetal pancreatic samples 10-22 weeks of gestational age (wga, was obtained by PCR-based high throughput screening with Taqman Low Density Arrays. This method led to identification of 212 microRNAs. The microRNAs were classified in 3 groups: Group number I contains 4 microRNAs with the increasing profile; II, 35 microRNAs with decreasing profile and III with 173 microRNAs, which remain unchanged. We calculated Pearson correlations between the expression profile of microRNAs and target mRNAs, predicted by TargetScan 5.1 and miRBase altgorithms, using genome-wide mRNA expression data. Group I correlated with the decreasing expression of 142 target mRNAs and Group II with the increasing expression of 876 target mRNAs. Most microRNAs correlate with multiple targets, just as mRNAs are targeted by multiple microRNAs. Among the identified targets are the genes and transcription factors known to play an essential role in pancreatic development. Conclusions We have determined specific groups of microRNAs in human fetal pancreas that change the degree of their expression throughout the development. A negative correlative analysis suggests an intertwined network of microRNAs and mRNAs collaborating with each other. This study provides information leading to potential two-way level of combinatorial control regulating gene expression through microRNAs targeting multiple mRNAs and, conversely, target mRNAs regulated in

  7. Degradation of amine-based water treatment polymers during chloramination as N-nitrosodimethylamine (NDMA) precursors.

    Science.gov (United States)

    Park, Sang-Hyuck; Wei, Shuting; Mizaikoff, Boris; Taylor, Amelia E; Favero, Cedrick; Huang, Ching-Hua

    2009-03-01

    Recent studies indicated that water treatment polymers such as poly(epichlorohydrin dimethylamine) (polyamine) and poly(diallyldimethylammonium chloride) (polyDADMAC) may form N-nitrosodimethylamine (NDMA) when in contact with chloramine water disinfectants. To minimize such potential risk and improve the polymer products, the mechanisms of how the polymers behave as NDMA precursors need to be elucidated. Direct chloramination of polymers and intermediate monomers in reagent water was conducted to probe the predominant mechanisms. The impact of polymer properties including polymer purity, polymer molecular weight and structure, residual dimethylamine (DMA), and other intermediate compounds involved in polymer synthesis, and reaction conditions such as pH, oxidant dose, and contact time on the NDMA formation potential (NDMA-FP) was investigated. Polymer degradation after reaction with chloramines was monitored at the molecular level using FT-IR and Raman spectroscopy. Overall, polyamines have greater NDMA-FP than polyDADMAC, and the NDMA formation from both polymers is strongly related to polymer degradation and DMA release during chloramination. Polyamines' tertiary amine chain ends play a major role in their NDMA-FP, while polyDADMACs' NDMA-FP is related to degradation of the quaternary ammonium ring group.

  8. High strength nanostructured Al-based alloys through optimized processing of rapidly quenched amorphous precursors.

    Science.gov (United States)

    Kim, Song-Yi; Lee, Gwang-Yeob; Park, Gyu-Hyeon; Kim, Hyeon-Ah; Lee, A-Young; Scudino, Sergio; Prashanth, Konda Gokuldoss; Kim, Do-Hyang; Eckert, Jürgen; Lee, Min-Ha

    2018-01-18

    We report the methods increasing both strength and ductility of aluminum alloys transformed from amorphous precursor. The mechanical properties of bulk samples produced by spark-plasma sintering (SPS) of amorphous Al-Ni-Co-Dy powders at temperatures above 673 K are significantly enhanced by in-situ crystallization of nano-scale intermetallic compounds during the SPS process. The spark plasma sintered Al 84 Ni 7 Co 3 Dy 6 bulk specimens exhibit 1433 MPa compressive yield strength and 1773 MPa maximum strength together with 5.6% plastic strain, respectively. The addition of Dy enhances the thermal stability of primary fcc Al in the amorphous Al-TM -RE alloy. The precipitation of intermetallic phases by crystallization of the remaining amorphous matrix plays important role to restrict the growth of the fcc Al phase and contributes to the improvement of the mechanical properties. Such fully crystalline nano- or ultrafine-scale Al-Ni-Co-Dy systems are considered promising for industrial application because their superior mechanical properties in terms of a combination of very high room temperature strength combined with good ductility.

  9. Size of the coming solar cycle 24 based on Ohl's Precursor Method, final estimate

    Directory of Open Access Journals (Sweden)

    R. P. Kane

    2010-07-01

    Full Text Available In Ohl's Precursor Method (Ohl, 1966, 1976, the geomagnetic activity during the declining phase of a sunspot cycle is shown to be well correlated with the size (maximum sunspot number Rz(max of the next cycle. For solar cycle 24, Kane (2007a used aa(min=15.5 (12-month running mean, which occurred during March–May of 2006 and made a preliminary estimate Rz(max=124±26 (12-month running mean. However, in the next few months, the aa index first increased and then decreased to a new low value of 14.8 in July 2007. With this new low value, the prediction was Rz(max=117±26 (12-month running mean. However, even this proved a false signal. Since then, the aa values have decreased considerably and the last 12-monthly value is 8.7, centered at May 2009. For solar cycle 24, using aa(min=8.7, the latest prediction is, Rz(max=58.0±25.0.

  10. Development and validation of a microRNA based diagnostic assay for primary tumor site classification of liver core biopsies

    DEFF Research Database (Denmark)

    Perell, Katharina; Vincent, Martin; Vainer, Ben

    2015-01-01

    for normal liver tissue contamination. Performance was estimated by cross-validation, followed by independent validation on 55 liver core biopsies with a tumor content as low as 10%. A microRNA classifier developed, using the statistical contamination model, showed an overall classification accuracy of 74...... on classification. MicroRNA profiling was performed using quantitative Real-Time PCR on formalin-fixed paraffin-embedded samples. 278 primary tumors and liver metastases, representing nine primary tumor classes, as well as normal liver samples were used as a training set. A statistical model was applied to adjust.......5% upon independent validation. Two-thirds of the samples were classified with high-confidence, with an accuracy of 92% on high-confidence predictions. A classifier trained without adjusting for liver tissue contamination, showed a classification accuracy of 38.2%. Our results indicate that surrounding...

  11. A Collagen-based Scaffold Delivering Exogenous MicroRNA-29B to Modulate Extracellular Matrix Remodeling

    OpenAIRE

    Monaghan, Michael; Browne, Shane; Schenke-Layland, Katja; Pandit, Abhay

    2014-01-01

    Directing appropriate extracellular matrix remodeling is a key aim of regenerative medicine strategies. Thus, antifibrotic interfering RNA (RNAi) therapy with exogenous microRNA (miR)-29B was proposed as a method to modulate extracellular matrix remodeling following cutaneous injury. It was hypothesized that delivery of miR-29B from a collagen scaffold will efficiently modulate the extracellular matrix remodeling response and reduce maladaptive remodeling such as aggressive deposition of coll...

  12. Signal amplification of microRNAs with modified strand displacement-based cycling probe technology.

    Science.gov (United States)

    Jia, Huning; Bu, Ying; Zou, Bingjie; Wang, Jianping; Kumar, Shalen; Pitman, Janet L; Zhou, Guohua; Song, Qinxin

    2016-10-24

    Micro ribose nucleic acids (miRNAs) play an important role in biological processes such as cell differentiation, proliferation and apoptosis. Therefore, miRNAs are potentially a powerful marker for monitoring cancer and diagnosis. Here, we present sensitive signal amplification for miRNAs based on modified cycling probe technology with strand displacement amplification. miRNA was captured by the template coupled with beads, and then the first cycle based on SDA was repeatedly extended to the nicking end, which was produced by the extension reaction of miRNA. The products generated by SDA are captured by a molecular beacon (MB), which is designed to initiate the second amplification cycle, with a similar principle to the cycling probe technology (CPT), which is based on repeated digestion of the DNA-RNA hybrid by the RNase H. After one sample enrichment and two steps of signal amplification, 0.1 pM of let-7a can be detected. The miRNA assay exhibits a great dynamic range of over 100 orders of magnitude and high specificity to clearly discriminate a single base difference in miRNA sequences. This isothermal amplification does not require any special temperature control instrument. The assay is also about signal amplification rather than template amplification, therefore minimising contamination issues. In addition, there is no need for the reverse transcription (RT) process. Thus the amplification is suitable for miRNA detection.

  13. Impact of the atomic layer deposition precursors diffusion on solid-state carbon nanotube based supercapacitors performances

    International Nuclear Information System (INIS)

    Fiorentino, Giuseppe; Vollebregt, Sten; Ishihara, Ryoichi; Sarro, Pasqualina M; Tichelaar, F D

    2015-01-01

    A study on the impact of atomic layer deposition (ALD) precursors diffusion on the performance of solid-state miniaturized nanostructure capacitor array is presented. Three-dimensional nanostructured capacitor array based on double conformal coating of multiwalled carbon nanotubes (MWCNTs) bundles is realized using ALD to deposit Al 2 O 3 as dielectric layer and TiN as high aspect-ratio conformal counter-electrode on 2 μm long MWCNT bundles. The devices have a small footprint (from 100 μm 2 to 2500 μm 2 ) and are realized using an IC wafer-scale manufacturing process with high reproducibility (≤0.3E-12F deviation). To evaluate the enhancement of the electrode surface, the measured capacitance values are compared to a lumped circuital model. The observed discrepancies are explained with a partial coating of the CNT, that determine a limited use of the available electrode surface area. To analyze the CNT coating effectiveness, the ALD precursors diffusions inside the CNT bundle is studied using a Knudsen diffusion mechanism. (paper)

  14. Impact of the atomic layer deposition precursors diffusion on solid-state carbon nanotube based supercapacitors performances

    Science.gov (United States)

    Fiorentino, Giuseppe; Vollebregt, Sten; Tichelaar, F. D.; Ishihara, Ryoichi; Sarro, Pasqualina M.

    2015-02-01

    A study on the impact of atomic layer deposition (ALD) precursors diffusion on the performance of solid-state miniaturized nanostructure capacitor array is presented. Three-dimensional nanostructured capacitor array based on double conformal coating of multiwalled carbon nanotubes (MWCNTs) bundles is realized using ALD to deposit Al2O3 as dielectric layer and TiN as high aspect-ratio conformal counter-electrode on 2 μm long MWCNT bundles. The devices have a small footprint (from 100 μm2 to 2500 μm2) and are realized using an IC wafer-scale manufacturing process with high reproducibility (≤0.3E-12F deviation). To evaluate the enhancement of the electrode surface, the measured capacitance values are compared to a lumped circuital model. The observed discrepancies are explained with a partial coating of the CNT, that determine a limited use of the available electrode surface area. To analyze the CNT coating effectiveness, the ALD precursors diffusions inside the CNT bundle is studied using a Knudsen diffusion mechanism.

  15. Influence of the precursor chemical composition on heavy metal adsorption properties of hemp (Cannabis Sativa fibers based biocarbon

    Directory of Open Access Journals (Sweden)

    Vukčević Marija M.

    2017-01-01

    Full Text Available Waste hemp (Cannabis sativa fibers were used as sustainable and renewable raw materials for production of low-cost biocarbon sorbent for heavy metals removal. Carbon precursors of different chemical composition were obtained by oxidative and alkaline treatments of hemp fibers. Influence of lignocellulosic precursor chemical composition on hemp fibers-based biocarbon (HFB characteristics was examined by BET surface area measurement, scanning electron microscopy and mass titration. It was found that lignin content and polymorphic transformation of cellulose increase the SBET of microporous HFBs, while hemicelluloses induce more homogeneous distribution of adsorption active sites. Heavy metal ions adsorption onto HFBs is primarily influenced by the amount of surface oxygen groups, while specific surface area plays a secondary role. Equilibrium data obtained for lead ions adsorption were analyzed by different nonlinear adsorption isotherms, and the best fitting model was chosen using standard deviation and Akaike information criterion (AICC. The maximum adsorption capacities of HFBs ranged from 103.1 to 116.3 mg Pb/g. Thermodynamic parameters showed that Pb2+ adsorption onto HFBs is a spontaneous and complex endothermic process, suggesting the coexistence of physisorption and chemisorption mechanisms. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. 172007 and Grant no. 172029

  16. Redefining high-risk patients with stage II colon cancer by risk index and microRNA-21: results from a population-based cohort

    DEFF Research Database (Denmark)

    Hansen, T F; Kjær-Frifeldt, S; Christensen, R D

    2014-01-01

    Background:The aim of the present study was to analyse the prognostic value of microRNA-21 (miRNA-21) in patients with stage II colon cancer aiming at a risk index for this group of patients.Methods:A population-based cohort of 554 patients was included. MicroRNA-21 was analysed by qPCR based...... on tumour tissue. An index was created using the coefficients obtained from a collective multiple Cox regression. The entire procedure was cross-validated (10-fold). The performance of the index was quantified by time-dependent receiver operating characteristics curves.Results:High miRNA-21 expression...... was associated with an unfavourable recurrence-free cancer-specific survival (RF-CSS), hazard ratio 1.35 (95% confidence interval, 1.03-1.76) (P=0.028). The generated RF-CSS index divided the traditional high-risk patients into subgroups with 5-year RF-CSS rates of 87% and 73%, respectively (P...

  17. Thermoset precursor

    International Nuclear Information System (INIS)

    Yamamoto, Y.

    1983-04-01

    This invention pertains to a distinctive thermoset precursor which is prepared by mixing a resin composition (A) which can be hardened by ionizing radiation, and a resin composition (B) which can be hardened by heat but cannot be hardened by, or is resistant to, ionizing radiation, and by coating or impregnating a molding or other substrate with a sheet or film of this mixture and irradiating this with an ionizing radiation. The principal components of composition (A) and (B) can be the following: (1) an acrylate or methacrylate and an epoxy resin and an epoxy resin hardener; (2) an unsaturated polyester resin and epoxy resin and an epoxy resin hardener; (3) a diacrylate or dimethacrylate or polyethylene glycol and an epoxy resin; (4) an epoxy acrylates or epoxy methacrylate obtained by the addition reaction of epoxy resin and acrylic or methacrylic acid

  18. Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection.

    Science.gov (United States)

    Chaudhary, Vrantika; Jangra, Sumit; Yadav, Neelam R

    2018-04-13

    Nanobiotechnology has the potential to revolutionize diverse sectors including medicine, agriculture, food, textile and pharmaceuticals. Disease diagnostics, therapeutics and crop protection strategies are fast emerging using nanomaterials preferably nanobiomaterials. It has potential for development of novel nanobiomolecules which offer several advantages over conventional treatment methods. RNA nanoparticles with many unique features are promising candidates in disease treatment. The miRNAs are involved in many biochemical and developmental pathways and their regulation in plants and animals. These appear to be a powerful tool for controlling various pathological diseases in human, plants and animals, however there are challenges associated with miRNA based nanotechnology. Several advancements made in the field of miRNA therapeutics make it an attractive approach, but a lot more has to be explored in nanotechnology assisted miRNA therapy. The miRNA based technologies can be employed for detection and combating crop diseases as well. Despite these potential advantages, nanobiotechnology applications in the agricultural sector are still in its infancy and have not yet made its mark in comparison with healthcare sector. The review provides a platform to discuss nature, role and use of miRNAs in nanobiotechnology applications.

  19. SERS-based inverse molecular sentinel (iMS) nanoprobes for multiplexed detection of microRNA cancer biomarkers in biological samples

    Science.gov (United States)

    Crawford, Bridget M.; Wang, Hsin-Neng; Fales, Andrew M.; Bowie, Michelle L.; Seewaldt, Victoria L.; Vo-Dinh, Tuan

    2017-02-01

    The development of sensitive and selective biosensing techniques is of great interest for clinical diagnostics. Here, we describe the development and application of a surface enhanced Raman scattering (SERS) sensing technology, referred to as "inverse Molecular Sentinel (iMS)" nanoprobes, for the detection of nucleic acid biomarkers in biological samples. This iMS nanoprobe involves the use of plasmonic-active nanostars as the sensing platform for a homogenous assay for multiplexed detection of nucleic acid biomarkers, including DNA, RNA and microRNA (miRNA). The "OFF-to-ON" signal switch is based on a non-enzymatic strand-displacement process and the conformational change of stem-loop (hairpin) oligonucleotide probes upon target binding. Here, we demonstrate the development of iMS nanoprobes for the detection of DNA sequences as well as a modified design of the nanoprobe for the detection of short (22-nt) microRNA sequences. The application of iMS nanoprobes to detect miRNAs in real biological samples was performed with total small RNA extracted from breast cancer cell lines. The multiplex capability of the iMS technique was demonstrated using a mixture of the two differently labeled nanoprobes to detect miR-21 and miR-34a miRNA biomarkers for breast cancer. The results of this study demonstrate the feasibility of applying the iMS technique for multiplexed detection of nucleic acid biomarkers, including short miRNAs molecules.

  20. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

    Directory of Open Access Journals (Sweden)

    Reis Patricia P

    2010-06-01

    Full Text Available Abstract Background MicroRNAs (miRs are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE tissue. Results Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p 35, we show that reproducibility between technical replicates, equivalent dilutions, and FFPE vs. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p Conclusion Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR platform, opening up a realm of research possibilities for retrospective studies.

  1. Polymeric precursors method for obtaining pigments based on Inorganic oxides of chromium and iron deposited on TiO2

    International Nuclear Information System (INIS)

    Silva, Everlania M. da; Galvao, Sheila B.; Paskocimas, C.A.

    2011-01-01

    The case study was the use of chromium oxides and iron, as a precursor in the synthesis of inorganic pigments. The synthesis was based on the dissolution of citric acid as a complexing agent, addition of metal oxides, such as ion chromophores; polymerization with ethylene glycol and doping with titanium oxide. Going through pre-calcination, breakdown, calcination at different temperatures (700, 900 and 1100 deg C resulting in pigments: green for pigment and chromium deposited on TiO2, orange for iron on TiO2. The thermal analysis (TG and DTA), evaluated their thermal decompositions, the XRD revealed the formation of crystalline phases such as iron titanate and chrome titanate; SEM showed the formation of hexagonal particles for both oxides. Under the different analysis, one can see the potential stability of pigments and powders, can be proposed its use as pigments in polymers. (author)

  2. MS2 VLP-based delivery of microRNA-146a inhibits autoantibody production in lupus-prone mice

    Directory of Open Access Journals (Sweden)

    Pan Y

    2012-12-01

    Full Text Available Yang Pan,1,2 Tingting Jia,1,2 Yuan Zhang,1,2 Kuo Zhang,1 Rui Zhang,1 Jinming Li,1 Lunan Wang11National Center for Clinical Laboratories, Beijing Hospital of the Ministry of Health, Beijing, People’s Republic of China; 2Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of ChinaBackground: Systemic lupus erythematosus (SLE is a chronic autoimmune disease characterized by the presence of pathogenic autoantibodies. Recent studies suggest that microRNAs (miRNAs play an essential role in immunoregulation and may be involved in the pathogenesis of SLE. Therefore, it was of interest to investigate the potential therapeutic application of miRNAs in SLE, a concept that has not been thoroughly investigated thus far. Virus-like particles (VLPs are a type of recombinant nanoparticle enveloped by certain proteins derived from the outer coat of a virus. Herein, we describe a novel miRNA-delivery approach via bacteriophage MS2 VLPs and investigate the therapeutic effects of miR-146a, a well-studied and SLE-related miRNA, in BXSB lupus-prone mice.Methods: VLPs containing miR-146a, and the control VLPs, were prepared using an Escherichia coli expression system and then administered to lupus-prone mice over a 12-day period. We performed an enzyme-linked immunosorbent assay to evaluate the anti-dsDNA antibody, autoantibody to nuclear antigen (ANA, total IgG and total IgM levels in serum. The expression of miR-146a was analyzed by qRT-PCR. SLE-related cytokines as well as some toll-like receptor signaling pathway molecules were also measured.Results: Treatment with MS2-miR146a VLP showed profound effects on lupus-prone BXSB mice, including an increased level of mature miR-146a, which led to a significant reduction in the expression of autoantibodies and total IgG. Remarkably, these mice also exhibited reduced levels of proinflammatorycytokines, including IFN-Interferon-α (IFN-α, Interleukin-1β (Il-1

  3. Place-based and data-rich citizen science as a precursor for conservation action.

    Science.gov (United States)

    Haywood, Benjamin K; Parrish, Julia K; Dolliver, Jane

    2016-06-01

    Environmental education strategies have customarily placed substantial focus on enhancing ecological knowledge and literacy with the hope that, upon discovering relevant facts and concepts, participants will be better equipped to process and dissect environmental issues and, therefore, make more informed decisions. The assumption is that informed citizens will become active citizens--enthusiastically lobbying for, and participating in, conservation-oriented action. We surveyed and interviewed and used performance data from 432 participants in the Coastal Observation and Seabird Survey Team (COASST), a scientifically rigorous citizen science program, to explore measurable change in and links between understanding and action. We found that participation in rigorous citizen science was associated with significant increases in participant knowledge and skills; a greater connection to place and, secondarily, to community; and an increasing awareness of the relative impact of anthropogenic activities on local ecosystems specifically through increasing scientific understanding of the ecosystem and factors affecting it. Our results suggest that a place-based, data-rich experience linked explicitly to local, regional, and global issues can lead to measurable change in individual and collective action, expressed in our case study principally through participation in citizen science and community action and communication of program results to personal acquaintances and elected officials. We propose the following tenets of conservation literacy based on emergent themes and the connections between them explicit in our data: place-based learning creates personal meaning making; individual experience nested within collective (i.e., program-wide) experience facilitates an understanding of the ecosystem process and function at local and regional scales; and science-based meaning making creates informed concern (i.e., the ability to discern both natural and anthropogenic forcing

  4. Polyether precursors of molecular recognition systems based on the 9,10-anthraquinone moiety

    Science.gov (United States)

    Wcisło, Anna; Cirocka, Anna; Zarzeczańska, Dorota; Niedziałkowski, Paweł; Nakonieczna, Sandra; Ossowski, Tadeusz

    2015-02-01

    A series of novel polyether derivatives of 9,10-anthraquinone (AQ) was synthesized and characterized by means of UV-Vis spectroscopy, acid-base titration and complexometric titration. The results were compared with 1-NEt2AQ and 1-NHEtAQ - model compounds of alkylaminoanthraquinones. Acetonitrile and methanol were used as solvents for determination of spectroscopic and acid-base properties. Complexometric titrations were carried out exclusively in acetonitrile. Spectral characteristic of these compounds strongly depends on pH. Addition of acid causes the decrease of absorption intensity and in some cases also a shift of the visible range band. The weakest base is the compound (2), and the strongest - compound (1), both in methanol and acetonitrile solution. The introduction of an additional substituent in the position 8 of the anthraquinone compound increases its basicity. The presence of metal ions causes changes in intensity of absorption (decrease for compounds (2) and (3) and increase with bathochromic shift for (1) and (4)). For the determination of the coordination properties aluminum (III) ions were chosen. The highest complex stability constant with Al (III) ions is observed for compound (1), and the weakest for compound (3). The elongation of the polyether chain decreases the stability of the complex formed.

  5. Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers

    NARCIS (Netherlands)

    Yousef, Malik; Nigatu, Dawit; Levy, Dalit; Allmer, Jens; Henkel, Werner

    2017-01-01

    Background: Diseases like cancer can manifest themselves through changes in protein abundance, and microRNAs (miRNAs) play a key role in the modulation of protein quantity. MicroRNAs are used throughout all kingdoms and have been shown to be exploited by viruses to modulate their host

  6. Biomarker MicroRNAs for Diagnosis of Oral Squamous Cell Carcinoma Identified Based on Gene Expression Data and MicroRNA-mRNA Network Analysis

    Science.gov (United States)

    Zhang, Hui; Li, Tangxin; Zheng, Linqing

    2017-01-01

    Oral squamous cell carcinoma is one of the most malignant tumors with high mortality rate worldwide. Biomarker discovery is critical for early diagnosis and precision treatment of this disease. MicroRNAs are small noncoding RNA molecules which often regulate essential biological processes and are good candidates for biomarkers. By integrative analysis of both the cancer-associated gene expression data and microRNA-mRNA network, miR-148b-3p, miR-629-3p, miR-27a-3p, and miR-142-3p were screened as novel diagnostic biomarkers for oral squamous cell carcinoma based on their unique regulatory abilities in the network structure of the conditional microRNA-mRNA network and their important functions. These findings were confirmed by literature verification and functional enrichment analysis. Future experimental validation is expected for the further investigation of their molecular mechanisms. PMID:29098014

  7. A population-based study of anxiety as a precursor for depression in childhood and adolescence

    Directory of Open Access Journals (Sweden)

    van den Bree Marianne BM

    2004-12-01

    Full Text Available Background Anxiety and depression co-occur in children and adolescents with anxiety commonly preceding depression. Although there is some evidence to suggest that the association between early anxiety and later depression is explained by a shared genetic aetiology, the contribution of environmental factors is less well examined and it is unknown whether anxiety itself is a phenotypic risk factor for later depression. These explanations of the association between early anxiety and later depression were evaluated. Methods Anxiety and depressive symptoms were assessed longitudinally in a U.K. population-based sample of 676 twins aged 5–17 at baseline. At baseline, anxiety and depression were assessed by parental questionnaire. Depression was assessed three years later by parental and adolescent questionnaire. Results Shared genetic effects between early anxiety and later depression were found. A model of a phenotypic risk effect from early anxiety on later depression provided a poor fit to the data. However, there were significant genetic effects specific to later depression, showing that early anxiety and later depression do not index entirely the same genetic risk. Conclusions Anxiety and depression are associated over time because they share a partly common genetic aetiology rather than because the anxiety phenotype leads to later depression.

  8. A population-based study of anxiety as a precursor for depression in childhood and adolescence.

    Science.gov (United States)

    Rice, Frances; van den Bree, Marianne B M; Thapar, Anita

    2004-12-13

    Anxiety and depression co-occur in children and adolescents with anxiety commonly preceding depression. Although there is some evidence to suggest that the association between early anxiety and later depression is explained by a shared genetic aetiology, the contribution of environmental factors is less well examined and it is unknown whether anxiety itself is a phenotypic risk factor for later depression. These explanations of the association between early anxiety and later depression were evaluated. Anxiety and depressive symptoms were assessed longitudinally in a U.K. population-based sample of 676 twins aged 5-17 at baseline. At baseline, anxiety and depression were assessed by parental questionnaire. Depression was assessed three years later by parental and adolescent questionnaire. Shared genetic effects between early anxiety and later depression were found. A model of a phenotypic risk effect from early anxiety on later depression provided a poor fit to the data. However, there were significant genetic effects specific to later depression, showing that early anxiety and later depression do not index entirely the same genetic risk. Anxiety and depression are associated over time because they share a partly common genetic aetiology rather than because the anxiety phenotype leads to later depression.

  9. Formation of crystalline InGaO₃(ZnO)n nanowires via the solid-phase diffusion process using a solution-based precursor.

    Science.gov (United States)

    Guo, Yujie; Van Bilzen, Bart; Locquet, Jean Pierre; Seo, Jin Won

    2015-12-11

    One-dimensional single crystalline InGaO3(ZnO)n (IGZO) nanostructures have great potential for various electrical and optical applications. This paper demonstrates for the first time, to our knowledge, a non-vacuum route for the synthesis of IGZO nanowires by annealing ZnO nanowires covered with solution-based IGZO precursor. This method results in nanowires with highly periodic IGZO superlattice structure. The phase transition of IGZO precursor during thermal treatment was systematically studied. Transmission electron microscopy studies reveal that the formation of the IGZO structure is driven by anisotropic inter-diffusion of In, Ga, and Zn atoms, and also by the crystallization of the IGZO precursor. Optical measurements using cathodoluminescence and UV-vis spectroscopy confirm that the nanowires consist of the IGZO compound with wide optical band gap and suppressed luminescence.

  10. Formation of crystalline InGaO_3(ZnO)_n nanowires via the solid-phase diffusion process using a solution-based precursor

    International Nuclear Information System (INIS)

    Guo, Yujie; Seo, Jin Won; Bilzen, Bart Van; Locquet, Jean Pierre

    2015-01-01

    One-dimensional single crystalline InGaO_3(ZnO)_n (IGZO) nanostructures have great potential for various electrical and optical applications. This paper demonstrates for the first time, to our knowledge, a non-vacuum route for the synthesis of IGZO nanowires by annealing ZnO nanowires covered with solution-based IGZO precursor. This method results in nanowires with highly periodic IGZO superlattice structure. The phase transition of IGZO precursor during thermal treatment was systematically studied. Transmission electron microscopy studies reveal that the formation of the IGZO structure is driven by anisotropic inter-diffusion of In, Ga, and Zn atoms, and also by the crystallization of the IGZO precursor. Optical measurements using cathodoluminescence and UV-vis spectroscopy confirm that the nanowires consist of the IGZO compound with wide optical band gap and suppressed luminescence. (paper)

  11. Preparation of (Bi,Pb)2Sr2Ca2Cu3Ox precursor powders by a modified polyethylene glycol based sol-gel process

    DEFF Research Database (Denmark)

    Grivel, Jean-Claude; Andersen, N.H.

    2002-01-01

    A modified sol-gel process based on polyethylene glycol has been developed for preparing (Bi,Pb)(2)Sr2Ca2Cu3Ox precursor powders in view of Ag-sheeted tape manufacture. A careful control of the pH and concentration temperature yields an amorphous gel, which can be converted to a fine and extremely...

  12. Synthesis and properties of nasicon prepared from different zirconia-based precursors

    Directory of Open Access Journals (Sweden)

    Fuentes, R. O.

    1999-12-01

    Full Text Available This work reports on the synthesis and characterization of NASICON prepared from SiO2, Na3PO4.12H2O and two types of zirconia: pure monoclinic ZrO2 and TZP (Tetragonal Polycrystalline Zirconia, with 3 mol% Y2O3 as raw materials. The classical ceramic method was used in all cases. SEM, XRD and DTA were used to follow the synthesis and sintering process, and impedance spectroscopy (IS was used to study the electrical properties of sintered pellets. Results obtained with different NASICON samples showed a significant role of composition and processing conditions on the electrical properties. Samples based on TZP, sintered at 1210ºC, exhibited densities of about 3.20 g/cm3 (98% of theoretical density of NASICON and ionic conductivities of about 2x10-3 S.cm-1 at room temperature a rather interesting result when compared with data obtained with the material prepared from pure ZrO2.

    Este trabajo trata de la síntesis y caracterización de NASICON preparado a partir de SiO2 , Na3PO4.12H2O y dos tipos de circonia, ZrO2 monoclínica pura y TZP (circonia policristalina tetragonal, con 3 moles% Y2O3 como materia prima. Se emplea el método cerámico clásico en todos los casos. Las técnicas de MEB, DRX y ATD se emplean para seguir la síntesis y el proceso de sinterización. La espectroscopia de impedancia compleja se emplea para estudiar las propiedades eléctricas de las muestras sinterizadas. Los resultados obtenidos con diferentes muestras de NASICON mostraron un papel significativo de la composición y condiciones de procesamiento sobre las propiedades eléctricas. Las muestras basadas en TZP, sinterizadas a 1210ºC, presentan densidades alrededor de 3.20 g/cm3 (98% de la densidad teórica del NASICON y conductividad iónica de 2x 10-3 5.cm-1 a temperatura ambiente, un resultado bastante interesante cuando se compara con datos obtenidos con material preparado de ZrO2 pura.

  13. Spectroelectrochemical detection of microRNA-155 based on functional RNA immobilization onto ITO/GNP nanopattern.

    Science.gov (United States)

    Mohammadniaei, Mohsen; Yoon, Jinho; Lee, Taek; Choi, Jeong-Woo

    2018-05-20

    We fabricated a microRNA biosensor using the combination of surface enhanced Raman spectroscopy (SERS) and electrochemical (EC) techniques. For the first time, the weaknesses of each techniques for microRNA detection was compensated by the other ones to give rise to the specific and wide-range detection of miR-155. A single stranded 3' methylene blue (MB) and 5' thiol-modified RNA (MB-ssRNA-SH) was designed to detect the target miR-155 and immobilized onto the gold nanoparticle-modified ITO (ITO/GNP). Upon the invasion of target strand, the double-stranded RNA transformed rapidly to an upright structure resulting in a notable decrease in SERS and redox signals of the MB. For the first time, by combination of SERS and EC techniques in a single platform we extended the dynamic range of both techniques from 10 pM to 450 nM (SERS: 10 pM-5 nM and EC: 5 nM-450 nM). As well, the SERS technique improved the detection limit of the EC method from 100 pM to 100 fM, while the EC method covered single-mismatch detection which was the SERS deficiency. The fabricated single-step biosensor possessing a good capability of miRNA detection in human serum, could be employed throughout the broad ranges of biomedical and bioelectronics applications. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Deciphering the porcine intestinal microRNA transcriptome

    Directory of Open Access Journals (Sweden)

    Keller Andreas

    2010-04-01

    Full Text Available Abstract Background While more than 700 microRNAs (miRNAs are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy. Results Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks. Conclusions In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.

  15. miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis.

    Science.gov (United States)

    Zhang, Hanyuan; Vieira Resende E Silva, Bruno; Cui, Juan

    2018-05-01

    Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes. In this article, we present microRNA Discovery (miRDis), a new small RNA sequencing data analysis pipeline for both endogenous and exogenous miRNA detection. Specifically, we developed and deployed a Web service that supports the annotation and expression profiling data of known host miRNAs and the detection of novel miRNAs, other noncoding RNAs, and the exogenous miRNAs from dietary species. As a proof-of-concept, we analyzed a set of human plasma sequencing data from a milk-feeding study where 225 human miRNAs were detected in the plasma samples and 44 show elevated expression after milk intake. By examining the bovine-specific sequences, data indicate that three bovine miRNAs (bta-miR-378, -181* and -150) are present in human plasma possibly because of the dietary uptake. Further evaluation based on different sets of public data demonstrates that miRDis outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources. The miRDis Web server is available at: http://sbbi.unl.edu/miRDis/index.php.

  16. Yak milk casein as potential precursor of angiotensin I-converting enzyme inhibitory peptides based on in silico proteolysis.

    Science.gov (United States)

    Lin, Kai; Zhang, Lan-Wei; Han, Xue; Xin, Liang; Meng, Zhao-Xu; Gong, Pi-Min; Cheng, Da-You

    2018-07-15

    Yak milk casein was selected as a potential precursor of bioactive peptides based on in silico analysis. Most notable among these are the angiotensin I-converting enzyme (ACE) inhibitory peptides. First, yak milk casein has high homology with cow milk casein by homologous analysis. The potential of yak milk casein for the releasing bioactive peptides was evaluated by determining the frequency of occurrence of fragments with a given activity. Through the BIOPEP database analysis, there are many bioactive peptides in yak milk casein sequences. Then, an in silico proteolysis using single or combined enzymes to obtained ACE inhibitory peptides was investigated. Cytotoxicity analysis using the online toxic prediction tool ToxinPred revealed that all in silico proteolysis derived ACE inhibitory peptides are non-cytotoxic. Overall, the present study highlights a in silico proteolysis approach to assist the yak milk casein releasing ACE inhibitory peptides and provides a guidance for the actual hydrolysis of proteins for the production of bioactive peptides. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Systematic Prediction of the Impacts of Mutations in MicroRNA Seed Sequences

    Directory of Open Access Journals (Sweden)

    Bhattacharya Anindya

    2017-05-01

    Full Text Available 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. The result provides a comprehensive reference for the functional assessment of the impacts of possible natural and artificial single nucleotide mutations in microRNA seed regions.

  18. Modulation of microRNA activity by semi-microRNAs (smiRNAs

    Directory of Open Access Journals (Sweden)

    Isabelle ePlante

    2012-06-01

    Full Text Available The ribonuclease Dicer plays a central role in the microRNA pathway by catalyzing the formation of 19 to 24-nucleotide (nt long microRNAs. Subsequently incorporated into Ago2 effector complexes, microRNAs are known to regulate messenger RNA (mRNA translation. Whether shorter RNA species derived from microRNAs exist and play a role in mRNA regulation remains unknown. Here, we report the serendipitous discovery of a 12-nt long RNA species corresponding to the 5’ region of the microRNA let-7, and tentatively termed semi-microRNA, or smiRNA. Using a smiRNA derived from the precursor of miR-223 as a model, we show that 12-nt long smiRNA species are devoid of any direct mRNA regulatory activity, as assessed in a reporter gene activity assay in transfected cultured human cells. However, smiR-223 was found to modulate the ability of the microRNA from which it derives to mediate translational repression or cleavage of reporter mRNAs. Our findings suggest that smiRNAs may be generated along the microRNA pathway and participate to the control of gene expression by regulating the activity of the related full-length mature microRNA in vivo.

  19. Targeting of microRNAs for therapeutics

    DEFF Research Database (Denmark)

    Stenvang, Jan; Lindow, Morten; Kauppinen, Sakari

    2008-01-01

    miRNAs (microRNAs) comprise a class of small endogenous non-coding RNAs that post-transcriptionally repress gene expression by base-pairing with their target mRNAs. Recent evidence has shown that miRNAs play important roles in a wide variety of human diseases, such as viral infections, cancer...

  20. Micro-RNAs

    DEFF Research Database (Denmark)

    Taipaleenmäki, H.; Hokland, L. B.; Chen, Li

    2012-01-01

    Osteoblast differentiation and bone formation (osteogenesis) are regulated by transcriptional and post-transcriptional mechanisms. Recently, a novel class of regulatory factors termed microRNAs has been identified as playing an important role in the regulation of many aspects of osteoblast biology...... including proliferation, differentiation, metabolism and apoptosis. Also, preliminary data from animal disease models suggest that targeting miRNAs in bone can be a novel approach to increase bone mass. This review highlights the current knowledge of microRNA biology and their role in bone formation...

  1. Precursor analyses - The use of deterministic and PSA based methods in the event investigation process at nuclear power plants

    International Nuclear Information System (INIS)

    2004-09-01

    The efficient feedback of operating experience (OE) is a valuable source of information for improving the safety and reliability of nuclear power plants (NPPs). It is therefore essential to collect information on abnormal events from both internal and external sources. Internal operating experience is analysed to obtain a complete understanding of an event and of its safety implications. Corrective or improvement measures may then be developed, prioritized and implemented in the plant if considered appropriate. Information from external events may also be analysed in order to learn lessons from others' experience and prevent similar occurrences at our own plant. The traditional ways of investigating operational events have been predominantly qualitative. In recent years, a PSA-based method called probabilistic precursor event analysis has been developed, used and applied on a significant scale in many places for a number of plants. The method enables a quantitative estimation of the safety significance of operational events to be incorporated. The purpose of this report is to outline a synergistic process that makes more effective use of operating experience event information by combining the insights and knowledge gained from both approaches, traditional deterministic event investigation and PSA-based event analysis. The PSA-based view on operational events and PSA-based event analysis can support the process of operational event analysis at the following stages of the operational event investigation: (1) Initial screening stage. (It introduces an element of quantitative analysis into the selection process. Quantitative analysis of the safety significance of nuclear plant events can be a very useful measure when it comes to selecting internal and external operating experience information for its relevance.) (2) In-depth analysis. (PSA based event evaluation provides a quantitative measure for judging the significance of operational events, contributors to

  2. Improved mapping of tropospheric air quality gases based on the Copernicus Sentinel 5 Precursor/TROPOMI mission

    Science.gov (United States)

    Van Roozendael, Michel; De Smedt, Isabelle; Theys, Nicolas; Danckaert, Thomas; Yu, Huan; Lerot, Christophe; van Gent, Jeroen; Vlietinck, Jonas

    2017-04-01

    Scheduled for launch in summer 2017, the Sentinel 5 Precursor (S5P) mission having onboard the TROPOMI payload will fly on a sun-synchronous polar orbit and provide daily global early-afternoon observations of a number of key atmospheric trace gases at the unprecedented spatial resolution of 7x3.5 km2. By the early 2020's, S5P will be complemented by geostationary observations from the Sentinel 4 UVN instrument to be delivered at hourly resolution over Europe, and by mid-morning global observations from the low-earth orbiting Sentinel 5 mission. Altogether these missions will form a constellation serving the needs of the Copernicus Atmospheric Monitoring Services (CAMS). Owing to their unprecedented spatial resolution and spectral performance, TROPOMI/S5P and the subsequent Sentinel 4 and 5 missions will significantly push forward monitoring capabilities addressing anthropogenic and natural emissions of air quality-related trace gases. They will also extend the long-term datasets from past and existing UV-Vis sensors (GOME, SCIAMACHY, OMI, GOME-2, OMPS). In this presentation, we explore the potential of S5P to improve on several aspects of the monitoring of tropospheric pollutants, with a focus on the short-lived species NO2, SO2 and HCHO. Based on algorithms designed at BIRA as part of TROPOMI/S5P and S4/S5 level-2 development projects, and their application to the current OMI and GOME-2 sensors, we illustrate and discuss the expected ability of the new sensors to detect smaller scale point sources with better accuracy and selectivity. The retrieval challenges associated with higher resolution measurements are also addressed.

  3. Signal-off Electrochemiluminescence Biosensor Based on Phi29 DNA Polymerase Mediated Strand Displacement Amplification for MicroRNA Detection.

    Science.gov (United States)

    Chen, Anyi; Gui, Guo-Feng; Zhuo, Ying; Chai, Ya-Qin; Xiang, Yun; Yuan, Ruo

    2015-06-16

    A target induced cycling strand displacement amplification (SDA) mediated by phi29 DNA polymerase (phi29) was first investigated and applied in a signal-off electrochemiluminescence (ECL) biosensor for microRNA (miRNA) detection. Herein, the target miRNA triggered the phi29-mediated SDA which could produce amounts of single-stranded DNA (assistant probe) with accurate and comprehensive nucleotide sequence. Then, the assistant probe hybridized with the capture probe and the ferrocene-labeled probe (Fc-probe) to form a ternary "Y" structure for ECL signal quenching by ferrocene. Therefore, the ECL intensity would decrease with increasing concentration of the target miRNA, and the sensitivity of biosensor would be promoted on account of the efficient signal amplification of the target induced cycling reaction. Besides, a self-enhanced Ru(II) ECL system was designed to obtain a stable and strong initial signal to further improve the sensitivity. The ECL assay for miRNA-21 detection is developed with excellent sensitivity of a concentration variation from 10 aM to 1.0 pM and limit of detection down to 3.3 aM.

  4. miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal

    Science.gov (United States)

    Chen, Liang; Heikkinen, Liisa; Wang, ChangLiang; Yang, Yang; Knott, K Emily

    2018-01-01

    Abstract Hundreds of bioinformatics tools have been developed for MicroRNA (miRNA) investigations including those used for identification, target prediction, structure and expression profile analysis. However, finding the correct tool for a specific application requires the tedious and laborious process of locating, downloading, testing and validating the appropriate tool from a group of nearly a thousand. In order to facilitate this process, we developed a novel database portal named miRToolsGallery. We constructed the portal by manually curating > 950 miRNA analysis tools and resources. In the portal, a query to locate the appropriate tool is expedited by being searchable, filterable and rankable. The ranking feature is vital to quickly identify and prioritize the more useful from the obscure tools. Tools are ranked via different criteria including the PageRank algorithm, date of publication, number of citations, average of votes and number of publications. miRToolsGallery provides links and data for the comprehensive collection of currently available miRNA tools with a ranking function which can be adjusted using different criteria according to specific requirements. Database URL: http://www.mirtoolsgallery.org PMID:29688355

  5. A facile synthesis of α-MnO2 used as a supercapacitor electrode material: The influence of the Mn-based precursor solutions on the electrochemical performance

    Science.gov (United States)

    Li, Wenyao; Xu, Jiani; Pan, Yishuang; An, Lei; Xu, Kaibing; Wang, Guangjin; Yu, Zhishui; Yu, Li; Hu, Junqing

    2015-12-01

    Three types of α-MnO2 nanomaterials are synthesized in different Mn-based precursor solutions by using a facile electrochemical deposition at the same depositional condition. The relationships between the precursor solutions and corresponding MnO2 nanomaterials' morphology as well as the electrochemical performance have been studied. As an electrode, electrochemical measurements show that the MnO2 deposited in MnCl2 precursor solution (MnO2-P3) exhibits an enhanced specific capacitance (318.9 F g-1 at 2 mV s-1). Moreover, this electrode demonstrates a good rate capability with 44% retention, which is higher than the MnO2-P1 deposited with Mn(CH3COOH)2 solution and the MnO2-P2 deposited with Mn(NO3)2 precursor solution. Besides, the specific capacitance of the MnO2-P3 electrode nearly has 98.2% retention after 2000 cycles, showing good long-term cycle stability. These findings show that the MnO2-P3 is a promising electrode material for supercapacitors.

  6. MicroRNA pharmacogenomics

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Shomron, Noam

    2011-01-01

    polymorphisms, copy number variations or differences in gene expression levels of drug metabolizing or transporting genes and drug targets. In this review paper, we focus instead on microRNAs (miRNAs): small noncoding RNAs, prevalent in metazoans, that negatively regulate gene expression in many cellular...

  7. Visible-light induced photoelectrochemical biosensor for the detection of microRNA based on Bi2S3 nanorods and streptavidin on an ITO electrode

    International Nuclear Information System (INIS)

    Wang, Mo; Yang, Zhiqing; Guo, Yunlong; Wang, Xinxu; Yin, Huanshun; Ai, Shiyun

    2015-01-01

    We demonstrate a photo-electrochemical biosensor for the sensitive and specific detection of microRNA using Bi 2 S 3 nanorods as a photoactive material and streptavidin as the unit that inhibits photocurrent. Bi 2 S 3 nanorods were synthesized hydrothermally in organic phase and displayed excellent light-to-current conversion efficiency. The Bi 2 S 3 was deposited on an indium tin oxide (ITO) slice and then modified with gold nanoparticles onto which biotinylated hairpin probe DNA was deposited as a monolayer. Following hybridization between the biotinylated probe DNA and the target microRNA, the stem-loop structure of the probe DNA was unfolded and the biotin directed outwards into the solution. Streptavidin was then added to bind to biotin via the strong streptavidin-biotin interactions. This causes the photocurrent of the modified ITO to decrease due to steric hindrance that blocks the transfer of electrons from added ascorbic acid to the surface of the electrode. The method has a detection limit as low as 3.5 fM of microRNA and can excellently discriminate even singly mismatched microRNA. The method was successfully applied to investigate the effect of abscisic acid on the expression level of microRNA-159a in seeds of Arabidopsis thaliana. We conclude that the assay presented here has a large potential as a method for quantification of microRNA and for studying the epigenetic regulation of flowering plants. (author)

  8. The EM Earthquake Precursor

    Science.gov (United States)

    Jones, K. B., II; Saxton, P. T.

    2013-12-01

    Many attempts have been made to determine a sound forecasting method regarding earthquakes and warn the public in turn. Presently, the animal kingdom leads the precursor list alluding to a transmission related source. By applying the animal-based model to an electromagnetic (EM) wave model, various hypotheses were formed, but the most interesting one required the use of a magnetometer with a differing design and geometry. To date, numerous, high-end magnetometers have been in use in close proximity to fault zones for potential earthquake forecasting; however, something is still amiss. The problem still resides with what exactly is forecastable and the investigating direction of EM. After the 1989 Loma Prieta Earthquake, American earthquake investigators predetermined magnetometer use and a minimum earthquake magnitude necessary for EM detection. This action was set in motion, due to the extensive damage incurred and public outrage concerning earthquake forecasting; however, the magnetometers employed, grounded or buried, are completely subject to static and electric fields and have yet to correlate to an identifiable precursor. Secondly, there is neither a networked array for finding any epicentral locations, nor have there been any attempts to find even one. This methodology needs dismissal, because it is overly complicated, subject to continuous change, and provides no response time. As for the minimum magnitude threshold, which was set at M5, this is simply higher than what modern technological advances have gained. Detection can now be achieved at approximately M1, which greatly improves forecasting chances. A propagating precursor has now been detected in both the field and laboratory. Field antenna testing conducted outside the NE Texas town of Timpson in February, 2013, detected three strong EM sources along with numerous weaker signals. The antenna had mobility, and observations were noted for recurrence, duration, and frequency response. Next, two

  9. Label-free fluorescence strategy for sensitive microRNA detection based on isothermal exponential amplification and graphene oxide.

    Science.gov (United States)

    Li, Wei; Hou, Ting; Wu, Min; Li, Feng

    2016-01-01

    MicroRNAs (miRNAs) play an important role in many biological processes, and have been regarded as potential targets and biomarkers in cancer diagnosis and therapy. Also, to meet the big challenge imposed by the characteristics of miRNAs, such as small size and vulnerability to enzymatic digestion, it is of great importance to develop accurate, sensitive and simple miRNA assays. Herein, we developed a label-free fluorescence strategy for sensitive miRNA detection by combining isothermal exponential amplification and the unique features of SYBR Green I (SG) and graphene oxide (GO), in which SG gives significantly enhanced fluorescence upon intercalation into double-stranded DNAs (dsDNAs), and GO selectively adsorbs miRNA, single-stranded DNA and SG, to protect miRNA from enzymatic digestion, and to quench the fluorescence of the adsorbed SG. In the presence of the target miRNA, the ingeniously designed hairpin probe (HP) is unfolded and the subsequent polymerization and strand displacement reaction takes place to initiate the target recycling process. The newly formed dsDNAs are then recognized and cleaved by the nicking enzyme, generating new DNA triggers with the same sequence as the target miRNA, which hybridize with intact HPs to initiate new extension reactions. As a result, the circular exponential amplification for target miRNA is achieved and large amount of dsDNAs are formed to generate significantly enhanced fluorescence upon the intercalation of SG. Thus sensitive and selective fluorescence miRNA detection is realized, and the detection limit of 3 fM is obtained. Besides, this method exhibits additional advantages of simplicity and low cost, since expensive and tedious labeling process is avoided. Therefore, the as-proposed label-free fluorescence strategy has great potential in the applications in miRNA-related clinical practices and biochemical researches. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Development of Ni-Based Catalysts Derived from Hydrotalcite-Like Compounds Precursors for Synthesis Gas Production via Methane or Ethanol Reforming

    OpenAIRE

    Ya-Li Du; Xu Wu; Qiang Cheng; Yan-Li Huang; Wei Huang

    2017-01-01

    As a favorably clean fuel, syngas (synthesis gas) production has been the focus of concern in past decades. Substantial literatures reported the syngas production by various catalytic reforming reactions particularly in methane or ethanol reforming. Among the developed catalysts in these reforming processes, Ni-based catalysts from hydrotalcite-like compounds (HTLcs) precursors have drawn considerable attention for their preferable structural traits. This review covers the recent literature r...

  11. Demonstrating the utility of boron based precursor molecules for selective area deposition in a scanning tunneling microscope

    International Nuclear Information System (INIS)

    Perkins, F.K.; Onellion, M.; Lee, S.; Bowben, T.A.

    1992-01-01

    The scanning tunneling microscope (STM) can be used to selectively deposit material from a gaseous precursor compound. Ultrasmall (less than a 100 nm across) spatial dimensions for selective area deposition may be achieved by this means. In this paper the authors outline a scheme foreselecting and designing main group cluster compounds and organometallics for this type of selective area deposition using nido-decaborane(14) as an example

  12. Automated electrochemical assembly of the protected potential TMG-chitotriomycin precursor based on rational optimization of the carbohydrate building block.

    Science.gov (United States)

    Nokami, Toshiki; Isoda, Yuta; Sasaki, Norihiko; Takaiso, Aki; Hayase, Shuichi; Itoh, Toshiyuki; Hayashi, Ryutaro; Shimizu, Akihiro; Yoshida, Jun-ichi

    2015-03-20

    The anomeric arylthio group and the hydroxyl-protecting groups of thioglycosides were optimized to construct carbohydrate building blocks for automated electrochemical solution-phase synthesis of oligoglucosamines having 1,4-β-glycosidic linkages. The optimization study included density functional theory calculations, measurements of the oxidation potentials, and the trial synthesis of the chitotriose trisaccharide. The automated synthesis of the protected potential N,N,N-trimethyl-d-glucosaminylchitotriomycin precursor was accomplished by using the optimized building block.

  13. Ionospheric earthquake precursors

    International Nuclear Information System (INIS)

    Bulachenko, A.L.; Oraevskij, V.N.; Pokhotelov, O.A.; Sorokin, V.N.; Strakhov, V.N.; Chmyrev, V.M.

    1996-01-01

    Results of experimental study on ionospheric earthquake precursors, program development on processes in the earthquake focus and physical mechanisms of formation of various type precursors are considered. Composition of experimental cosmic system for earthquake precursors monitoring is determined. 36 refs., 5 figs

  14. QbD based approach for optimization of Tenofovir disoproxil fumarate loaded liquid crystal precursor with improved permeability

    Directory of Open Access Journals (Sweden)

    Sharvil Patil

    2017-11-01

    Full Text Available BCS class III drugs suffer from a drawback of low permeability even though they have high aqueous solubility. The objective of current work was to screen the suitability of glyceryl monooleate (GMO/Pluronic F127 cubic phase liquid crystals precursors for permeation enhancement and in turn the bioavailability of tenofovir disoproxil fumarate (TDF, a BCS class III drug. Spray-drying method was used for preparation of TDF loaded liquid crystal precursors (LCP consisting of GMO/Pluronic F127 and lactose monohydrate with an ability to in situ transform into stable cubic phases upon hydration. The quality by design (QbD approach (Factorial design was used for batch optimization. Spherical TDF loaded LCP as revealed by scanning electron microscopy photographs when hydrated and analyzed by small angle X-ray scattering confirmed formation of cubic phase. Differential scanning calorimetry and X-ray diffraction studies confirmed the molecular dispersion of TDF in polymer matrix and also suggested the conversion of TDF from crystalline to amorphous form. In vitro TDF release from prepared LCP showed controlled drug release over a period of 10 h. Further ex vivo studies revealed permeation enhancing activity of prepared LCP, which was highest when tested in presence of digestive enzyme extract. Thus, formulation of stable liquid crystal powder precursor can serve as an alternative for designing oral delivery system for drugs with low permeability.

  15. Gene function analysis by artificial microRNAs in Physcomitrella patens.

    KAUST Repository

    Khraiwesh, Basel; Fattash, Isam; Arif, Muhammad Asif; Frank, Wolfgang

    2011-01-01

    MicroRNAs (miRNAs) are ~21 nt long small RNAs transcribed from endogenous MIR genes which form precursor RNAs with a characteristic hairpin structure. miRNAs control the expression of cognate target genes by binding to reverse complementary

  16. NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs.

    Directory of Open Access Journals (Sweden)

    Elize A Shirdel

    2011-02-01

    Full Text Available MicroRNAs are a class of small RNAs known to regulate gene expression at the transcript level, the protein level, or both. Since microRNA binding is sequence-based but possibly structure-specific, work in this area has resulted in multiple databases storing predicted microRNA:target relationships computed using diverse algorithms. We integrate prediction databases, compare predictions to in vitro data, and use cross-database predictions to model the microRNA:transcript interactome--referred to as the micronome--to study microRNA involvement in well-known signalling pathways as well as associations with disease. We make this data freely available with a flexible user interface as our microRNA Data Integration Portal--mirDIP (http://ophid.utoronto.ca/mirDIP.mirDIP integrates prediction databases to elucidate accurate microRNA:target relationships. Using NAViGaTOR to produce interaction networks implicating microRNAs in literature-based, KEGG-based and Reactome-based pathways, we find these signalling pathway networks have significantly more microRNA involvement compared to chance (p<0.05, suggesting microRNAs co-target many genes in a given pathway. Further examination of the micronome shows two distinct classes of microRNAs; universe microRNAs, which are involved in many signalling pathways; and intra-pathway microRNAs, which target multiple genes within one signalling pathway. We find universe microRNAs to have more targets (p<0.0001, to be more studied (p<0.0002, and to have higher degree in the KEGG cancer pathway (p<0.0001, compared to intra-pathway microRNAs.Our pathway-based analysis of mirDIP data suggests microRNAs are involved in intra-pathway signalling. We identify two distinct classes of microRNAs, suggesting a hierarchical organization of microRNAs co-targeting genes both within and between pathways, and implying differential involvement of universe and intra-pathway microRNAs at the disease level.

  17. Tissue-Based MicroRNAs as Predictors of Biochemical Recurrence after Radical Prostatectomy: What Can We Learn from Past Studies?

    Directory of Open Access Journals (Sweden)

    Zhongwei Zhao

    2017-09-01

    Full Text Available With the increasing understanding of the molecular mechanism of the microRNAs (miRNAs in prostate cancer (PCa, the predictive potential of miRNAs has received more attention by clinicians and laboratory scientists. Compared with the traditional prognostic tools based on clinicopathological variables, including the prostate-specific antigen, miRNAs may be helpful novel molecular biomarkers of biochemical recurrence for a more accurate risk stratification of PCa patients after radical prostatectomy and may contribute to personalized treatment. Tissue samples from prostatectomy specimens are easily available for miRNA isolation. Numerous studies from different countries have investigated the role of tissue-miRNAs as independent predictors of disease recurrence, either alone or in combination with other clinicopathological factors. For this purpose, a PubMed search was performed for articles published between 2008 and 2017. We compiled a profile of dysregulated miRNAs as potential predictors of biochemical recurrence and discussed their current clinical relevance. Because of differences in analytics, insufficient power and the heterogeneity of studies, and different statistical evaluation methods, limited consistency in results was obvious. Prospective multi-institutional studies with larger sample sizes, harmonized analytics, well-structured external validations, and reasonable study designs are necessary to assess the real prognostic information of miRNAs, in combination with conventional clinicopathological factors, as predictors of biochemical recurrence.

  18. Identifying MicroRNAs and Transcript Targets in Jatropha Seeds

    Science.gov (United States)

    Galli, Vanessa; Guzman, Frank; de Oliveira, Luiz F. V.; Loss-Morais, Guilherme; Körbes, Ana P.; Silva, Sérgio D. A.; Margis-Pinheiro, Márcia M. A. N.; Margis, Rogério

    2014-01-01

    MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs. PMID:24551031

  19. Precursor Ion Scan Mode-Based Strategy for Fast Screening of Polyether Ionophores by Copper-Induced Gas-Phase Radical Fragmentation Reactions.

    Science.gov (United States)

    Crevelin, Eduardo J; Possato, Bruna; Lopes, João L C; Lopes, Norberto P; Crotti, Antônio E M

    2017-04-04

    The potential of copper(II) to induce gas-phase fragmentation reactions in macrotetrolides, a class of polyether ionophores produced by Streptomyces species, was investigated by accurate-mass electrospray tandem mass spectrometry (ESI-MS/MS). Copper(II)/copper(I) transition directly induced production of diagnostic acylium ions with m/z 199, 185, 181, and 167 from α-cleavages of [macrotetrolides + Cu] 2+ . A UPLC-ESI-MS/MS methodology based on the precursor ion scan of these acylium ions was developed and successfully used to identify isodinactin (1), trinactin (2), and tetranactin (3) in a crude extract of Streptomyces sp. AMC 23 in the precursor ion scan mode. In addition, copper(II) was also used to induce radical fragmentation reactions in the carboxylic acid polyether ionophore nigericin. The resulting product ions with m/z 755 and 585 helped to identify nigericin in a crude extract of Streptomyces sp. Eucal-26 by means of precursor ion scan experiments, demonstrating that copper-induced fragmentation reactions can potentially identify different classes of polyether ionophores rapidly and selectively.

  20. New group III precursors for the MOVPE of GaAs and InP based material

    International Nuclear Information System (INIS)

    Hostaler, M.; Pohl, L.; Brauers, A.; Balk, P.; Frese, V.; Hovel, R.; Regel, G.K.; Hardtdegen, H.

    1989-01-01

    This paper presents proposals for the synthesis of several group III metal organics (In, Ga, Al compounds) and preliminary results on their use in the MOVPE (metal organic vapor phase epitaxy) of III-V semiconductors. The common feature of all these precursors is that they are saturated by inter- or intramolecular coordination. They are even non-pyrophoric and air resistant which is an interesting aspect with respect to safe handling. In addition, the compounds are liquid at room temperature with a low but sufficient vapor pressure for MOVPE without additional heating of the source

  1. Common features of microRNA target prediction tools

    Directory of Open Access Journals (Sweden)

    Sarah M. Peterson

    2014-02-01

    Full Text Available The human genome encodes for over 1800 microRNAs, which are short noncoding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one microRNA to target multiple gene transcripts, microRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of microRNA targets is a critical initial step in identifying microRNA:mRNA target interactions for experimental validation. The available tools for microRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to microRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all microRNA target prediction tools, four main aspects of the microRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MicroRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

  2. Preparation of iron molybdate catalysts for methanol to formaldehyde oxidation based on ammonium molybdoferrate(II precursor

    Directory of Open Access Journals (Sweden)

    N.V. Nikolenko

    2018-03-01

    Full Text Available It was demonstrated that iron molybdate catalysts for methanol oxidation can be prepared using Fe(II as a precursor instead of Fe(III. This would allow for reduction of acidity of preparation solutions as well as elimination of Fe(III oxide impurities which are detrimental for the process selectivity. The system containing Fe(II and Mo(VI species in aqueous solution was investigated using UV–Vis spectroscopy. It was demonstrated that three types of chemical reactions occur in the Fe(II–Mo(VI system: (i formation of complexes between Fe(II and molybdate(VI ions, (ii inner sphere oxidation of coordinated Fe(II by Mo(VI and (iii decomposition of the Fe–Mo complexes to form scarcely soluble Fe(III molybdate, Mo(VI hydrous trioxide and molybdenum blue. Solid molybdoferrate(II prepared by interaction of Fe(II and Mo(VI in solution was characterized by EDXA, TGA, DTA and XRD and a scheme of its thermal evolution proposed. The iron molybdate catalyst prepared from Fe(II precursor was tested in methanol-to-formaldehyde oxidation in a continuous flow fixed-bed reactor to show similar activity and selectivity to the conventional catalyst prepared with the use of Fe(III.

  3. A ratiometric electrochemical biosensor for the exosomal microRNAs detection based on bipedal DNA walkers propelled by locked nucleic acid modified toehold mediate strand displacement reaction.

    Science.gov (United States)

    Zhang, Jing; Wang, Liang-Liang; Hou, Mei-Feng; Xia, Yao-Kun; He, Wen-Hui; Yan, An; Weng, Yun-Ping; Zeng, Lu-Peng; Chen, Jing-Hua

    2018-04-15

    Sensitive and selective detection of microRNAs (miRNAs) in cancer cells derived exosomes have attracted rapidly growing interest owing to their potential in diagnostic and prognostic applications. Here, we design a ratiometric electrochemical biosensor based on bipedal DNA walkers for the attomolar detection of exosomal miR-21. In the presence of miR-21, DNA walkers are activated to walk continuously along DNA tracks, resulting in conformational changes as well as considerable increases of the signal ratio produced by target-respond and target-independent reporters. With the signal cascade amplification of DNA walkers, the biosensor exhibits ultrahigh sensitivity with the limit of detection (LOD) down to 67 aM. Furthermore, owing to the background-correcting function of target-independent reporters termed as reference reporters, the biosensor is robust and stable enough to be applied in the detection of exosomal miR-21 extracted from breast cancer cell lines and serums. In addition, because locked nucleic acid (LNA) modified toehold mediate strand displacement reaction (TMSDR) has extraordinary discriminative ability, the biosensor displays excellent selectivity even against the single-base-mismatched target. It is worth mentioning that our sensor is regenerative and stable for at least 5 cycles without diminution in sensitivity. In brief, the high sensitivity, selectivity and reproducibility, together with cheap, make the proposed biosensor a promising approach for exosomal miRNAs detection, in conjunction with early point-of-care testing (POCT) of cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Annotation of mammalian primary microRNAs

    Directory of Open Access Journals (Sweden)

    Enright Anton J

    2008-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are important regulators of gene expression and have been implicated in development, differentiation and pathogenesis. Hundreds of miRNAs have been discovered in mammalian genomes. Approximately 50% of mammalian miRNAs are expressed from introns of protein-coding genes; the primary transcript (pri-miRNA is therefore assumed to be the host transcript. However, very little is known about the structure of pri-miRNAs expressed from intergenic regions. Here we annotate transcript boundaries of miRNAs in human, mouse and rat genomes using various transcription features. The 5' end of the pri-miRNA is predicted from transcription start sites, CpG islands and 5' CAGE tags mapped in the upstream flanking region surrounding the precursor miRNA (pre-miRNA. The 3' end of the pri-miRNA is predicted based on the mapping of polyA signals, and supported by cDNA/EST and ditags data. The predicted pri-miRNAs are also analyzed for promoter and insulator-associated regulatory regions. Results We define sets of conserved and non-conserved human, mouse and rat pre-miRNAs using bidirectional BLAST and synteny analysis. Transcription features in their flanking regions are used to demarcate the 5' and 3' boundaries of the pri-miRNAs. The lengths and boundaries of primary transcripts are highly conserved between orthologous miRNAs. A significant fraction of pri-miRNAs have lengths between 1 and 10 kb, with very few introns. We annotate a total of 59 pri-miRNA structures, which include 82 pre-miRNAs. 36 pri-miRNAs are conserved in all 3 species. In total, 18 of the confidently annotated transcripts express more than one pre-miRNA. The upstream regions of 54% of the predicted pri-miRNAs are found to be associated with promoter and insulator regulatory sequences. Conclusion Little is known about the primary transcripts of intergenic miRNAs. Using comparative data, we are able to identify the boundaries of a significant proportion of

  5. MicroRNA profiling in intraocular medulloepitheliomas.

    Directory of Open Access Journals (Sweden)

    Deepak P Edward

    Full Text Available To study the differential expression of microRNA (miRNA profiles between intraocular medulloepithelioma (ME and normal control tissue (CT.Total RNA was extracted from formalin fixed paraffin embedded (FFPE intraocular ME (n=7 and from age matched ciliary body controls (n=8. The clinical history and phenotype was recorded. MiRNA profiles were determined using the Affymetrix GeneChip miRNA Arrays analyzed using expression console 1.3 software. Validation of significantly dysregulated miRNA was confirmed by quantitative real-time PCR. The web-based DNA Intelligent Analysis (DIANA-miRPath v2.0 was used to perform enrichment analysis of differentially expressed (DE miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG pathway.The pathologic evaluation revealed one benign (benign non-teratoid, n=1 and six malignant tumors (malignant teratoid, n=2; malignant non-teratoid, n = 4. A total of 88 miRNAs were upregulated and 43 miRNAs were downregulated significantly (P<0.05 in the tumor specimens. Many of these significantly dysregulated miRNAs were known to play various roles in carcinogenesis and tumor behavior. RT-PCR validated three significantly upregulated miRNAs and three significantly downregulated miRNAs namely miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p and miR-211. Many DE miRNAs that were significant in ME tumors showed dysregulation in retinoblastoma, glioblastoma, and precursor, normal and reactive human cartilage. Enriched pathway analysis suggested a significant association of upregulated miRNAs with 15 pathways involved in prion disease and several types of cancer. The pathways involving significantly downregulated miRNAs included the toll-like receptor (TLR (p<4.36E-16 and Nuclear Factor kappa B (NF-κB signaling pathways (p<9.00E-06.We report significantly dysregulated miRNAs in intraocular ME tumors, which exhibited abnormal profiles in other cancers as well such as retinoblastoma and glioblastoma. Pathway analysis

  6. Metallorganic chemical vapor deposition and atomic layer deposition approaches for the growth of hafnium-based thin films from dialkylamide precursors for advanced CMOS gate stack applications

    Science.gov (United States)

    Consiglio, Steven P.

    To continue the rapid progress of the semiconductor industry as described by Moore's Law, the feasibility of new material systems for front end of the line (FEOL) process technologies needs to be investigated, since the currently employed polysilicon/SiO2-based transistor system is reaching its fundamental scaling limits. Revolutionary breakthroughs in complementary-metal-oxide-semiconductor (CMOS) technology were recently announced by Intel Corporation and International Business Machines Corporation (IBM), with both organizations revealing significant progress in the implementation of hafnium-based high-k dielectrics along with metal gates. This announcement was heralded by Gordon Moore as "...the biggest change in transistor technology since the introduction of polysilicon gate MOS transistors in the late 1960s." Accordingly, the study described herein focuses on the growth of Hf-based dielectrics and Hf-based metal gates using chemical vapor-based deposition methods, specifically metallorganic chemical vapor deposition (MOCVD) and atomic layer deposition (ALD). A family of Hf source complexes that has received much attention recently due to their desirable properties for implementation in wafer scale manufacturing is the Hf dialkylamide precursors. These precursors are room temperature liquids and possess sufficient volatility and desirable decomposition characteristics for both MOCVD and ALD processing. Another benefit of using these sources is the existence of chemically compatible Si dialkylamide sources as co-precursors for use in Hf silicate growth. The first part of this study investigates properties of MOCVD-deposited HfO2 and HfSixOy using dimethylamido Hf and Si precursor sources using a customized MOCVD reactor. The second part of this study involves a study of wet and dry surface pre-treatments for ALD growth of HfO2 using tetrakis(ethylmethylamido)hafnium in a wafer scale manufacturing environment. The third part of this study is an investigation of

  7. Association of microRNA-125a and microRNA-499a polymorphisms in chronic periodontitis in a sample south Indian population: A hospital-based genetic association study.

    Science.gov (United States)

    Venugopal, Priyanka; Lavu, Vamsi; Rao, Suresh Ranga; Venkatesan, Vettriselvi

    2017-10-05

    Periodontitis is a chronic inflammatory disease, caused by interaction between periodontopathic bacteria and the host immune response. MicroRNAs are small, single-stranded molecules, which play a key role in the regulation of diverse biological processes. Dysregulation of microRNAs function can lead to several diseases such as autoimmune and chronic inflammatory diseases. The objective of the study was to determine the association between selected single nucleotide polymorphisms in miR-125a, miR-499 and LIN28 homology A with chronic periodontitis susceptibility in a sample population from south India. Genotyping of the single nucleotide polymorphisms in miR-125a (rs41275794, rs12976445, rs10404453 and rs12975333), miR-499 (rs3746444) and LIN28 homolog A (rs3811463) was performed in DNA from288 controls (individuals with healthy gingiva) and 262 cases (chronic periodontitis patients) by direct dye-terminator sequencing. Disease association analysis revealed a significant association of the variant alleles of the miR-499a polymorphism (rs3746444) in chronic periodontitis [OR=2.07; 95%CI (1.35-3.17)]. The risk associated C-allele frequency was found to be higher in chronic periodontitis subjects as compared to that of healthy individuals. Similar results were also observed in the dominant model [OR=2.42; 95% CI (1.67-3.51)]. The recessive model for miR-125a polymorphism (rs12976445) was also found to be statistically significant with OR=1.54 and 95% CI (1.03-2.30). The haplotype "GCGGCA" was found to be higher in chronic periodontitis subjects than in healthy individuals. Pairwise linkage disequilibrium analysis exhibited that the polymorphisms, rs41275794 and rs12976445 in miR-125a, were in strong linkage equilibrium (D'=0.97). Epistatic interaction by multifactorial dimensionality reduction analysis revealed that the genotypes of the polymorphisms of miR-125a (rs41275794, rs12976445, rs10404453), miR-499a (rs3746444) and LIN28 (rs3811463) were interacting

  8. miRBase: annotating high confidence microRNAs using deep sequencing data.

    Science.gov (United States)

    Kozomara, Ana; Griffiths-Jones, Sam

    2014-01-01

    We describe an update of the miRBase database (http://www.mirbase.org/), the primary microRNA sequence repository. The latest miRBase release (v20, June 2013) contains 24 521 microRNA loci from 206 species, processed to produce 30 424 mature microRNA products. The rate of deposition of novel microRNAs and the number of researchers involved in their discovery continue to increase, driven largely by small RNA deep sequencing experiments. In the face of these increases, and a range of microRNA annotation methods and criteria, maintaining the quality of the microRNA sequence data set is a significant challenge. Here, we describe recent developments of the miRBase database to address this issue. In particular, we describe the collation and use of deep sequencing data sets to assign levels of confidence to miRBase entries. We now provide a high confidence subset of miRBase entries, based on the pattern of mapped reads. The high confidence microRNA data set is available alongside the complete microRNA collection at http://www.mirbase.org/. We also describe embedding microRNA-specific Wikipedia pages on the miRBase website to encourage the microRNA community to contribute and share textual and functional information.

  9. Development of Ni-Based Catalysts Derived from Hydrotalcite-Like Compounds Precursors for Synthesis Gas Production via Methane or Ethanol Reforming

    Directory of Open Access Journals (Sweden)

    Ya-Li Du

    2017-02-01

    Full Text Available As a favorably clean fuel, syngas (synthesis gas production has been the focus of concern in past decades. Substantial literatures reported the syngas production by various catalytic reforming reactions particularly in methane or ethanol reforming. Among the developed catalysts in these reforming processes, Ni-based catalysts from hydrotalcite-like compounds (HTLcs precursors have drawn considerable attention for their preferable structural traits. This review covers the recent literature reporting syngas production with Ni-based catalysts from HTLc precursors via methane or ethanol reforming. The discussion was initiated with catalyst preparation (including conventional and novel means, followed by subsequent thermal treatment processes, then composition design and the addition of promoters in these catalysts. As Ni-based catalysts have thermodynamic potential to deactivate because of carbon deposition or metal sintering, measures for dealing with these problems were finally summarized. To obtain optimal catalytic performances and resultantly better syngas production, based on analyzing the achievements of the references, some perspectives were finally proposed.

  10. An "off-on" electrochemiluminescent biosensor based on DNAzyme-assisted target recycling and rolling circle amplifications for ultrasensitive detection of microRNA.

    Science.gov (United States)

    Zhang, Pu; Wu, Xiaoyan; Yuan, Ruo; Chai, Yaqin

    2015-03-17

    In this study, an off-on switching of a dual amplified electrochemiluminescence (ECL) biosensor based on Pb(2+)-induced DNAzyme-assisted target recycling and rolling circle amplification (RCA) was constructed for microRNA (miRNA) detection. First, the primer probe with assistant probe and miRNA formed Y junction which was cleaved with the addition of Pb(2+) to release miRNA. Subsequently, the released miRNA could initiate the next recycling process, leading to the generation of numerous intermediate DNA sequences (S2). Afterward, bare glassy carbon electrode (GCE) was immersed into HAuCl4 solution to electrodeposit a Au nanoparticle layer (depAu), followed by the assembly of a hairpin probe (HP). Then, dopamine (DA)-modified DNA sequence (S1) was employed to hybridize with HP, which switching off the sensing system. This is the first work that employs DA to quench luminol ECL signal, possessing the biosensor ultralow background signal. Afterward, S2 produced by the target recycling process was loaded onto the prepared electrode to displace S1 and served as an initiator for RCA. With rational design, numerous repeated DNA sequences coupling with hemin to form hemin/G-quadruplex were generated, which could exhibit strongly catalytic toward H2O2, thus amplified the ECL signal and switched the ON state of the sensing system. The liner range for miRNA detection was from 1.0 fM to 100 pM with a low detection limit down to 0.3 fM. Moreover, with the high sensitivity and specificity induced by the dual signal amplification, the proposed miRNA biosensor holds great potential for analysis of other interesting tumor markers.

  11. Label-Free Platform for MicroRNA Detection Based on the Fluorescence Quenching of Positively Charged Gold Nanoparticles to Silver Nanoclusters.

    Science.gov (United States)

    Miao, Xiangmin; Cheng, Zhiyuan; Ma, Haiyan; Li, Zongbing; Xue, Ning; Wang, Po

    2018-01-16

    A novel strategy was developed for microRNA-155 (miRNA-155) detection based on the fluorescence quenching of positively charged gold nanoparticles [(+)AuNPs] to Ag nanoclusters (AgNCs). In the designed system, DNA-stabilized Ag nanoclusters (DNA/AgNCs) were introduced as fluorescent probes, and DNA-RNA heteroduplexes were formed upon the addition of target miRNA-155. Meanwhile, the (+)AuNPs could be electrostatically adsorbed on the negatively charged single-stranded DNA (ssDNA) or DNA-RNA heteroduplexes to quench the fluorescence signal. In the presence of duplex-specific nuclease (DSN), DNA-RNA heteroduplexes became a substrate for the enzymatic hydrolysis of the DNA strand to yield a fluorescence signal due to the diffusion of AgNCs away from (+)AuNPs. Under the optimal conditions, (+)AuNPs displayed very high quenching efficiency to AgNCs, which paved the way for ultrasensitive detection with a low detection limit of 33.4 fM. In particular, the present strategy demonstrated excellent specificity and selectivity toward the detection of target miRNA against control miRNAs, including mutated miRNA-155, miRNA-21, miRNA-141, let-7a, and miRNA-182. Moreover, the practical application value of the system was confirmed by the evaluation of the expression levels of miRNA-155 in clinical serum samples with satisfactory results, suggesting that the proposed sensing platform is promising for applications in disease diagnosis as well as the fundamental research of biochemistry.

  12. Highly sensitive and label-free electrochemical detection of microRNAs based on triple signal amplification of multifunctional gold nanoparticles, enzymes and redox-cycling reaction.

    Science.gov (United States)

    Liu, Lin; Xia, Ning; Liu, Huiping; Kang, Xiaojing; Liu, Xiaoshuan; Xue, Chan; He, Xiaoling

    2014-03-15

    MicroRNAs (miRNAs) are believed to be important for cancer diagnosis and prognosis, serving as reliable molecular biomarkers. In this work, we presented a label-free and highly sensitive electrochemical genosensor for miRNAs detection with the triple signal amplification of gold nanoparticles (AuNPs), alkaline phosphatase (ALP) and p-aminophenol (p-AP) redox cycling. The label-free strategy is based on the difference in the structures of RNA and DNA. Specifically, miRNAs were first captured by the pre-immobilized DNA probes on a gold electrode. Next, the cis-diol group of ribose sugar at the end of the miRNAs chain allowed 3-aminophenylboronic acid (APBA)/biotin-modified multifunctional AuNPs (denoted as APBA-biotin-AuNPs) to be attached through the formation of a boronate ester covalent bond, which facilitated the capture of streptavidin-conjugated alkaline phosphatase (SA-ALP) via the biotin-streptavidin interaction. After the addition of the 4-aminophenylphosphate (p-APP) substrate, the enzymatic conversion from p-APP to p-AP occurred. The resulting p-AP could be cycled by a chemical reducing reagent after its electro-oxidization on the electrode (known as p-AP redox cycling), thus enabling an increase in the anodic current. As a result, the current increased linearly with the miRNAs concentration over a range of 10 fM-5 pM, and a detection limit of 3 fM was achieved. We believe that this work will be valuable for the design of new types of label-free and sensitive electrochemical biosensors. © 2013 Published by Elsevier B.V.

  13. Novel Strategy to Control Transgene Expression Mediated by a Sendai Virus-Based Vector Using a Nonstructural C Protein and Endogenous MicroRNAs.

    Directory of Open Access Journals (Sweden)

    Masayuki Sano

    Full Text Available Tissue-specific control of gene expression is an invaluable tool for studying various biological processes and medical applications. Efficient regulatory systems have been utilized to control transgene expression in various types of DNA viral or integrating viral vectors. However, existing regulatory systems are difficult to transfer into negative-strand RNA virus vector platforms because of significant differences in their transcriptional machineries. In this study, we developed a novel strategy for regulating transgene expression mediated by a cytoplasmic RNA vector based on a replication-defective and persistent Sendai virus (SeVdp. Because of the capacity of Sendai virus (SeV nonstructural C proteins to specifically inhibit viral RNA synthesis, overexpression of C protein significantly reduced transgene expression mediated by SeVdp vectors. We found that SeV C overexpression concomitantly reduced SeVdp mRNA levels and genomic RNA synthesis. To control C expression, target sequences for an endogenous microRNA were incorporated into the 3' untranslated region of the C genes. Incorporation of target sequences for miR-21 into the SeVdp vector restored transgene expression in HeLa cells by decreasing C expression. Furthermore, the SeVdp vector containing target sequences for let-7a enabled cell-specific control of transgene expression in human fibroblasts and induced pluripotent stem cells. Our findings demonstrate that SeV C can be used as an effective regulator for controlling transgene expression. This strategy will contribute to efficient and less toxic SeVdp-mediated gene transfer in various biological applications.

  14. Design and Synthesis of Novel Antimicrobial Acyclic and Heterocyclic Dyes and Their Precursors for Dyeing and/or Textile Finishing Based on 2-N-Acylamino-4,5,6,7-tetrahydro-benzo[b]thiophene Systems

    Directory of Open Access Journals (Sweden)

    Rafat Milad Mohareb

    2011-07-01

    Full Text Available A series of novel polyfunctionalized acyclic and heterocyclic dye precursors and their respective azo (hydrazone counterpart dyes and dye precursors based on conjugate enaminones and/or enaminonitrile moieties were synthesized. The dyes and their precursors are based on 2-cyano-N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl-acetamide, 2-ethoxycarbonyl-N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl-acetamide or 2-phenylcarbamoyl-N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl-acetamide systems as precursors. The latter compounds were used to synthesize polyfunctional thiophene-, thiazole-, pyrazole, pyridine-, pyrimidine-, oxazine-, as well as acyclic moieties. The dyes and dye precursors were characterized by elemental analysis and spectral methods. All dyes and their precursors were screened in vitro and evaluated for both their antibacterial and antifungal activities. MIC data of the novel dye systems and their respective precursors showed significant antimicrobial activity against most tested organisms. Some compounds exhibited comparable or even higher efficiency than selected standards. Dyes were applied at 5% depth for disperse dyeing of nylon, acetate and polyester fabrics. Their spectral characteristics and fastness properties were measured and evaluated.

  15. Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

    Science.gov (United States)

    Sewer, Alain; Gubian, Sylvain; Kogel, Ulrike; Veljkovic, Emilija; Han, Wanjiang; Hengstermann, Arnd; Peitsch, Manuel C; Hoeng, Julia

    2014-05-17

    High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the "common reference design" and processed as "pseudo-single-channel". They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription-polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data

  16. Bioinspired magnetite synthesis via solid precursor phases

    NARCIS (Netherlands)

    Lenders, J.J.M.; Mirabello, G.; Sommerdijk, N.A.J.M.

    2016-01-01

    Living organisms often exploit solid but poorly ordered mineral phases as precursors in the biomineralization of their inorganic body parts. Generally speaking, such precursor-based approaches allow the organisms-without the need of high supersaturation levels-to accumulate significant quantities of

  17. Accurate microRNA target prediction correlates with protein repression levels

    Directory of Open Access Journals (Sweden)

    Simossis Victor A

    2009-09-01

    Full Text Available Abstract Background MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and disease. Results DIANA-microT 3.0 is an algorithm for microRNA target prediction which is based on several parameters calculated individually for each microRNA and combines conserved and non-conserved microRNA recognition elements into a final prediction score, which correlates with protein production fold change. Specifically, for each predicted interaction the program reports a signal to noise ratio and a precision score which can be used as an indication of the false positive rate of the prediction. Conclusion Recently, several computational target prediction programs were benchmarked based on a set of microRNA target genes identified by the pSILAC method. In this assessment DIANA-microT 3.0 was found to achieve the highest precision among the most widely used microRNA target prediction programs reaching approximately 66%. The DIANA-microT 3.0 prediction results are available online in a user friendly web server at http://www.microrna.gr/microT

  18. Identified EM Earthquake Precursors

    Science.gov (United States)

    Jones, Kenneth, II; Saxton, Patrick

    2014-05-01

    Many attempts have been made to determine a sound forecasting method regarding earthquakes and warn the public in turn. Presently, the animal kingdom leads the precursor list alluding to a transmission related source. By applying the animal-based model to an electromagnetic (EM) wave model, various hypotheses were formed, but the most interesting one required the use of a magnetometer with a differing design and geometry. To date, numerous, high-end magnetometers have been in use in close proximity to fault zones for potential earthquake forecasting; however, something is still amiss. The problem still resides with what exactly is forecastable and the investigating direction of EM. After a number of custom rock experiments, two hypotheses were formed which could answer the EM wave model. The first hypothesis concerned a sufficient and continuous electron movement either by surface or penetrative flow, and the second regarded a novel approach to radio transmission. Electron flow along fracture surfaces was determined to be inadequate in creating strong EM fields, because rock has a very high electrical resistance making it a high quality insulator. Penetrative flow could not be corroborated as well, because it was discovered that rock was absorbing and confining electrons to a very thin skin depth. Radio wave transmission and detection worked with every single test administered. This hypothesis was reviewed for propagating, long-wave generation with sufficient amplitude, and the capability of penetrating solid rock. Additionally, fracture spaces, either air or ion-filled, can facilitate this concept from great depths and allow for surficial detection. A few propagating precursor signals have been detected in the field occurring with associated phases using custom-built loop antennae. Field testing was conducted in Southern California from 2006-2011, and outside the NE Texas town of Timpson in February, 2013. The antennae have mobility and observations were noted for

  19. A dynamic dilution system-based evaluation of the procedure adopted for determining ozone precursor volatile compounds.

    Science.gov (United States)

    Palluau, Fabienne; Mirabel, Philippe; Millet, Maurice

    2005-02-01

    A dynamic dilution system was created to evaluate the performance and the reliability of ozone precursor volatile organic compound (VOC) sampling ("TO-Can" canisters) and analysis (thermal desorption/gas chromatography/flame ionisation detection) techniques used by the "Laboratoire Interregional de Chimie du Grand Est (LIC)". Different atmospheres of VOCs were generated at concentrations between 0.8 and 25 ppb, with temperatures of 0, 10, 20 and 30 degrees C, and with relative humidities of 0, 30, 50, 70 and 90%. These conditions are generally representative of those commonly observed in ambient air in the eastern France. This dynamic dilution allows the simulation of a wide range of scenarios (concentrations, temperatures and relative humidities). After assessing the capacity and performance of the system, it was applied in order to evaluate the recoveries and stabilities of VOCs from canisters used for the collection and analysis of two mixtures of VOCs. The first mixture contained six alkanes (ethane, propane, butane, pentane, hexane and heptane), and the second contained five alkenes (ethene, propene, butene, 1-pentene and 1-hexene), five aromatics (benzene, toluene, ethylbenzene, m-xylene and o-xylene), acetylene, and 1,3-butadiene. No significant losses of alkanes from the canisters were observed after 21 days of storage, and good recoveries of alkanes from the canisters (>80%) were obtained regardless of the concentration, the temperature and the relative humidity. However, losses of certain aromatics were noted at low relative humidity.

  20. CID-miRNA: A web server for prediction of novel miRNA precursors in human genome

    International Nuclear Information System (INIS)

    Tyagi, Sonika; Vaz, Candida; Gupta, Vipin; Bhatia, Rohit; Maheshwari, Sachin; Srinivasan, Ashwin; Bhattacharya, Alok

    2008-01-01

    microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at (http://mirna.jnu.ac.in/cidmirna/)

  1. Plant MicroRNA Prediction by Supervised Machine Learning Using C5.0 Decision Trees

    Directory of Open Access Journals (Sweden)

    Philip H. Williams

    2012-01-01

    Full Text Available MicroRNAs (miRNAs are nonprotein coding RNAs between 20 and 22 nucleotides long that attenuate protein production. Different types of sequence data are being investigated for novel miRNAs, including genomic and transcriptomic sequences. A variety of machine learning methods have successfully predicted miRNA precursors, mature miRNAs, and other nonprotein coding sequences. MirTools, mirDeep2, and miRanalyzer require “read count” to be included with the input sequences, which restricts their use to deep-sequencing data. Our aim was to train a predictor using a cross-section of different species to accurately predict miRNAs outside the training set. We wanted a system that did not require read-count for prediction and could therefore be applied to short sequences extracted from genomic, EST, or RNA-seq sources. A miRNA-predictive decision-tree model has been developed by supervised machine learning. It only requires that the corresponding genome or transcriptome is available within a sequence window that includes the precursor candidate so that the required sequence features can be collected. Some of the most critical features for training the predictor are the miRNA:miRNA∗ duplex energy and the number of mismatches in the duplex. We present a cross-species plant miRNA predictor with 84.08% sensitivity and 98.53% specificity based on rigorous testing by leave-one-out validation.

  2. Gene function analysis by artificial microRNAs in Physcomitrella patens.

    KAUST Repository

    Khraiwesh, Basel

    2011-01-01

    MicroRNAs (miRNAs) are ~21 nt long small RNAs transcribed from endogenous MIR genes which form precursor RNAs with a characteristic hairpin structure. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences resulting in cleavage or translational inhibition of the target RNA. Artificial miRNAs (amiRNAs) can be generated by exchanging the miRNA/miRNA sequence of endogenous MIR precursor genes, while maintaining the general pattern of matches and mismatches in the foldback. Thus, for functional gene analysis amiRNAs can be designed to target any gene of interest. During the last decade the moss Physcomitrella patens emerged as a model plant for functional gene analysis based on its unique ability to integrate DNA into the nuclear genome by homologous recombination which allows for the generation of targeted gene knockout mutants. In addition to this, we developed a protocol to express amiRNAs in P. patens that has particular advantages over the generation of knockout mutants and might be used to speed up reverse genetics approaches in this model species.

  3. Plant MicroRNA Prediction by Supervised Machine Learning Using C5.0 Decision Trees.

    Science.gov (United States)

    Williams, Philip H; Eyles, Rod; Weiller, Georg

    2012-01-01

    MicroRNAs (miRNAs) are nonprotein coding RNAs between 20 and 22 nucleotides long that attenuate protein production. Different types of sequence data are being investigated for novel miRNAs, including genomic and transcriptomic sequences. A variety of machine learning methods have successfully predicted miRNA precursors, mature miRNAs, and other nonprotein coding sequences. MirTools, mirDeep2, and miRanalyzer require "read count" to be included with the input sequences, which restricts their use to deep-sequencing data. Our aim was to train a predictor using a cross-section of different species to accurately predict miRNAs outside the training set. We wanted a system that did not require read-count for prediction and could therefore be applied to short sequences extracted from genomic, EST, or RNA-seq sources. A miRNA-predictive decision-tree model has been developed by supervised machine learning. It only requires that the corresponding genome or transcriptome is available within a sequence window that includes the precursor candidate so that the required sequence features can be collected. Some of the most critical features for training the predictor are the miRNA:miRNA(∗) duplex energy and the number of mismatches in the duplex. We present a cross-species plant miRNA predictor with 84.08% sensitivity and 98.53% specificity based on rigorous testing by leave-one-out validation.

  4. Fluorescence-based codetection with protein markers reveals distinct cellular compartments for altered MicroRNA expression in solid tumors

    DEFF Research Database (Denmark)

    Sempere, Lorenzo F; Preis, Meir; Yezefski, Todd

    2010-01-01

    of altered miRNA expression in solid tumors, we developed a sensitive fluorescence-based in situ hybridization (ISH) method to visualize miRNA accumulation within individual cells in formalin-fixed, paraffin-embedded tissue specimens. This ISH method was implemented to be compatible with routine clinical...

  5. Immunofluorescence-based screening identifies germ cell associated microRNA 302 as an antagonist to p63 expression

    DEFF Research Database (Denmark)

    Scheel, Andreas Hans Joachim; Beyer, Ulrike; Agami, Reuven

    2009-01-01

    The tumor suppressor homologue p63 is required for proper skin and limb development, but specific isoforms of it also act as a "guardian of the germline." To gain insight into the regulation of p63 expression, we performed immunofluorescence-based screening assays. Using a large collection of micro...

  6. Efficient Planar Structured Perovskite Solar Cells with Enhanced Open-Circuit Voltage and Suppressed Charge Recombination Based on a Slow Grown Perovskite Layer from Lead Acetate Precursor.

    Science.gov (United States)

    Li, Cong; Guo, Qiang; Wang, Zhibin; Bai, Yiming; Liu, Lin; Wang, Fuzhi; Zhou, Erjun; Hayat, Tasawar; Alsaedi, Ahmed; Tan, Zhan'ao

    2017-12-06

    For planar structured organic-inorganic hybrid perovskite solar cells (PerSCs) with the poly(3,4-ethylenedioxythiophene:polystyrene sulfonate) (PEDOT:PSS) hole transport layer, the open-circuit voltage (V oc ) of the device is limited to be about 1.0 V, resulting in inferior performance in comparison with TiO 2 -based planar counterparts. Therefore, increasing V oc of the PEDOT:PSS-based planar device is an important way to enhance the efficiency of the PerSCs. Herein, we demonstrate a novel approach for perovskite film formation and the film is formed by slow growth from lead acetate precursor via a one-step spin-coating process without the thermal annealing (TA) process. Because the perovskite layer grows slowly and naturally, high-quality perovskite film can be achieved with larger crystalline particles, less defects, and smoother surface morphology. Ultraviolet absorption, X-ray diffraction, scanning electron microscopy, steady-state fluorescence spectroscopy (photoluminescence), and time-resolved fluorescence spectroscopy are used to clarify the crystallinity, morphology, and internal defects of perovskite thin films. The power conversion efficiency of p-i-n PerSCs based on slow-grown film (16.33%) shows greatly enhanced performance compared to that of the control device based on traditional thermally annealed perovskite film (14.33%). Furthermore, the V oc of the slow-growing device reaches 1.12 V, which is 0.1 V higher than that of the TA device. These findings indicate that slow growth of the perovskite layer from lead acetate precursor is a promising approach to achieve high-quality perovskite film for high-performance PerSCs.

  7. Intronic microRNAs

    International Nuclear Information System (INIS)

    Ying, S.-Y.; Lin, S.-L.

    2005-01-01

    MicroRNAs (miRNAs), small single-stranded regulatory RNAs capable of interfering with intracellular mRNAs that contain partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. MiRNA was originally discovered in the intergenic regions of the Caenorhabditis elegans genome as native RNA fragments that modulate a wide range of genetic regulatory pathways during animal development. However, neither RNA promoter nor polymerase responsible for miRNA biogenesis was determined. Recent findings of intron-derived miRNA in C. elegans, mouse, and human have inevitably led to an alternative pathway for miRNA biogenesis, which relies on the coupled interaction of Pol-II-mediated pre-mRNA transcription and intron excision, occurring in certain nuclear regions proximal to genomic perichromatin fibrils

  8. Earthquakes: hydrogeochemical precursors

    Science.gov (United States)

    Ingebritsen, Steven E.; Manga, Michael

    2014-01-01

    Earthquake prediction is a long-sought goal. Changes in groundwater chemistry before earthquakes in Iceland highlight a potential hydrogeochemical precursor, but such signals must be evaluated in the context of long-term, multiparametric data sets.

  9. In Vitro and In Vivo Evaluation of Sol-Gel Derived TiO2 Coatings Based on a Variety of Precursors and Synthesis Conditions

    Directory of Open Access Journals (Sweden)

    Krzysztof Marycz

    2014-01-01

    Full Text Available The effect of synthesis way of TiO2 coatings on biocompatibility of transplanted materials using an in vitro and in vivo rat model was investigated. TiO2 layers were synthesized by a nonaqueous sol-gel dip-coating method on stainless steel 316L substrates applying two different precursors and their combination. Morphology and topography of newly formed biomaterials were determined as well as chemical composition and elemental distribution of a surface samples. In vitro tests were conducted by adipose-derived mesenchymal stem cells cultured on TiO2 coatings and stainless steel without coatings to assess the bioreactivity of obtained materials. A positive biological effect of TiO2/316L/1 coatings—based on titanium(IV ethoxide—was found in both in vitro and in vivo models. The TiO2/316L/1 exhibited the highest roughness and the lowest titanium concentration in TiO2 than TiO2/316L/2—based on titanium(IV propoxide and TiO2/316L/3—based on both above-mentioned precursors. The proper fibroblast-like morphology and higher proliferation rate of cells cultured on TiO2/316L/1 were observed when compared to the other biomaterials. No inflammatory response in the bone surrounding implant covered by each of the obtained TiO2 was present. Our results showed that improvement of routinely used stainless steel 316L with TiO2/316L/1 layer can stimulate beneficial biological response.

  10. From cell biology to immunology: Controlling metastatic progression of cancer via microRNA regulatory networks.

    Science.gov (United States)

    Park, Jae Hyon; Theodoratou, Evropi; Calin, George A; Shin, Jae Il

    2016-01-01

    Recently, the study of microRNAs has expanded our knowledge of the fundamental processes of cancer biology and the underlying mechanisms behind tumor metastasis. Extensive research in the fields of microRNA and its novel mechanisms of actions against various cancers has more recently led to the trial of a first cancer-targeted microRNA drug, MRX34. Yet, these microRNAs are mostly being studied and clinically trialed solely based on the understanding of their cell biologic effects, thus, neglecting the important immunologic effects that are sometimes opposite of the cell biologic effects. Here, we summarize both the cell biologic and immunologic effects of various microRNAs and discuss the importance of considering both effects before using them in clinical settings. We stress the importance of understanding the miRNA's effect on cancer metastasis from a "systems" perspective before developing a miRNA-targeted therapeutic in treating cancer metastasis.

  11. Ratiometric FRET-based detection of DNA and micro-RNA on the surface using TIRF detection

    International Nuclear Information System (INIS)

    Matveeva, Evgenia G.; Gryczynski, Zygmunt; Stewart, Donald R.; Gryczynski, Ignacy

    2010-01-01

    A new FRET-based method for the ratiometric detection of DNA oligomers on a surface using TIRF detection mode is reported. The dual-labeled system consisting of two hybridized oligomers, Cy3oligoY:Cy5oligoX was immobilized on the surface, and the total internal reflection fluorescence (TIRF) was used to detect emission signals from the surface. Two signals, green and red, which originated from the green donor Cy3 and the red acceptor Cy5, have been simultaneously detected. When the target single-stranded complimentary oligomer was present in the solution, this oligomer replaced the Cy3oligoY in the donor:acceptor complex on the surface and the ratio of red-to-green signal was dramatically changed. This detection scheme is generally applicable to the detection of DNA or RNA on a surface.

  12. Self-assembled SnO2 micro- and nanosphere-based gas sensor thick films from an alkoxide-derived high purity aqueous colloid precursor

    Science.gov (United States)

    Kelp, G.; Tätte, T.; Pikker, S.; Mändar, H.; Rozhin, A. G.; Rauwel, P.; Vanetsev, A. S.; Gerst, A.; Merisalu, M.; Mäeorg, U.; Natali, M.; Persson, I.; Kessler, V. G.

    2016-03-01

    Tin oxide is considered to be one of the most promising semiconductor oxide materials for use as a gas sensor. However, a simple route for the controllable build-up of nanostructured, sufficiently pure and hierarchical SnO2 structures for gas sensor applications is still a challenge. In the current work, an aqueous SnO2 nanoparticulate precursor sol, which is free of organic contaminants and sorbed ions and is fully stable over time, was prepared in a highly reproducible manner from an alkoxide Sn(OR)4 just by mixing it with a large excess of pure neutral water. The precursor is formed as a separate liquid phase. The structure and purity of the precursor is revealed using XRD, SAXS, EXAFS, HRTEM imaging, FTIR, and XRF analysis. An unconventional approach for the estimation of the particle size based on the quantification of the Sn-Sn contacts in the structure was developed using EXAFS spectroscopy and verified using HRTEM. To construct sensors with a hierarchical 3D structure, we employed an unusual emulsification technique not involving any additives or surfactants, using simply the extraction of the liquid phase, water, with the help of dry butanol under ambient conditions. The originally generated crystalline but yet highly reactive nanoparticles form relatively uniform spheres through self-assembly and solidify instantly. The spheres floating in butanol were left to deposit on the surface of quartz plates bearing sputtered gold electrodes, producing ready-for-use gas sensors in the form of ca. 50 μm thick sphere-based-films. The films were dried for 24 h and calcined at 300 °C in air before use. The gas sensitivity of the structures was tested in the temperature range of 150-400 °C. The materials showed a very quickly emerging and reversible (20-30 times) increase in electrical conductivity as a response to exposure to air containing 100 ppm of H2 or CO and short (10 s) recovery times when the gas flow was stopped.Tin oxide is considered to be one of the

  13. High-performance oxygen reduction catalysts in both alkaline and acidic fuel cells based on pre-treating carbon material and iron precursor

    Energy Technology Data Exchange (ETDEWEB)

    Song, Ping; Barkholtz, Heather M.; Wang, Ying; Xu, Weilin; Liu, Dijia; Zhuang, Lin

    2017-12-01

    We demonstrate a new and simple method for pre-treating the carbon material and iron precursor to prepare oxygen reduction reaction (ORR) catalysts, which can produce super-high performance and stability in alkaline solution, with high performance in acid solution. This strategy using cheap materials is simply controllable. Moreover, it has achieved smaller uniform nanoparticles to exhibit high stability, and the synergetic effect of Fe and N offered much higher performance in ORR than commercial Pt/C, with high maximum power density in alkaline and acid fuel cell test. So it can make this kind of catalysts be the most promising alternatives of Pt-based catalysts with best performance/price.

  14. Genome-wide characterization of microRNA in foxtail millet (Setaria italica).

    Science.gov (United States)

    Yi, Fei; Xie, Shaojun; Liu, Yuwei; Qi, Xin; Yu, Jingjuan

    2013-12-13

    MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood. In this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing. We predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.

  15. Single-source-precursor synthesis of dense SiC/HfC(x)N(1-x)-based ultrahigh-temperature ceramic nanocomposites.

    Science.gov (United States)

    Wen, Qingbo; Xu, Yeping; Xu, Binbin; Fasel, Claudia; Guillon, Olivier; Buntkowsky, Gerd; Yu, Zhaoju; Riedel, Ralf; Ionescu, Emanuel

    2014-11-21

    A novel single-source precursor was synthesized by the reaction of an allyl hydrido polycarbosilane (SMP10) and tetrakis(dimethylamido)hafnium(iv) (TDMAH) for the purpose of preparing dense monolithic SiC/HfC(x)N(1-x)-based ultrahigh temperature ceramic nanocomposites. The materials obtained at different stages of the synthesis process were characterized via Fourier transform infrared (FT-IR) as well as nuclear magnetic resonance (NMR) spectroscopy. The polymer-to-ceramic transformation was investigated by means of MAS NMR and FT-IR spectroscopy as well as thermogravimetric analysis (TGA) coupled with in situ mass spectrometry. Moreover, the microstructural evolution of the synthesized SiHfCN-based ceramics annealed at different temperatures ranging from 1300 °C to 1800 °C was characterized by elemental analysis, X-ray diffraction, Raman spectroscopy and transmission electron microscopy (TEM). Based on its high temperature behavior, the amorphous SiHfCN-based ceramic powder was used to prepare monolithic SiC/HfC(x)N(1-x)-based nanocomposites using the spark plasma sintering (SPS) technique. The results showed that dense monolithic SiC/HfC(x)N(1-x)-based nanocomposites with low open porosity (0.74 vol%) can be prepared successfully from single-source precursors. The average grain size of both HfC0.83N0.17 and SiC phases was found to be less than 100 nm after SPS processing owing to a unique microstructure: HfC0.83N0.17 grains were embedded homogeneously in a β-SiC matrix and encapsulated by in situ formed carbon layers which acted as a diffusion barrier to suppress grain growth. The segregated Hf-carbonitride grains significantly influenced the electrical conductivity of the SPS processed monolithic samples. While Hf-free polymer-derived SiC showed an electrical conductivity of ca. 1.8 S cm(-1), the electrical conductivity of the Hf-containing material was analyzed to be ca. 136.2 S cm(-1).

  16. High-­Performance Carbon Molecular Sieve Gas Separation Membranes Based on a Carbon-­Rich Intrinsically Microporous Polyimide Precursor

    KAUST Repository

    Hazazi, Khalid

    2018-01-01

    of the polyimide precursor using a well-defined heating protocol in a horizontal tube furnace up to 1000 °C. A nitrogen purge was kept inside the furnace to remove all the evolved by-products as the precursor started to decompose and carbonize. The microstructures

  17. Identification of reference genes for relative quantification of circulating microRNAs in bovine serum.

    Directory of Open Access Journals (Sweden)

    In-Seon Bae

    Full Text Available Circulating microRNAs in body fluids have been implicated as promising biomarkers for physiopathology disorders. Currently, the expression levels of circulating microRNAs are estimated by reverse transcription quantitative real-time polymerase chain reaction. Use of appropriate reference microRNAs for normalization is critical for accurate microRNA expression analysis. However, no study has systematically investigated reference genes for evaluating circulating microRNA expression in cattle. In this study, we describe the identification and characterization of appropriate reference microRNAs for use in the normalization of circulating microRNA levels in bovine serum. We evaluated the expression stability of ten candidate reference genes in bovine serum by using reverse transcription quantitative real-time polymerase chain reaction. Data were analyzed using geNorm, NormFinder, and BestKeeper statistical algorithms. The results consistently showed that a combination of miR-93 and miR-127 provided the most stably expressed reference. The suitability of these microRNAs was validated, and even when compared among different genders or breeds, the combination of miR-93 and miR-127 was ranked as the most stable microRNA reference. Therefore, we conclude that this combination is the optimal endogenous reference for reverse transcription quantitative real-time polymerase chain reaction-based detection of microRNAs in bovine serum. The data presented in this study are crucial to successful biomarker discovery and validation for the diagnosis of physiopathological conditions in cattle.

  18. Simultaneous visualization of the subfemtomolar expression of microRNA and microRNA target gene using HILO microscopy.

    Science.gov (United States)

    Lin, Yi-Zhen; Ou, Da-Liang; Chang, Hsin-Yuan; Lin, Wei-Yu; Hsu, Chiun; Chang, Po-Ling

    2017-09-01

    The family of microRNAs (miRNAs) not only plays an important role in gene regulation but is also useful for the diagnosis of diseases. A reliable method with high sensitivity may allow researchers to detect slight fluctuations in ultra-trace amounts of miRNA. In this study, we propose a sensitive imaging method for the direct probing of miR-10b (miR-10b-3p, also called miR-10b*) and its target ( HOXD10 mRNA) in fixed cells based on the specific recognition of molecular beacons combined with highly inclined and laminated optical sheet (HILO) fluorescence microscopy. The designed dye-quencher-labelled molecular beacons offer excellent efficiencies of fluorescence resonance energy transfer that allow us to detect miRNA and the target mRNA simultaneously in hepatocellular carcinoma cells using HILO fluorescence microscopy. Not only can the basal trace amount of miRNA be observed in each individual cell, but the obtained images also indicate that this method is useful for monitoring the fluctuations in ultra-trace amounts of miRNA when the cells are transfected with a miRNA precursor or a miRNA inhibitor (anti-miR). Furthermore, a reasonable causal relation between the miR-10b and HOXD10 expression levels was observed in miR-10b* precursor-transfected cells and miR-10b* inhibitor-transfected cells. The trends of the miRNA alterations obtained using HILO microscopy completely matched the RT-qPCR data and showed remarkable reproducibility (the coefficient of variation [CV] = 0.86%) and sensitivity (<1.0 fM). This proposed imaging method appears to be useful for the simultaneous visualisation of ultra-trace amounts of miRNA and target mRNA and excludes the procedures for RNA extraction and amplification. Therefore, the visualisation of miRNA and the target mRNA should facilitate the exploration of the functions of ultra-trace amounts of miRNA in fixed cells in biological studies and may serve as a powerful tool for diagnoses based on circulating cancer cells.

  19. Precursor incident program at EDF

    International Nuclear Information System (INIS)

    Fourest, B.; Maliverney, B.; Rozenholc, M.; Piovesan, C.

    1998-01-01

    The precursor program was started by EDF in 1994, after an investigation of the US NRC's Accident Sequence Precursor Program. Since then, reported operational events identified as Safety Outstanding Events have been analyzed whenever possible using probabilistic methods based on PSAs. Analysis provides an estimate of the remaining protection against core damage at the time the incident occurred. Measuring the incidents' severity enables to detect incidents important regarding safety. Moreover, the most efficient feedback actions can be derived from the main accident sequences identified through the analysis. Therefore, incident probabilistic analysis provides a way to assess priorities in terms of treatment and resource allocation, and so, to implement countermeasures preventing further occurrence and development of the most significant incidents. As some incidents cannot be analyzed using this method, probabilistic analysis can only be one among the methods used to assess the nuclear power plants' safety level. Nevertheless, it provides an interesting complement to classical methods of deterministic studies. (author)

  20. Single-source-precursor synthesis of dense SiC/HfCxN1-x-based ultrahigh-temperature ceramic nanocomposites

    Science.gov (United States)

    Wen, Qingbo; Xu, Yeping; Xu, Binbin; Fasel, Claudia; Guillon, Olivier; Buntkowsky, Gerd; Yu, Zhaoju; Riedel, Ralf; Ionescu, Emanuel

    2014-10-01

    A novel single-source precursor was synthesized by the reaction of an allyl hydrido polycarbosilane (SMP10) and tetrakis(dimethylamido)hafnium(iv) (TDMAH) for the purpose of preparing dense monolithic SiC/HfCxN1-x-based ultrahigh temperature ceramic nanocomposites. The materials obtained at different stages of the synthesis process were characterized via Fourier transform infrared (FT-IR) as well as nuclear magnetic resonance (NMR) spectroscopy. The polymer-to-ceramic transformation was investigated by means of MAS NMR and FT-IR spectroscopy as well as thermogravimetric analysis (TGA) coupled with in situ mass spectrometry. Moreover, the microstructural evolution of the synthesized SiHfCN-based ceramics annealed at different temperatures ranging from 1300 °C to 1800 °C was characterized by elemental analysis, X-ray diffraction, Raman spectroscopy and transmission electron microscopy (TEM). Based on its high temperature behavior, the amorphous SiHfCN-based ceramic powder was used to prepare monolithic SiC/HfCxN1-x-based nanocomposites using the spark plasma sintering (SPS) technique. The results showed that dense monolithic SiC/HfCxN1-x-based nanocomposites with low open porosity (0.74 vol%) can be prepared successfully from single-source precursors. The average grain size of both HfC0.83N0.17 and SiC phases was found to be less than 100 nm after SPS processing owing to a unique microstructure: HfC0.83N0.17 grains were embedded homogeneously in a β-SiC matrix and encapsulated by in situ formed carbon layers which acted as a diffusion barrier to suppress grain growth. The segregated Hf-carbonitride grains significantly influenced the electrical conductivity of the SPS processed monolithic samples. While Hf-free polymer-derived SiC showed an electrical conductivity of ca. 1.8 S cm-1, the electrical conductivity of the Hf-containing material was analyzed to be ca. 136.2 S cm-1.A novel single-source precursor was synthesized by the reaction of an allyl hydrido

  1. Combinatorial microRNA target predictions

    DEFF Research Database (Denmark)

    Krek, Azra; Grün, Dominic; Poy, Matthew N.

    2005-01-01

    MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript1, 2, 3. Different combinations of microRNAs are expressed...... in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published micro......RNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. We find that vertebrate microRNAs target, on average, roughly 200 transcripts each. Furthermore, our results...

  2. Label-free and ultrasensitive electrochemiluminescence detection of microRNA based on long-range self-assembled DNA nanostructures

    International Nuclear Information System (INIS)

    Liu, Ting; Chen, Xian; Hong, Cheng-Yi; Xu, Xiao-Ping; Yang, Huang-Hao

    2014-01-01

    Electrochemiluminescence (ECL) integrates the advantages of electrochemical detection and chemiluminescent techniques. The method has received particular attention because it is highly sensitive and selective, has a wide linear range but low reagent costs. The use of nanomaterials with their unique physical and chemical properties has led to new kinds of biosensors that exhibit high sensitivity and stability. Compared to other nanomaterials, DNA nanostructures are more biocompatible, more hydrophilic, and thus less prone to nonspecific adsorption onto the electrode surface. We describe here a label-free and ultrasensitive ECL biosensor for detecting a cancer-associated microRNA at a femtomolar level. We have designed two auxiliary probes that cause the formation of a long-range self-assembly in the form of a μm-long 1-dimensional DNA concatamer. These can be used as carriers for signal amplification. The intercalation of the ECL probe Ru(phen) 3 2+ into the grooves of the concatamers leads to a substantial increase in ECL intensity. This amplified sensor shows high selectivity for discriminating complementary target and other mismatched RNAs. The biosensor enables the quantification of the expression of microRNA-21 in MCF-7 cells. It also displays very low limits of detection and provides an alternative approach for the detection of RNA or DNA detection in diagnostics and gene analysis. (author)

  3. Kinetic removal of haloacetonitrile precursors by photo-based advanced oxidation processes (UV/H2O2, UV/O3, and UV/H2O2/O3).

    Science.gov (United States)

    Srithep, Sirinthip; Phattarapattamawong, Songkeart

    2017-06-01

    The objective of the study is to evaluate the performance of conventional treatment process (i.e., coagulation, flocculation, sedimentation and sand filtration) on the removals of haloacetonitrile (HAN) precursors. In addition, the removals of HAN precursors by photo-based advanced oxidation processes (Photo-AOPs) (i.e., UV/H 2 O 2 , UV/O 3 , and UV/H 2 O 2 /O 3 ) are investigated. The conventional treatment process was ineffective to remove HAN precursors. Among Photo-AOPs, the UV/H 2 O 2 /O 3 was the most effective process for removing HAN precursors, followed by UV/H 2 O 2 , and UV/O 3 , respectively. For 20min contact time, the UV/H 2 O 2 /O 3 , UV/H 2 O 2 , and UV/O 3 suppressed the HAN formations by 54, 42, and 27% reduction. Increasing ozone doses from 1 to 5 mgL -1 in UV/O 3 systems slightly improved the removals of HAN precursors. Changes in pH (6-8) were unaffected most of processes (i.e., UV, UV/H 2 O 2 , and UV/H 2 O 2 /O 3 ), except for the UV/O 3 system that its efficiency was low in the weak acid condition. The pseudo first-order kinetic constant for removals of dichloroacetonitrile precursors (k' DCANFP ) by the UV/H 2 O 2 /O 3 , UV/H 2 O 2 and standalone UV systems were 1.4-2.8 orders magnitude higher than the UV/O 3 process. The kinetic degradation of dissolved organic nitrogen (DON) tended to be higher than the k' DCANFP value. This study firstly differentiates the kinetic degradation between DON and HAN precursors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. MicroRNA and cancer

    DEFF Research Database (Denmark)

    Jansson, Martin D; Lund, Anders H

    2012-01-01

    biological phenomena and pathologies. The best characterized non-coding RNA family consists in humans of about 1400 microRNAs for which abundant evidence have demonstrated fundamental importance in normal development, differentiation, growth control and in human diseases such as cancer. In this review, we...... summarize the current knowledge and concepts concerning the involvement of microRNAs in cancer, which have emerged from the study of cell culture and animal model systems, including the regulation of key cancer-related pathways, such as cell cycle control and the DNA damage response. Importantly, micro...

  5. A systematic review of overlapping microRNA patterns in systemic sclerosis and idiopathic pulmonary fibrosis.

    Science.gov (United States)

    Bagnato, Gianluca; Roberts, William Neal; Roman, Jesse; Gangemi, Sebastiano

    2017-06-30

    Lung fibrosis can be observed in systemic sclerosis and in idiopathic pulmonary fibrosis, two disorders where lung involvement carries a poor prognosis. Although much has been learned about the pathogenesis of these conditions, interventions capable of reversing or, at the very least, halting disease progression are not available. Recent studies point to the potential role of micro messenger RNAs (microRNAs) in cancer and tissue fibrogenesis. MicroRNAs are short non-coding RNA sequences (20-23 nucleotides) that are endogenous, evolutionarily conserved and encoded in the genome. By acting on several genes, microRNAs control protein expression. Considering the above, we engaged in a systematic review of the literature in search of overlapping observations implicating microRNAs in the pathogenesis of both idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc). Our objective was to uncover top microRNA candidates for further investigation based on their mechanisms of action and their potential for serving as targets for intervention against lung fibrosis. Our review points to microRNAs of the -29 family, -21-5p and -92a-3p, -26a-5p and let-7d-5p as having distinct and counter-balancing actions related to lung fibrosis. Based on this, we speculate that readjusting the disrupted balance between these microRNAs in lung fibrosis related to SSc and IPF may have therapeutic potential. Copyright ©ERS 2017.

  6. Stability, Reactivity, and Constituent Interaction in TiSe2-Based Metastable Misfit Layer Compounds Synthesized from Designed Amorphous Precursors

    Science.gov (United States)

    Merrill, Devin R.

    A series of intergrowth compounds with the basic formula [(MSe) 1+delta]m(TiSe2)n are reported. The compounds are prepared from modulated elemental reactants and display interesting structural and electronic behavior. Section 1 of this dissertation outlines initial attempts to characterize constituent interaction. The first member of the SnSe based subclass is reported and displays the highest Seebeck coefficient of any m = n = 1 compound reported to date, and a surprising amount of order is observed, compared to previously reported compounds. With properly established deposition parameters, the synthesis was extended to included the m = 2-4 compounds. These compounds display interesting electronic behavior that suggests the band structure shifts considerably as the SnSe block is expanded, affecting the interaction between the constituent layers. The first compound based on BiSe is then reported, suggesting that the Bi structure donates more conduction electrons to the band structure. Targeted substitution through kinetic control is the focus of Section 2, and a family of (PbxSn1-xSe)1+deltaTiSe 2 is reported over the entire range of x, even though a miscibility gap exists in the bulk PbxSn1-xSe system. The resulting alloyed intergrowth compounds also display equal or higher mobility than the end members, suggesting modulation doping could be used to affect transport properties. As a proof of principle, the analogous system based on a Bi xSn1-xSe constituent was prepared to attempt to systematically affect carrier concentration. It was found that while carrier concentration can be controlled, the evolving structure affects the doping efficiency of the Bi atoms and mobility in the structure. Section 3 outlines attempts to form higher order TiSe2-based heterostructures and the important chemical considerations observed during the preparation of these materials. The 3 component systems in the Pb-Sn-Ti-Se system can be formed at low temperature, with SnSe2 rather than

  7. IAP-Based Cell Sorting Results in Homogeneous Transplantable Dopaminergic Precursor Cells Derived from Human Pluripotent Stem Cells

    Directory of Open Access Journals (Sweden)

    Daniela Lehnen

    2017-10-01

    Full Text Available Human pluripotent stem cell (hPSC-derived mesencephalic dopaminergic (mesDA neurons can relieve motor deficits in animal models of Parkinson's disease (PD. Clinical translation of differentiation protocols requires standardization of production procedures, and surface-marker-based cell sorting is considered instrumental for reproducible generation of defined cell products. Here, we demonstrate that integrin-associated protein (IAP is a cell surface marker suitable for enrichment of hPSC-derived mesDA progenitor cells. Immunomagnetically sorted IAP+ mesDA progenitors showed increased expression of ventral midbrain floor plate markers, lacked expression of pluripotency markers, and differentiated into mature dopaminergic (DA neurons in vitro. Intrastriatal transplantation of IAP+ cells sorted at day 16 of differentiation in a rat model of PD resulted in functional recovery. Grafts from sorted IAP+ mesDA progenitors were more homogeneous in size and DA neuron density. Thus, we suggest IAP-based sorting for reproducible prospective enrichment of mesDA progenitor cells in clinical cell replacement strategies.

  8. A test to measure the minimum burning pressure of water-based commercial explosives and their precursors

    Energy Technology Data Exchange (ETDEWEB)

    Turcotte, R.; Feng, H.; Badeen, C.M.; Goldthorp, S.; Johnson, C. [Natural Resources Canada, Ottawa, ON (Canada). Canadian Explosives Research Laboratory; Chan, S.K. [Orica Canada Inc., Brownsburg-Chatham, PQ (Canada)

    2009-05-15

    This paper described a testing protocol developed to measure the minimum burning pressure (MBP) of ammonium nitrate water-based emulsions (AWEs). Oxidizer solutions were prepared in a stainless steel beaker. A modified commercial mixer was used to emulsify the oil-surfactant phase with the oxidizer solutions and blend dry ingredients. Five high water content AWEs were then prepared and placed in pressurized vessels. Samples were ignited using a straight length of nichrome wire. Emulsion samples were transferred into a cylindrical test cell painted with non-conductive paint. Copper conductor leg-wires were connected to electrodes passing through the body of the vessel. When samples were equilibrated to the desired initial pressure, a constant current was supplied to the hot wire. Solid state relays were used to switch the current power supply on and off. Hot wire voltage signals were used to obtain temperature profiles for onset and ignition temperatures. The procedure to perform the MBP measurements was based on 3 types of classifying events, namely (1) no reaction, (2) partial reaction, and (3) slow decomposition. Results of the tests demonstrated that the 5 emulsions exhibited large differences in respective MBP values. Data from the study will be used to develop standards for the authorization of high explosives in Canada. 15 refs., 1 tab., 3 figs.

  9. IAP-Based Cell Sorting Results in Homogeneous Transplantable Dopaminergic Precursor Cells Derived from Human Pluripotent Stem Cells.

    Science.gov (United States)

    Lehnen, Daniela; Barral, Serena; Cardoso, Tiago; Grealish, Shane; Heuer, Andreas; Smiyakin, Andrej; Kirkeby, Agnete; Kollet, Jutta; Cremer, Harold; Parmar, Malin; Bosio, Andreas; Knöbel, Sebastian

    2017-10-10

    Human pluripotent stem cell (hPSC)-derived mesencephalic dopaminergic (mesDA) neurons can relieve motor deficits in animal models of Parkinson's disease (PD). Clinical translation of differentiation protocols requires standardization of production procedures, and surface-marker-based cell sorting is considered instrumental for reproducible generation of defined cell products. Here, we demonstrate that integrin-associated protein (IAP) is a cell surface marker suitable for enrichment of hPSC-derived mesDA progenitor cells. Immunomagnetically sorted IAP + mesDA progenitors showed increased expression of ventral midbrain floor plate markers, lacked expression of pluripotency markers, and differentiated into mature dopaminergic (DA) neurons in vitro. Intrastriatal transplantation of IAP + cells sorted at day 16 of differentiation in a rat model of PD resulted in functional recovery. Grafts from sorted IAP + mesDA progenitors were more homogeneous in size and DA neuron density. Thus, we suggest IAP-based sorting for reproducible prospective enrichment of mesDA progenitor cells in clinical cell replacement strategies. Copyright © 2017 Miltenyi Biotec GmbH. Published by Elsevier Inc. All rights reserved.

  10. Serum microRNA-1 and microRNA-133a levels reflect myocardial steatosis in uncomplicated type 2 diabetes

    NARCIS (Netherlands)

    Gonzalo-Calvo, D. de; Meer, R.W. van der; Rijzewijk, L.J.; Smit, J.W.A.; Revuelta-Lopez, E.; Nasarre, L.; Escola-Gil, J.C.; Lamb, H.J.; Llorente-Cortes, V.

    2017-01-01

    Using in vitro, in vivo and patient-based approaches, we investigated the potential of circulating microRNAs (miRNAs) as surrogate biomarkers of myocardial steatosis, a hallmark of diabetic cardiomyopathy. We analysed the cardiomyocyte-enriched miRNA signature in serum from patients with

  11. Further Development of an Exhaled microRNA Biomarker of Lung Cancer Risk

    Science.gov (United States)

    2017-08-01

    AWARD NUMBER: W81XWH-16-1-0328 TITLE: Further Development of an Exhaled microRNA Biomarker of Lung Cancer Risk PRINCIPAL INVESTIGATOR: Dr...4. TITLE AND SUBTITLE Further Development of an Exhaled microRNA Biomarker of Lung Cancer Risk 5b. GRANT NUMBER W81XWH 16-1-0328 5c. PROGRAM...devise a non-invasive airway based exhaled microRNA metric for lung cancer risk, initial work to be tested in a case control study. We expanded the

  12. A pyrazolyl-based thiolato single-source precursor for the selective synthesis of isotropic copper-deficient copper(I) sulfide nanocrystals: synthesis, optical and photocatalytic activity

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, Gopinath; Santra, Ananyakumari; Bera, Pradip; Acharjya, Moumita [Vidyasagar University, Post Graduate Department of Chemistry, Panskura Banamali College (India); Jana, Sumanta [Indian Institute of Engineering Science and Technology (IIEST), Department of Chemistry (India); Chattopadhyay, Dipankar [University of Calcutta, Department of Polymer Science and Technology (India); Mondal, Anup [Indian Institute of Engineering Science and Technology (IIEST), Department of Chemistry (India); Seok, Sang Il [Korea Research Institute of Chemical Technology, KRICT-EPFL Global Research Laboratory, Division of Advanced Materials (Korea, Republic of); Bera, Pulakesh, E-mail: pbera.pbc.chem@gmail.com [Vidyasagar University, Post Graduate Department of Chemistry, Panskura Banamali College (India)

    2016-10-15

    Hexagonal copper-deficient copper(I) sulfide (Cu{sub 2-x}S, x = 0.03, 0.2) nanocrystals (NCs) are synthesized from a newly prepared single-source precursor (SP), [Cu(bdpa){sub 2}][CuCl{sub 2}], where bdpa is benzyl 3,5-dimethyl-pyrazole-1-carbodithioate. The SP is crystallized with space group Pī and possesses a distorted tetrahedron structure with a CuN{sub 2}S{sub 2} chromophore where the central copper is in +1 oxidation state. Distortion in copper(I) structure and the low decomposition temperature of SP make it favorable for the low-temperature solvent-assisted selective growth of high-copper content sulfides. The nucleation and growth of Cu{sub 2-x}S (x = 0.03, 0.2) are effectively controlled by the SP and the solvent in the solvothermal decomposition process. During decomposition, fragment benzyl thiol (PhCH{sub 2}SH) from SP effectively passivates the nucleus leading to spherical nanocrystals. Further, solvent plays an important role in the selective thermochemical transformation of Cu{sup I}-complex to Cu{sub 2-x}S (x = 0.03, 0.2) NCs. The chelating binders (solvent) like ethylene diamine (EN) and ethylene glycol (EG) prefer to form spherical Cu{sub 1.97}S nanoparticles (djurleite), whereas nonchelating hydrazine hydrate (HH) shows the tendency to furnish hexagonal platelets of copper-deficient Cu{sub 1.8}S. The optical band gap values (2.25–2.50 eV) show quantum confinement effect in the structure. The synthesized NCs display excellent catalytic activity (~87 %) toward photodegradation of organic dyes like Congo Red (CR) and Methylene Blue (MB).Graphical abstractA pyrazolyl-based thiolato single-source precursor for the selective synthesis of isotropic copper-deficient copper(I) sulfide nanocrystals: Synthesis, optical and photocatalytic activity.Gopinath Mondal, Ananyakumari Santra, Pradip Bera, Moumita Acharjya, Sumanta Jana, Dipankar Chattopadhyay, Anup Mondal, Sang Il Seok, Pulakesh Bera.

  13. High expression of microRNA-625-3p is associated with poor response to first-line oxaliplatin based treatment of metastatic colorectal cancer

    DEFF Research Database (Denmark)

    Rasmussen, Mads Heilskov; Jensen, Niels; Tarpgaard, Line Schmidt

    2013-01-01

    The backbone of current cytotoxic treatment of metastatic colorectal cancer (mCRC) consists of a fluoropyrimidine together with either oxaliplatin (XELOX/FOLFOX) or irinotecan (XELIRI/FOLFIRI). With an overall objective response rate of approximately 50% for either treatment combination, a major...... analyses showed that miR-625-3p was not dysregulated between normal and cancer samples, nor was its expression associated with recurrence of stage II or III disease, indicating that miR-625-3p solely is a response marker. Finally, we also found that these miRNAs were up-regulated in oxaliplatin resistant...... unsolved problem is that no predictors of response to these treatments are available. To address this issue, we profiled 742 microRNAs in laser-capture microdissected cancer cells from responding and non-responding patients receiving XELOX/FOLFOX as first-line treatment for mCRC, and identified, among...

  14. Molecular precursor derived silicon boron carbonitride/carbon nanotube and silicon oxycarbide/carbon nanotube composite nanowires for energy based applications

    Science.gov (United States)

    Bhandavat, Romil

    Molecular precursor derived ceramics (also known as polymer-derived ceramics or PDCs) are high temperature glasses that have been studied for applications involving operation at elevated temperatures. Prepared from controlled thermal degradation of liquid-phase organosilicon precursors, these ceramics offer remarkable engineering properties such as resistance to crystallization up to 1400 °C, semiconductor behavior at high temperatures and intense photoluminescence. These properties are a direct result of their covalent bonded amorphous network and free (-sp2) carbon along with mixed Si/B/C/N/O bonds, which otherwise can not be obtained through conventional ceramic processing techniques. This thesis demonstrates synthesis of a unique core/shell type nanowire structure involving either siliconboroncarbonitride (SiBCN) or siliconoxycarbide (SiOC) as the shell with carbon nanotube (CNT) acting as the core. This was made possible by liquid phase functionalization of CNT surfaces with respective polymeric precursor (e.g., home-made boron-modified polyureamethylvinylsilazane for SiBCN/CNT and commercially obtained polysiloxane for SiOC/CNT), followed by controlled pyrolysis in inert conditions. This unique architecture has several benefits such as high temperature oxidation resistance (provided by the ceramic shell), improved electrical conductivity and mechanical toughness (attributed to the CNT core) that allowed us to explore its use in energy conversion and storage devices. The first application involved use of SiBCN/CNT composite as a high temperature radiation absorbant material for laser thermal calorimeter. SiBCN/CNT spray coatings on copper substrate were exposed to high energy laser beams (continuous wave at 10.6 mum 2.5 kW CO2 laser, 10 seconds) and resulting change in its microstructure was studied ex-situ. With the aid of multiple techniques we ascertained the thermal damage resistance to be 15 kW/cm -2 with optical absorbance exceeding 97%. This represents

  15. OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

    Science.gov (United States)

    Huang, Jingshan; Gutierrez, Fernando; Strachan, Harrison J; Dou, Dejing; Huang, Weili; Smith, Barry; Blake, Judith A; Eilbeck, Karen; Natale, Darren A; Lin, Yu; Wu, Bin; Silva, Nisansa de; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming; Ruttenberg, Alan

    2016-01-01

    As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field. In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software.

  16. Characterization of retrovirus-based reporter viruses pseudotyped with the precursor membrane and envelope glycoproteins of four serotypes of dengue viruses

    International Nuclear Information System (INIS)

    Hu, H.-P.; Hsieh, S.-C.; King, C.-C.; Wang, W.-K.

    2007-01-01

    In this study, we successfully established retrovirus-based reporter viruses pseudotyped with the precursor membrane and envelope (PrM/E) proteins of each of the four serotypes of dengue viruses, which caused the most important arboviral diseases in this century. Co-sedimentation of the dengue E protein and HIV-1 core proteins by sucrose gradient analysis of the pseudotype reporter virus of dengue virus type 2, D2(HIVluc), and detection of HIV-1 core proteins by immunoprecipitation with anti-E monoclonal antibody suggested that dengue viral proteins were incorporated into the pseudotype viral particles. The infectivity in target cells, as assessed by the luciferase activity, can be inhibited by the lysosomotropic agents, suggesting a pH-dependent mechanism of entry. Amino acid substitutions of the leucine at position 107, a critical residue at the fusion loop of E protein, with lysine resulted in severe impairment in infectivity, suggesting that entry of the pseudotype reporter virus is mediated through the fusogenic properties of E protein. With more and more dengue viral sequences available from different outbreaks worldwide, this sensitive and convenient tool has the potential to facilitate molecular characterization of the PrM/E proteins of dengue field isolates

  17. Evidence for X-chromosomal schizophrenia associated with microRNA alterations.

    Directory of Open Access Journals (Sweden)

    Jinong Feng

    2009-07-01

    Full Text Available Schizophrenia is a severe disabling brain disease affecting about 1% of the population. Individual microRNAs (miRNAs affect moderate downregulation of gene expression. In addition, components required for miRNA processing and/or function have also been implicated in X-linked mental retardation, neurological and neoplastic diseases, pointing to the wide ranging involvement of miRNAs in disease.To explore the role of miRNAs in schizophrenia, 59 microRNA genes on the X-chromosome were amplified and sequenced in males with (193 and without (191 schizophrenia spectrum disorders to test the hypothesis that ultra-rare mutations in microRNA collectively contribute to the risk of schizophrenia. Here we provide the first association of microRNA gene dysfunction with schizophrenia. Eight ultra-rare variants in the precursor or mature miRNA were identified in eight distinct miRNA genes in 4% of analyzed males with schizophrenia. One ultra-rare variant was identified in a control sample (with a history of depression (8/193 versus 1/191, p = 0.02 by one-sided Fisher's exact test, odds ratio = 8.2. These variants were not found in an additional 7,197 control X-chromosomes.Functional analyses of ectopically expressed copies of the variant miRNA precursors demonstrate loss of function, gain of function or altered expression levels. While confirmation is required, this study suggests that microRNA mutations can contribute to schizophrenia.

  18. Human Milk MicroRNA and Total RNA Differ Depending on Milk Fractionation.

    Science.gov (United States)

    Alsaweed, Mohammed; Hepworth, Anna R; Lefèvre, Christophe; Hartmann, Peter E; Geddes, Donna T; Hassiotou, Foteini

    2015-10-01

    MicroRNA have been recently discovered in human milk signifying potentially important functions for both the lactating breast and the infant. Whilst human milk microRNA have started to be explored, little data exist on the evaluation of sample processing, and analysis to ensure that a full spectrum of microRNA can be obtained. Human milk comprises three main fractions: cells, skim milk, and lipids. Typically, the skim milk fraction has been measured in isolation despite evidence that the lipid fraction may contain more microRNA. This study aimed to standardize isolation of microRNA and total RNA from all three fractions of human milk to determine the most appropriate sampling and analysis procedure for future studies. Three different methods from eight commercially available kits were tested for their efficacy in extracting total RNA and microRNA from the lipid, skim, and cell fractions of human milk. Each fraction yielded different concentrations of RNA and microRNA, with the highest quantities found in the cell and lipid fractions, and the lowest in skim milk. The column-based phenol-free method was the most efficient extraction method for all three milk fractions. Two microRNAs were expressed and validated in the three milk fractions by qPCR using the three recommended extraction kits for each fraction. High expression levels were identified in the skim and lipid milk factions for these microRNAs. These results suggest that careful consideration of both the human milk sample preparation and extraction protocols should be made prior to embarking upon research in this area. © 2015 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.

  19. The Role of microRNAs in the Pathogenesis of Herpesvirus Infection.

    Science.gov (United States)

    Piedade, Diogo; Azevedo-Pereira, José Miguel

    2016-06-02

    MicroRNAs (miRNAs) are small non-coding RNAs important in gene regulation. They are able to regulate mRNA translation through base-pair complementarity. Cellular miRNAs have been involved in the regulation of nearly all cellular pathways, and their deregulation has been associated with several diseases such as cancer. Given the importance of microRNAs to cell homeostasis, it is no surprise that viruses have evolved to take advantage of this cellular pathway. Viruses have been reported to be able to encode and express functional viral microRNAs that target both viral and cellular transcripts. Moreover, viral inhibition of key proteins from the microRNA pathway and important changes in cellular microRNA pool have been reported upon viral infection. In addition, viruses have developed multiple mechanisms to avoid being targeted by cellular microRNAs. This complex interaction between host and viruses to control the microRNA pathway usually favors viral infection and persistence by either reducing immune detection, avoiding apoptosis, promoting cell growth, or promoting lytic or latent infection. One of the best examples of this virus-host-microRNA interplay emanates from members of the Herperviridae family, namely the herpes simplex virus type 1 and type 2 (HSV-1 and HSV-2), human cytomegalovirus (HCMV), human herpesvirus 8 (HHV-8), and the Epstein-Barr virus (EBV). In this review, we will focus on the general functions of microRNAs and the interactions between herpesviruses, human hosts, and microRNAs and will delve into the related mechanisms that contribute to infection and pathogenesis.

  20. Nanostructured protic ionic liquids retain nanoscale features in aqueous solution while precursor Brønsted acids and bases exhibit different behavior.

    Science.gov (United States)

    Greaves, Tamar L; Kennedy, Danielle F; Weerawardena, Asoka; Tse, Nicholas M K; Kirby, Nigel; Drummond, Calum J

    2011-03-10

    Small- and wide-angle X-ray scattering (SWAXS) has been used to investigate the effect that water has on the nanoscale structure of protic ionic liquids (PILs) along with their precursor Brønsted acids and bases. The series of PILs consisted of primary, secondary, and tertiary alkylammonium cations in conjunction with formate, nitrate, or glycolate anions. Significant differences were observed for these systems. The nanoscale aggregates present in neat protic ionic liquids were shown to be stable in size on dilution to high concentrations of water, indicating that the water is localized in the ionic region and has little effect on the nonpolar domains. The Brønsted acid-water solutions did not display nanostructure at any water concentration. Primary amine Brønsted bases formed aggregates in water, which generally displayed characteristics of poorly structured microemulsions or a form of bicontinuous phase. Exceptions were butyl- and pentylamine with high water concentrations, for which the SWAXS patterns fitted well to the Teubner-Strey model for microemulsions. Brønsted base amines containing multiple alkyl chains or hydroxyl groups did not display nanostructure at any water concentration. IR spectroscopy was used to investigate the nature of water in the various solutions. For low PIL concentrations, the water was predominately present as bulk water for PIL molar fractions less than 0.4-0.5. At high PIL concentrations, in addition to the bulk water, there was a significant proportion of perturbed water, which is water influenced in some way by the cations and anions. The molecular state of the water in the studied amines was predominately present as bulk water, with smaller contributions from perturbed water than was seen in the PILs. © 2011 American Chemical Society

  1. Synthesis and gas permeation properties of a novel thermally-rearranged polybenzoxazole made from an intrinsically microporous hydroxyl-functionalized triptycene-based polyimide precursor

    KAUST Repository

    Alghunaimi, Fahd; Ghanem, Bader; Wang, Yingge; Salinas, Octavio; Alaslai, Nasser Y.; Pinnau, Ingo

    2017-01-01

    A hydroxyl-functionalized triptycene-based polyimide of intrinsic microporosity (TDA1-APAF) was converted to a polybenzoxazole (PBO) by heat treatment at 460 °C under nitrogen atmosphere. TDA1-APAF treated for 15 min (TR 460) resulted in a PBO conversion of 95% based on a theoretical weight loss of 11.7 wt% of the polyimide precursor. The BET surface area of the TR 460 (680 m2 g−1) was significantly higher than that of the TDA1-APAF polyimide (260 m2 g−1) as determined by nitrogen adsorption at −196 °C. Heating TDA1-APAF for 30 min (TRC 460) resulted in a weight loss of 13.5 wt%, indicating full conversion to PBO and partial main-chain degradation. The TR 460 membrane displayed excellent O2 permeability of 311 Barrer coupled with an O2/N2 selectivity of 5.4 and CO2 permeability of 1328 Barrer with a CO2/CH4 selectivity of 27. Interestingly, physical aging over 150 days resulted in enhanced O2/N2 selectivity of 6.3 with an O2 permeability of 185 Barrer. The novel triptycene-based TR 460 PBO outperformed all previously reported APAF-polyimide-based PBOs with gas permeation performance close to recently reported polymers located on the 2015 O2/N2 upper bound. Based on this study, thermally-rearranged membranes from hydroxyl-functionalized triptycene-based polyimides are promising candidate membrane materials for air separation, specifically in applications where space and weight of membrane systems are of utmost importance such as nitrogen production for inert atmospheres in fuel lines and tanks on aircrafts and off-shore oil- or natural gas platforms. Mixed-gas permeation experiments also demonstrated good performance of the TR 460 membrane for natural gas sweetening with a CO2 permeability of ∼1000 Barrer and CO2/CH4 selectivity of 22 at a typical CO2 wellhead partial pressure of 10 bar.

  2. Synthesis and gas permeation properties of a novel thermally-rearranged polybenzoxazole made from an intrinsically microporous hydroxyl-functionalized triptycene-based polyimide precursor

    KAUST Repository

    Alghunaimi, Fahd

    2017-06-06

    A hydroxyl-functionalized triptycene-based polyimide of intrinsic microporosity (TDA1-APAF) was converted to a polybenzoxazole (PBO) by heat treatment at 460 °C under nitrogen atmosphere. TDA1-APAF treated for 15 min (TR 460) resulted in a PBO conversion of 95% based on a theoretical weight loss of 11.7 wt% of the polyimide precursor. The BET surface area of the TR 460 (680 m2 g−1) was significantly higher than that of the TDA1-APAF polyimide (260 m2 g−1) as determined by nitrogen adsorption at −196 °C. Heating TDA1-APAF for 30 min (TRC 460) resulted in a weight loss of 13.5 wt%, indicating full conversion to PBO and partial main-chain degradation. The TR 460 membrane displayed excellent O2 permeability of 311 Barrer coupled with an O2/N2 selectivity of 5.4 and CO2 permeability of 1328 Barrer with a CO2/CH4 selectivity of 27. Interestingly, physical aging over 150 days resulted in enhanced O2/N2 selectivity of 6.3 with an O2 permeability of 185 Barrer. The novel triptycene-based TR 460 PBO outperformed all previously reported APAF-polyimide-based PBOs with gas permeation performance close to recently reported polymers located on the 2015 O2/N2 upper bound. Based on this study, thermally-rearranged membranes from hydroxyl-functionalized triptycene-based polyimides are promising candidate membrane materials for air separation, specifically in applications where space and weight of membrane systems are of utmost importance such as nitrogen production for inert atmospheres in fuel lines and tanks on aircrafts and off-shore oil- or natural gas platforms. Mixed-gas permeation experiments also demonstrated good performance of the TR 460 membrane for natural gas sweetening with a CO2 permeability of ∼1000 Barrer and CO2/CH4 selectivity of 22 at a typical CO2 wellhead partial pressure of 10 bar.

  3. Polymeric precursors method for obtaining pigments based on Inorganic oxides of chromium and iron deposited on TiO{sub 2}; Metodo dos precursores polimericos para obtencao de pigmentos inorganicos a base de oxidos de cromo e de ferro, depositados sobre TiO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-07-01

    The case study was the use of chromium oxides and iron, as a precursor in the synthesis of inorganic pigments. The synthesis was based on the dissolution of citric acid as a complexing agent, addition of metal oxides, such as ion chromophores; polymerization with ethylene glycol and doping with titanium oxide. Going through pre-calcination, breakdown, calcination at different temperatures (700, 900 and 1100 deg C resulting in pigments: green for pigment and chromium deposited on TiO2, orange for iron on TiO2. The thermal analysis (TG and DTA), evaluated their thermal decompositions, the XRD revealed the formation of crystalline phases such as iron titanate and chrome titanate; SEM showed the formation of hexagonal particles for both oxides. Under the different analysis, one can see the potential stability of pigments and powders, can be proposed its use as pigments in polymers. (author)

  4. Preparation of thin films, with base to precursor materials of type Cu-In-Se elaborated by electrodeposition for the solar cells elaboration

    International Nuclear Information System (INIS)

    Fernandez, A.M.

    1999-01-01

    Thin films of chalcogenide compounds are promising because they have excellent optoelectronic characteristics to be applied in solar cells. In particular, CuInSe 2 and Cd Te thin films have shown high solar to electrical conversion efficiency. However, this efficiency is limited by the method of preparation, in this case, physical vapor deposition techniques are used. In order to increase the area of deposition t is necessary to use chemical methods, for example, electrodeposition technique. In this paper, the preparation of Cu-In-Se precursors thin films by electrochemical method is reported. These precursors were used to build solar cells with 7.9 % of efficiency. (Author)

  5. Circulating MicroRNAs in Plasma of Hepatitis B e Antigen Positive Children Reveal Liver-Specific Target Genes

    DEFF Research Database (Denmark)

    Winther, Thilde Nordmann; Jacobsen, Kari Stougaard; Mirza, Aashiq Hussain

    2014-01-01

    Background and Aim. Hepatitis B e antigen positive (HBeAg-positive) children are at high risk of severe complications such as hepatocellular carcinoma and cirrhosis. Liver damage is caused by the host immune response to infected hepatocytes, and we hypothesise that specific microRNAs play a role...... in this complex interaction between virus and host. The study aimed to identify microRNAs with aberrant plasma expressions in HBeAg-positive children and with liver-specific target genes. Methods. By revisiting our previous screen of microRNA plasma levels in HBeAg-positive and HBeAg-negative children...... with chronic hepatitis B (CHB) and in healthy controls, candidate microRNAs with aberrant plasma expressions in HBeAg-positive children were identified. MicroRNAs targeting liver-specific genes were selected based on bioinformatics analysis and validated by qRT-PCR using plasma samples from 34 HBe...

  6. Blood microRNAs in Low or No Risk Ischemic Stroke Patients

    Directory of Open Access Journals (Sweden)

    Jun Rong Tan

    2013-01-01

    Full Text Available Ischemic stroke is a multi-factorial disease where some patients present themselves with little or no risk factors. Blood microRNA expression profiles are becoming useful in the diagnosis and prognosis of human diseases. We therefore investigated the blood microRNA profiles in young stroke patients who presented with minimal or absence of risk factors for stroke such as type 2 diabetes, dyslipidemia and hypertension. Blood microRNA profiles from these patients varied with stroke subtypes as well as different functional outcomes (based on modified Rankin Score. These microRNAs have been shown to target genes that are involved in stroke pathogenesis. The findings from our study suggest that molecular mechanisms in stroke pathogenesis involving low or no risk ischemic stroke patients could differ substantially from those with pre-existing risk factors.

  7. HPV16 RNA patterns defined by novel high-throughput RT-qPCR as triage marker in HPV-based cervical cancer precursor screening.

    Science.gov (United States)

    Höfler, Daniela; Böhmer, Gerd; von Wasielewski, Reinhard; Neumann, Heinrich; Halec, Gordana; Holzinger, Dana; Dondog, Bolormaa; Gissmann, Lutz; Pawlita, Michael; Schmitt, Markus

    2015-09-01

    Cervical cancer precursor screening by HPV testing has a low positive predictive value for advanced lesion. HPV16 RNA patterns characteristic for HPV16-transformed cells but based on laborious, cost-intensive singleplex NASBA reactions promised high value in triaging HPV16 DNA-positive women. We developed two high-throughput reverse transcriptase quantitative (RT-q) PCR assays for the HPV16 transcripts E6*I, E1^E4 and E1C and the cellular transcript ubiquitin C and analysed RNA of 158 singly HPV16 DNA-positive cervical cell samples archived in PreservCyt buffer for the presence of transformation-associated HPV16 RNA patterns, i.e., upregulation of E6*I relative to E1^E4 and/or presence of E1C. HPV16 RNA pattern analyses classified 85% of 58 samples diagnosed ≤CIN1 (no cytologically and histologically detectable cervical lesion or CIN grade 1) as negative and 90% of 59 samples diagnosed as ≥CIN3 (CIN grade 3 or invasive cancer) as positive. Among 41 CIN grade 2 samples representing an intermediate lesion group, 49% were HPV16 RNA patterns-positive. Interestingly, 3 of 4 HPV16 RNA patterns-positive lesions initially diagnosed as ≤CIN1 at follow-up 5-24 months later had progressed to ≥CIN2. We successfully developed and validated a second generation of HPV16 RNA patterns assay by rapid RT-qPCR as triage marker for HPV16 DNA-positive women offering clinical utility to distinguish between the need for immediate colposcopy and continued observation. Limited follow-up data suggests that HPV16 RNA patterns-positivity in ≤CIN1 lesions can predict disease progression. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Identification of neglected cestode Taenia multiceps microRNAs by illumina sequencing and bioinformatic analysis

    Science.gov (United States)

    2013-01-01

    Background Worldwide, but especially in developing countries, coenurosis of sheep and other livestock is caused by Taenia multiceps larvae, and zoonotic infections occur in humans. Infections frequently lead to host death, resulting in huge socioeconomic losses. MicroRNAs (miRNAs) have important roles in the post-transcriptional regulation of a large number of animal genes by imperfectly binding target mRNAs. To date, there have been no reports of miRNAs in T. multiceps. Results In this study, we obtained 12.8 million high quality raw reads from adult T. multiceps small RNA library using Illumina sequencing technology. A total of 796 conserved miRNA families (containing 1,006 miRNAs) from 170,888 unique miRNAs were characterized using miRBase (Release 17.0). Here, we selected three conserved miRNA/miRNA* (antisense strand) duplexes at random and amplified their corresponding precursors using a PCR-based method. Furthermore, 20 candidate novel miRNA precursors were verified by genomic PCR. Among these, six corresponding T. multiceps miRNAs are considered specific for Taeniidae because no homologs were found in other species annotated in miRBase. In addition, 181,077 target sites within T. multiceps transcriptome were predicted for 20 candidate newly miRNAs. Conclusions Our large-scale investigation of miRNAs in adult T. multiceps provides a substantial platform for improving our understanding of the molecular regulation of T. multiceps and other cestodes development. PMID:23941076

  9. Let-7 microRNAs are developmentally regulated in circulating human erythroid cells

    Directory of Open Access Journals (Sweden)

    Reed Christopher

    2009-11-01

    Full Text Available Abstract Background MicroRNAs are ~22nt-long small non-coding RNAs that negatively regulate protein expression through mRNA degradation or translational repression in eukaryotic cells. Based upon their importance in regulating development and terminal differentiation in model systems, erythrocyte microRNA profiles were examined at birth and in adults to determine if changes in their abundance coincide with the developmental phenomenon of hemoglobin switching. Methods Expression profiling of microRNA was performed using total RNA from four adult peripheral blood samples compared to four cord blood samples after depletion of plasma, platelets, and nucleated cells. Labeled RNAs were hybridized to custom spotted arrays containing 474 human microRNA species (miRBase release 9.1. Total RNA from Epstein-Barr virus (EBV-transformed lymphoblastoid cell lines provided a hybridization reference for all samples to generate microRNA abundance profile for each sample. Results Among 206 detected miRNAs, 79% of the microRNAs were present at equivalent levels in both cord and adult cells. By comparison, 37 microRNAs were up-regulated and 4 microRNAs were down-regulated in adult erythroid cells (fold change > 2; p let-7 miRNA family consistently demonstrated increased abundance in the adult samples by array-based analyses that were confirmed by quantitative PCR (4.5 to 18.4 fold increases in 6 of 8 let-7 miRNA. Profiling studies of messenger RNA (mRNA in these cells additionally demonstrated down-regulation of ten let-7 target genes in the adult cells. Conclusion These data suggest that a consistent pattern of up-regulation among let-7 miRNA in circulating erythroid cells occurs in association with hemoglobin switching during the fetal-to-adult developmental transition in humans.

  10. Regulation of immune responses and tolerance: the microRNA perspective

    Science.gov (United States)

    Chen, Chang-Zheng; Schaffert, Steven; Fragoso, Rita; Loh, Christina

    2013-01-01

    Summary Much has been learned about the molecular and cellular components critical for the control of immune responses and tolerance. It remains a challenge, however, to control the immune response and tolerance at the system level without causing significant toxicity to normal tissues. Recent studies suggest that microRNA (miRNA) genes, an abundant class of non-coding RNA genes that produce characteristic approximately 22 nucleotides small RNAs, play important roles in immune cells. In this article, we discuss emerging knowledge regarding the functions of miRNA genes in the immune system. We delve into the roles of miRNAs in regulating signaling strength and threshold, homeostasis, and the dynamics of the immune response and tolerance during normal and pathogenic immunological conditions. We also present observations based on analyzes of miR-181 family genes that indicate the potential functions of primary and/ or precursor miRNAs in target recognition and explore the impact of these findings on target identification. Finally, we illustrate that despite the subtle effects of miRNAs on gene expression, miRNAs have the potential to influence the outcomes of normal and pathogenic immune responses by controlling the quantitative and dynamic aspects of immune responses. Tuning miRNA functions in immune cells, through gain- and loss-of-function approaches in mice, may reveal novel approach to restore immune equilibrium from pathogenic conditions, such as autoimmune disease and leukemia, without significant toxicity. PMID:23550642

  11. Quantitative risk trends deriving from PSA-based event analyses. Analysis of results from U.S.NRC's accident sequence precursor program

    International Nuclear Information System (INIS)

    Watanabe, Norio

    2004-01-01

    The United States Nuclear Regulatory Commission (U.S.NRC) has been carrying out the Accident Sequence Precursor (ASP) Program to identify and categorize precursors to potential severe core damage accident sequences using the probabilistic safety assessment (PSA) technique. The ASP Program has identified a lot of risk significant events as precursors that occurred at U.S. nuclear power plants. Although the results from the ASP Program include valuable information that could be useful for obtaining and characterizing risk significant insights and for monitoring risk trends in nuclear power industry, there are only a few attempts to determine and develop the trends using the ASP results. The present study examines and discusses quantitative risk trends for the industry level, using two indicators, that is, the occurrence frequency of precursors and the annual core damage probability, deriving from the results of the ASP analysis. It is shown that the core damage risk at U.S. nuclear power plants has been lowered and the likelihood of risk significant events has been remarkably decreasing. As well, the present study demonstrates that two risk indicators used here can provide quantitative information useful for examining and monitoring the risk trends and/or risk characteristics in nuclear power industry. (author)

  12. MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors.

    Directory of Open Access Journals (Sweden)

    Katerina Gkirtzou

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are small, single stranded RNAs with a key role in post-transcriptional regulation of thousands of genes across numerous species. While several computational methods are currently available for identifying miRNA genes, accurate prediction of the mature miRNA remains a challenge. Existing approaches fall short in predicting the location of mature miRNAs but also in finding the functional strand(s of miRNA precursors. METHODOLOGY/PRINCIPAL FINDINGS: Here, we present a computational tool that incorporates a Naive Bayes classifier to identify mature miRNA candidates based on sequence and secondary structure information of their miRNA precursors. We take into account both positive (true mature miRNAs and negative (same-size non-mature miRNA sequences examples to optimize sensitivity as well as specificity. Our method can accurately predict the start position of experimentally verified mature miRNAs for both human and mouse, achieving a significantly larger (often double performance accuracy compared with two existing methods. Moreover, the method exhibits a very high generalization performance on miRNAs from two other organisms. More importantly, our method provides direct evidence about the features of miRNA precursors which may determine the location of the mature miRNA. We find that the triplet of positions 7, 8 and 9 from the mature miRNA end towards the closest hairpin have the largest discriminatory power, are relatively conserved in terms of sequence composition (mostly contain a Uracil and are located within or in very close proximity to the hairpin loop, suggesting the existence of a possible recognition site for Dicer and associated proteins. CONCLUSIONS: This work describes a novel algorithm for identifying the start position of mature miRNA(s produced by miRNA precursors. Our tool has significantly better (often double performance than two existing approaches and provides new insights about the potential use

  13. MicroRNA in Human Glioma

    Energy Technology Data Exchange (ETDEWEB)

    Li, Mengfeng, E-mail: limf@mail.sysu.edu.cn [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Li, Jun [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Liu, Lei; Li, Wei [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Yang, Yi [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Yuan, Jie [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Key Laboratory of Functional Molecules from Oceanic Microorganisms (Sun Yat-sen University), Department of Education of Guangdong Province, Guangzhou 510080 (China)

    2013-10-23

    Glioma represents a serious health problem worldwide. Despite advances in surgery, radiotherapy, chemotherapy, and targeting therapy, the disease remains one of the most lethal malignancies in humans, and new approaches to improvement of the efficacy of anti-glioma treatments are urgently needed. Thus, new therapeutic targets and tools should be developed based on a better understanding of the molecular pathogenesis of glioma. In this context, microRNAs (miRNAs), a class of small, non-coding RNAs, play a pivotal role in the development of the malignant phenotype of glioma cells, including cell survival, proliferation, differentiation, tumor angiogenesis, and stem cell generation. This review will discuss the biological functions of miRNAs in human glioma and their implications in improving clinical diagnosis, prediction of prognosis, and anti-glioma therapy.

  14. MicroRNA in Human Glioma

    International Nuclear Information System (INIS)

    Li, Mengfeng; Li, Jun; Liu, Lei; Li, Wei; Yang, Yi; Yuan, Jie

    2013-01-01

    Glioma represents a serious health problem worldwide. Despite advances in surgery, radiotherapy, chemotherapy, and targeting therapy, the disease remains one of the most lethal malignancies in humans, and new approaches to improvement of the efficacy of anti-glioma treatments are urgently needed. Thus, new therapeutic targets and tools should be developed based on a better understanding of the molecular pathogenesis of glioma. In this context, microRNAs (miRNAs), a class of small, non-coding RNAs, play a pivotal role in the development of the malignant phenotype of glioma cells, including cell survival, proliferation, differentiation, tumor angiogenesis, and stem cell generation. This review will discuss the biological functions of miRNAs in human glioma and their implications in improving clinical diagnosis, prediction of prognosis, and anti-glioma therapy

  15. MicroRNA involvement in glioblastoma pathogenesis

    International Nuclear Information System (INIS)

    Novakova, Jana; Slaby, Ondrej; Vyzula, Rostislav; Michalek, Jaroslav

    2009-01-01

    MicroRNAs are endogenously expressed regulatory noncoding RNAs. Altered expression levels of several microRNAs have been observed in glioblastomas. Functions and direct mRNA targets for these microRNAs have been relatively well studied over the last years. According to these data, it is now evident, that impairment of microRNA regulatory network is one of the key mechanisms in glioblastoma pathogenesis. MicroRNA deregulation is involved in processes such as cell proliferation, apoptosis, cell cycle regulation, invasion, glioma stem cell behavior, and angiogenesis. In this review, we summarize the current knowledge of miRNA functions in glioblastoma with an emphasis on its significance in glioblastoma oncogenic signaling and its potential to serve as a disease biomarker and a novel therapeutic target in oncology.

  16. MicroRNA function in Drosophila melanogaster.

    Science.gov (United States)

    Carthew, Richard W; Agbu, Pamela; Giri, Ritika

    2017-05-01

    Over the last decade, microRNAs have emerged as critical regulators in the expression and function of animal genomes. This review article discusses the relationship between microRNA-mediated regulation and the biology of the fruit fly Drosophila melanogaster. We focus on the roles that microRNAs play in tissue growth, germ cell development, hormone action, and the development and activity of the central nervous system. We also discuss the ways in which microRNAs affect robustness. Many gene regulatory networks are robust; they are relatively insensitive to the precise values of reaction constants and concentrations of molecules acting within the networks. MicroRNAs involved in robustness appear to be nonessential under uniform conditions used in conventional laboratory experiments. However, the robust functions of microRNAs can be revealed when environmental or genetic variation otherwise has an impact on developmental outcomes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Ternary Electrochemiluminescence System Based on Rubrene Microrods as Luminophore and Pt Nanomaterials as Coreaction Accelerator for Ultrasensitive Detection of MicroRNA from Cancer Cells.

    Science.gov (United States)

    Liu, Jia-Li; Tang, Zhi-Ling; Zhuo, Ying; Chai, Ya-Qin; Yuan, Ruo

    2017-09-05

    As the only endogenous coreactant in the electrochemiluminescence (ECL) system, the dissolved O 2 was the ideal candidate due to the mild reaction and easy operation, but compared to S 2 O 8 2- , the dissolved O 2 with weaker redox activity suffers from the poor enhancement effect of the luminophore, which restricted the further application in bioanalysis. Here, a high-intense ECL signal was gained by the employing of Pt nanomaterials as a coreaction accelerator to generate more of the intermediate of dissolved O 2 to promote the coreaction efficiency. On the basis of a new ternary ECL system of Pt nanomaterials as the coreaction accelerator, dissolved O 2 as the coreactant, and a neotype rubrene microrods as the luminophore, an efficient "on-off-on" solid-state ECL switch platfrom was designed for ultrasensitive microRNA (miRNA) detection with a background reduction strategy of ferrocene-labeled single-stranded DNA (Fc-DNA) as a quencher. In the presence of miRNA 141, the Pt nanoparticles labeled hairpin (HP1/PtNPs) was opened to produce plenty of Pt nanoparticles labeled output DNA (S1/PtNPs) and release the miRNA-141 to participate in the next cycle. Then, the S1/PtNPs were captured on the surface of the electrode by the complementary strand to obtain the super "signal on" state with extremely high ECL signal. This novel solid-state ECL platform exhibited excellent sensitivity from 10 aM to 100 pM with a detection limit of 2.1 aM, which provided a new approach for ultrasensitive ECL bioanalysis.

  18. Lessons learned on probabilistic methodology for precursor analyses

    International Nuclear Information System (INIS)

    Babst, Siegfried; Wielenberg, Andreas; Gaenssmantel, Gerhard

    2016-01-01

    Based on its experience in precursor assessment of operating experience from German NPP and related international activities in the field, GRS has identified areas for enhancing probabilistic methodology. These are related to improving the completeness of PSA models, to insufficiencies in probabilistic assessment approaches, and to enhancements of precursor assessment methods. Three examples from the recent practice in precursor assessments illustrating relevant methodological insights are provided and discussed in more detail. Our experience reinforces the importance of having full scope, current PSA models up to Level 2 PSA and including hazard scenarios for precursor analysis. Our lessons learned include that PSA models should be regularly updated regarding CCF data and inclusion of newly discovered CCF mechanisms or groups. Moreover, precursor classification schemes should be extended to degradations and unavailabilities of the containment function. Finally, PSA and precursor assessments should put more emphasis on the consideration of passive provisions for safety, e. g. by sensitivity cases.

  19. Lessons learned on probabilistic methodology for precursor analyses

    Energy Technology Data Exchange (ETDEWEB)

    Babst, Siegfried [Gesellschaft fuer Anlagen- und Reaktorsicherheit (GRS) gGmbH, Berlin (Germany); Wielenberg, Andreas; Gaenssmantel, Gerhard [Gesellschaft fuer Anlagen- und Reaktorsicherheit (GRS) gGmbH, Garching (Germany)

    2016-11-15

    Based on its experience in precursor assessment of operating experience from German NPP and related international activities in the field, GRS has identified areas for enhancing probabilistic methodology. These are related to improving the completeness of PSA models, to insufficiencies in probabilistic assessment approaches, and to enhancements of precursor assessment methods. Three examples from the recent practice in precursor assessments illustrating relevant methodological insights are provided and discussed in more detail. Our experience reinforces the importance of having full scope, current PSA models up to Level 2 PSA and including hazard scenarios for precursor analysis. Our lessons learned include that PSA models should be regularly updated regarding CCF data and inclusion of newly discovered CCF mechanisms or groups. Moreover, precursor classification schemes should be extended to degradations and unavailabilities of the containment function. Finally, PSA and precursor assessments should put more emphasis on the consideration of passive provisions for safety, e. g. by sensitivity cases.

  20. Growth of hexagonal NaGdF{sub 4} nanocrystals based on cubic Ln{sup 3+}: CaF{sub 2} precursors and the multi-color upconversion emissions

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Lei; Chen, Daqin, E-mail: dqchen@fjirsm.ac.cn; Yu, Yunlong; Zhang, Rui; Ling, Hang; Xu, Ju; Huang, Feng; Wang, Yuansheng, E-mail: yswang@fjirsm.ac.cn

    2014-04-05

    Graphical abstract: We reported a novel hetero-valence cation exchange route to synthesize Ln: NaGdF4 upconversion nanocrystals for the first time. -- Highlights: • The Ln3+: NaGdF4 nanocrystals were synthesized based on the Ln3+: CaF2 precursors. • The microstructures of nanocrystals were characterized. • The multi-color upconversion emissions were easily realized. -- Abstract: Lanthanide-doped upconversion nanomaterials have attracted great attention recently for their potential applications in the fields of bio-label, three-dimensional display, solar cell and so on. In this article, we report a new strategy to prepare hexagonal Ln{sup 3+}:NaGdF{sub 4} upconversion nanocrystals. Unlike the routine way of synthesizing NaGdF{sub 4} nanocrystals through nucleation and growth, the formation of hexagonal NaGdF{sub 4} nanocrystals herein is realized based on the Ln{sup 3+}-doped cubic CaF{sub 2} precursors, following a hetero-valence cation exchange process between Gd{sup 3+}/Na{sup +} and Ca{sup 2+}. Evidently, Ln{sup 3+} dopants in the CaF{sub 2} precursors are retained in the finally formed hexagonal NaGdF{sub 4} nanocrystals and, subsequently, multi-color upconversion emissions are easily realized by simply adjusting the Ln{sup 3+} dopant species and contents in the CaF{sub 2} precursors. This novel hetero-valence cation exchange route may open up a new pathway to synthesize nanomaterials that cannot be fabricated directly.

  1. Report on Fukushima Daiichi NPP precursor events

    International Nuclear Information System (INIS)

    2014-01-01

    The main questions to be answered by this report were: The Fukushima Daiichi NPP accident, could it have been prevented? If there is a next severe accident, may it be prevented? To answer the first question, the report addressed several aspects. First, the report investigated whether precursors to the Fukushima Daiichi NPP accident existed in the operating experience; second, the reasons why these precursors did not evolve into a severe accident. Third, whether lessons learned from these precursor events were adequately considered by member countries; and finally, if the operating experience feedback system needs to be improved, based on the previous analysis. To address the second question which is much more challenging, the report considered precursor events identified through a search and analysis of the IRS database and also precursors events based on risk significance. Both methods can point out areas where further work may be needed, even if it depends heavily on design and site-specific factors. From the operating experience side, more efforts are needed to ensure timely and full implementation of lessons learnt from precursor events. Concerning risk considerations, a combined use of risk precursors and operating experience may drive to effective changes to plants to reduce risk. The report also contains a short description and evaluation of selected precursors that are related to the course of the Fukushima Daiichi NPP accident. The report addresses the question whether operating experience feedback can be effectively used to identify plant vulnerabilities and minimize potential for severe core damage accidents. Based on several of the precursor events national or international in-depth evaluations were started. The vulnerability of NPPs due to external and internal flooding has clearly been addressed. In addition to the IRS based investigation, the WGRISK was asked to identify important precursor events based on risk significance. These precursors have

  2. Lunar Robotic Precursor Missions Using Electric Propulsion

    OpenAIRE

    Winski, Richard G.

    2006-01-01

    A trade study is carried out for the design of electric propulsion based lunar robotic precursor missions. The focus is to understand the relationships between payload mass delivered, electric propulsion power, and trip time. The results are compared against a baseline system using chemical propulsion with LOX/H2. The major differences between the chemical propulsion based and electric propulsion based systems are presented in terms of the payload mass and trip time. It is shown that solar e...

  3. MicroRNA target finding by comparative genomics.

    Science.gov (United States)

    Friedman, Robin C; Burge, Christopher B

    2014-01-01

    MicroRNAs (miRNAs) have been implicated in virtually every metazoan biological process, exerting a widespread impact on gene expression. MicroRNA repression is conferred by relatively short "seed match" sequences, although the degree of repression varies widely for individual target sites. The factors controlling whether, and to what extent, a target site is repressed are not fully understood. As an alternative to target prediction based on sequence alone, comparative genomics has emerged as an invaluable tool for identifying miRNA targets that are conserved by natural selection, and hence likely effective and important. Here we present a general method for quantifying conservation of miRNA seed match sites, separating it from background conservation, controlling for various biases, and predicting miRNA targets. This method is useful not only for generating predictions but also as a tool for empirically evaluating the importance of various target prediction criteria.

  4. Computational methods for ab initio detection of microRNAs

    Directory of Open Access Journals (Sweden)

    Malik eYousef

    2012-10-01

    Full Text Available MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the Microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed.

  5. MicroRNAs in Prostate Cancer

    Science.gov (United States)

    2008-11-01

    lymphoma. Genes Chromosom. Cancer 39:167–69 131. O’Connell RM, Taganov KD, Boldin MP, Cheng G, Baltimore D. 2007. MicroRNA-155 is induced during the...carcinoma. J. Virol. 81:1033–36 155. Xi Y, Nakajima G, Gavin E, Morris CG, Kudo K, et al. 2007. Systematic analysis of microRNA expression of RNA extracted ...diversity. miRNAs were extracted from the unique sequences by searching against miRNA database (miRbase release 10.0; http://microrna.sanger.ac.uk

  6. Role of MicroRNAs in Renin-Angiotensin-Aldosterone System-Mediated Cardiovascular Inflammation and Remodeling

    Directory of Open Access Journals (Sweden)

    Maricica Pacurari

    2015-01-01

    Full Text Available MicroRNAs are endogenous regulators of gene expression either by inhibiting translation or protein degradation. Recent studies indicate that microRNAs play a role in cardiovascular disease and renin-angiotensin-aldosterone system- (RAAS- mediated cardiovascular inflammation, either as mediators or being targeted by RAAS pharmacological inhibitors. The exact role(s of microRNAs in RAAS-mediated cardiovascular inflammation and remodeling is/are still in early stage of investigation. However, few microRNAs have been shown to play a role in RAAS signaling, particularly miR-155, miR-146a/b, miR-132/122, and miR-483-3p. Identification of specific microRNAs and their targets and elucidating microRNA-regulated mechanisms associated RAS-mediated cardiovascular inflammation and remodeling might lead to the development of novel pharmacological strategies to target RAAS-mediated vascular pathologies. This paper reviews microRNAs role in inflammatory factors mediating cardiovascular inflammation and RAAS genes and the effect of RAAS pharmacological inhibition on microRNAs and the resolution of RAAS-mediated cardiovascular inflammation and remodeling. Also, this paper discusses the advances on microRNAs-based therapeutic approaches that may be important in targeting RAAS signaling.

  7. Direct preparation of Al-base alloys from their oxides/metal precursors in the eutectic LiCl–KCl melt

    International Nuclear Information System (INIS)

    Gao, Bingliang; Zhu, Hao; Xia, Yuxiang; Shi, Zhongning; Hu, Xianwei; Wang, Zhaowen

    2016-01-01

    A study was carried out on the preparation of Al–Cu–Li alloy from their oxides/metal precursors using the method of electro-deoxidation in the eutectic LiCl–KCl melt at 648 K. Cyclic voltammetry was used to characterize the system. The samples were prepared by potentiostatic electrolysis at −1.0 V to −2.0 V (vs. Ag + /Ag) for 5 h. XRD analysis shows that Li 2 O is not electrochemically reduced to Li at −1.0 V (vs. Ag + /Ag) or more negative potential. During the preparation process of Al–Cu–Li alloy, lithium peroxide is formed as an intermediate compound. Al–Cu–Li alloy is chemically prepared through the reaction between aluminum and lithium peroxide by heating of Al–Cu–Li 2 O precursors in KCl–LiCl–LiF melt at 1023 K. Eelectro-deoxidation in LiCl–KCl melt can increase the lithium content in the final alloy product. Al–Mg and Al–Nd alloy were also prepared by using the same method from their mixture of aluminum and corresponding oxide, respectively. Al–Nd alloy can only be obtained at the temperature above 773 K. Al–Li alloy could not be obtained in eutectic CaCl 2 –LiCl melt because of formation of calcium aluminates. - Highlights: • Al–Cu–Li alloy was prepared using electrochemical deoxidation of Al–Cu–Li 2 O precursor in eutectic KCl–LiCl melt at 648 K. • Al–Nd alloy was successfully produced by the same method at 773 K. • CaCl 2 –LiCl melt is not a good choice for preparing Al–Li alloy because of formation of calcium aluminate.

  8. Direct preparation of Al-base alloys from their oxides/metal precursors in the eutectic LiCl–KCl melt

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Bingliang, E-mail: blgao@mail.neu.edu.cn; Zhu, Hao; Xia, Yuxiang; Shi, Zhongning; Hu, Xianwei; Wang, Zhaowen

    2016-04-25

    A study was carried out on the preparation of Al–Cu–Li alloy from their oxides/metal precursors using the method of electro-deoxidation in the eutectic LiCl–KCl melt at 648 K. Cyclic voltammetry was used to characterize the system. The samples were prepared by potentiostatic electrolysis at −1.0 V to −2.0 V (vs. Ag{sup +}/Ag) for 5 h. XRD analysis shows that Li{sub 2}O is not electrochemically reduced to Li at −1.0 V (vs. Ag{sup +}/Ag) or more negative potential. During the preparation process of Al–Cu–Li alloy, lithium peroxide is formed as an intermediate compound. Al–Cu–Li alloy is chemically prepared through the reaction between aluminum and lithium peroxide by heating of Al–Cu–Li{sub 2}O precursors in KCl–LiCl–LiF melt at 1023 K. Eelectro-deoxidation in LiCl–KCl melt can increase the lithium content in the final alloy product. Al–Mg and Al–Nd alloy were also prepared by using the same method from their mixture of aluminum and corresponding oxide, respectively. Al–Nd alloy can only be obtained at the temperature above 773 K. Al–Li alloy could not be obtained in eutectic CaCl{sub 2}–LiCl melt because of formation of calcium aluminates. - Highlights: • Al–Cu–Li alloy was prepared using electrochemical deoxidation of Al–Cu–Li{sub 2}O precursor in eutectic KCl–LiCl melt at 648 K. • Al–Nd alloy was successfully produced by the same method at 773 K. • CaCl{sub 2}–LiCl melt is not a good choice for preparing Al–Li alloy because of formation of calcium aluminate.

  9. Chemical and structural changes in polyamide based organic–inorganic hybrid materials upon incorporation of SeS{sub 2}O{sub 6}{sup 2−} precursor

    Energy Technology Data Exchange (ETDEWEB)

    Krylova, V.; Dukstienė, N.; Žalenkienė, S. [Department of Physical and Inorganic Chemistry, Kaunas University of Technology, Radvilenu st. " 1" 9" , LT-50254, Kaunas (Lithuania); Baltrusaitis, J., E-mail: job314@lehigh.edu [Department of Chemical and Biomolecular Engineering, Lehigh University, B336 Iacocca Hall, 111 Research Drive, Bethlehem, PA 18015 (United States)

    2017-01-15

    Highlights: • We investigated deposited and diffused K{sub 2}SeS{sub 2}O{sub 6} into polyamide 6 (PA 6). • AAS showed Se:S molar ratio = 1:2 within the PA. • Various decomposition products were detected within the polymer. • Measured bandgap shifted towards lower light absorption energies. - Abstract: Composite organic-inorganic functional materials are of significant importance in various applications of science and technology. In this work, physicochemical characterization of such composite materials obtained after the exposure of polyamide PA 6 to K{sub 2}SeS{sub 2}O{sub 6} precursor solution was performed. Chalcogenized polymer surface was characterized using X-ray diffraction, infrared, and UV–vis spectroscopies while their bulk chemical analysis was performed using atomic absorption spectroscopy. Crystallite size was not found to change with the exposure to K{sub 2}SeS{sub 2}O{sub 6} precursor but PA 6 chain–chain separation decreased. Importantly, infrared and X-ray analyses showed chemical bonding taking place between the PA 6 and SeS{sub 2}O{sub 6}{sup 2−} ions via −NH− functional group. A distinct change in bandgap, E{sub g}, value was observed in UV–vis spectra due to the presence of SeS{sub 2}O{sub 6}{sup 2−}, SeSO{sub 3}{sup 2−} and Se{sub 2}S{sub 2}O{sub 6}{sup 2−} ions formed via decomposition of the precursor material in acidic medium. After extended 4 h chalcogenation a distinct absorption due to the elemental selenium was also observed as obtained from Tauc plots.

  10. Synthesis and characterization of sulfonated polymers for ionomeric membranes based on styrene copolymers; Sintese e caracterizacao de precursores sulfonados para membranas polimericas a base de copolimeros estirenicos

    Energy Technology Data Exchange (ETDEWEB)

    Becker, C.M.; Forte, M.M.C.; Amico, S.C. [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Escola de Engenharia. Lab. de Materiais Polimericos (LAPOL)], e-mail: crismbecker@yahoo.com.br, e-mail: mmcforte@ufrgs.br, e-mail: amico@ufrgs.br; Vargas, J.V.C. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Engenharia Mecanica], e-mail: jvargas@demec.ufpr.br

    2006-07-01

    Polymer electrolyte membrane fuel cell (PEMFC) have emerged strongly as a viable alternative for power source owing to their high energy efficiency and environmental friendliness. Currently, Nafion is the most frequently used membrane even though it has a high cost. The objective of this work is to synthesize sulfonated polymers, based on styrene copolymers, with different sulfonation degrees as an alternative material for fuel cell membranes. Acetyl sulfate was used to carry out the sulfonation and the resulting polymers were characterized by Fourier Transform Infra-red (FTIR), thermogravimetric analysis (TGA) and degree of substitution or sulfonation (DS). The polyelectrolytes were evaluated regarding their ion exchange capacity (IEC) and conductivity. The results demonstrated that increasing the sulfonic acid content of the polymer results in higher IEC, conductivity and water uptake. (author)

  11. Performance comparison of digital microRNA profiling technologies applied on human breast cancer cell lines.

    Directory of Open Access Journals (Sweden)

    Erik Knutsen

    Full Text Available MicroRNA profiling represents an important first-step in deducting individual RNA-based regulatory function in a cell, tissue, or at a specific developmental stage. Currently there are several different platforms to choose from in order to make the initial miRNA profiles. In this study we investigate recently developed digital microRNA high-throughput technologies. Four different platforms were compared including next generation SOLiD ligation sequencing and Illumina HiSeq sequencing, hybridization-based NanoString nCounter, and miRCURY locked nucleic acid RT-qPCR. For all four technologies, full microRNA profiles were generated from human cell lines that represent noninvasive and invasive tumorigenic breast cancer. This study reports the correlation between platforms, as well as a more extensive analysis of the accuracy and sensitivity of data generated when using different platforms and important consideration when verifying results by the use of additional technologies. We found all the platforms to be highly capable for microRNA analysis. Furthermore, the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS and RT-qPCR. Based on these findings we propose new guidelines and considerations when performing microRNA profiling.

  12. Centrifugation: an important pre-analytic procedure that influences plasma microRNA quantification during blood processing.

    Science.gov (United States)

    Zheng, Xiao-Hui; Cui, Cui; Zhou, Xin-Xi; Zeng, Yi-Xin; Jia, Wei-Hua

    2013-12-01

    Circulating microRNAs are robustly present in plasma or serum and have become a research focus as biomarkers for tumor diagnosis and prognosis. Centrifugation is a necessary procedure for obtaining high-quality blood supernatant. Herein, we investigated one-step and two-step centrifugations, two centrifugal methods routinely used in microRNA study, to explore their effects on plasma microRNA quantification. The microRNAs obtained from one-step and two-step centrifugations were quantified by microarray and TaqMan-based real-time quantitative polymerase chain reaction (Q-PCR). Dynamic light scattering was performed to explore the difference underlying the two centrifugal methods. The results from the microarray containing 1,347 microRNAs showed that the signal detection rate was greatly decreased in the plasma sample prepared by two-step centrifugation. More importantly, the microRNAs missing in this plasma sample could be recovered and detected in the precipitate generated from the second centrifugation. Consistent with the results from microarray, a marked decrease of three representative microRNAs in two-step centrifugal plasma was validated by Q-PCR. According to the size distribution of all nanoparticles in plasma, there were fewer nanoparticles with size >1,000 nm in two-step centrifugal plasma. Our experiments directly demonstrated that different centrifugation methods produced distinct quantities of plasma microRNAs. Thus, exosomes or protein complexes containing microRNAs may be involved in large nanoparticle formation and may be precipitated after two-step centrifugation. Our results remind us that sample processing methods should be first considered in conducting research.

  13. Inhibition of Mef2a Enhances Neovascularization via Post-transcriptional Regulation of 14q32 MicroRNAs miR-329 and miR-494

    Directory of Open Access Journals (Sweden)

    Sabine M.J. Welten

    2017-06-01

    Full Text Available Improving the efficacy of neovascularization is a promising strategy to restore perfusion of ischemic tissues in patients with peripheral arterial disease. The 14q32 microRNA cluster is highly involved in neovascularization. The Mef2a transcription factor has been shown to induce transcription of the microRNAs within this cluster. We inhibited expression of Mef2a using gene-silencing oligonucleotides (GSOs in an in vivo hind limb ischemia model. Treatment with GSO-Mef2a clearly improved blood flow recovery within 3 days (44% recovery versus 25% recovery in control and persisted until 14 days after ischemia induction (80% recovery versus 60% recovery in control. Animals treated with GSO-Mef2a showed increased arteriogenesis and angiogenesis in the relevant muscle tissues. Inhibition of Mef2a decreased expression of 14q32 microRNAs miR-329 (p = 0.026 and miR-494 (trend, p = 0.06, but not of other 14q32 microRNAs, nor of 14q32 microRNA precursors. Because Mef2a did not influence 14q32 microRNA transcription, we hypothesized it functions as an RNA-binding protein that influences processing of 14q32 microRNA miR-329 and miR-494. Mef2A immunoprecipitation followed by RNA isolation and rt/qPCR confirmed direct binding of MEF2A to pri-miR-494, supporting this hypothesis. Our study demonstrates a novel function for Mef2a in post-ischemic neovascularization via post-transcriptional regulation of 14q32 microRNAs miR-329 and miR-494.

  14. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata

    Directory of Open Access Journals (Sweden)

    Yu Huaping

    2010-07-01

    Full Text Available Abstract Background MicroRNAs (miRNAs play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. Results In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata which is an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues. Based on sequence similarity and hairpin structure prediction, we found that 156,639 reads representing 63 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates whose precursors were all potentially generated from citrus ESTs. In addition, five miRNA* sequences were also sequenced. These sequences had not been earlier described in other plant species and accumulation of the 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes including one encoding IRX12 copper ion binding/oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata. Conclusion Deep sequencing of short RNAs from C. trifoliata flowers and fruits identified 10 new potential miRNAs and 42 highly conserved miRNA families, indicating that specific miRNAs exist in C. trifoliata. These results show that regulatory miRNAs exist in agronomically important trifoliate orange

  15. Prediction of guide strand of microRNAs from its sequence and secondary structure

    Directory of Open Access Journals (Sweden)

    Ahmed Firoz

    2009-04-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are produced by the sequential processing of a long hairpin RNA transcript by Drosha and Dicer, an RNase III enzymes, and form transitory small RNA duplexes. One strand of the duplex, which incorporates into RNA-induced silencing complex (RISC and silences the gene expression is called guide strand, or miRNA; while the other strand of duplex is degraded and called the passenger strand, or miRNA*. Predicting the guide strand of miRNA is important for better understanding the RNA interference pathways. Results This paper describes support vector machine (SVM models developed for predicting the guide strands of miRNAs. All models were trained and tested on a dataset consisting of 329 miRNA and 329 miRNA* pairs using five fold cross validation technique. Firstly, models were developed using mono-, di-, and tri-nucleotide composition of miRNA strands and achieved the highest accuracies of 0.588, 0.638 and 0.596 respectively. Secondly, models were developed using split nucleotide composition and achieved maximum accuracies of 0.553, 0.641 and 0.602 for mono-, di-, and tri-nucleotide respectively. Thirdly, models were developed using binary pattern and achieved the highest accuracy of 0.708. Furthermore, when integrating the secondary structure features with binary pattern, an accuracy of 0.719 was seen. Finally, hybrid models were developed by combining various features and achieved maximum accuracy of 0.799 with sensitivity 0.781 and specificity 0.818. Moreover, the performance of this model was tested on an independent dataset that achieved an accuracy of 0.80. In addition, we also compared the performance of our method with various siRNA-designing methods on miRNA and siRNA datasets. Conclusion In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex. This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their

  16. How the RNA isolation method can affect microRNA microarray results

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

    2011-01-01

    RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...

  17. Enumeration of minimal stoichiometric precursor sets in metabolic networks.

    Science.gov (United States)

    Andrade, Ricardo; Wannagat, Martin; Klein, Cecilia C; Acuña, Vicente; Marchetti-Spaccamela, Alberto; Milreu, Paulo V; Stougie, Leen; Sagot, Marie-France

    2016-01-01

    What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux. Although considering the stoichiometry makes the problem harder, it enables to obtain biologically reasonable precursor sets that we call stoichiometric. Recently a method to enumerate all minimal stoichiometric precursor sets was proposed in the literature. The relationship between topological and stoichiometric precursor sets had however not yet been studied. Such relationship between topological and stoichiometric precursor sets is highlighted. We also present two algorithms that enumerate all minimal stoichiometric precursor sets. The first one is of theoretical interest only and is based on the above mentioned relationship. The second approach solves a series of mixed integer linear programming problems. We compared the computed minimal precursor sets to experimentally obtained growth media of several Escherichia coli strains using genome-scale metabolic networks. The results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr.

  18. MicroRNAs in right ventricular remodelling.

    Science.gov (United States)

    Batkai, Sandor; Bär, Christian; Thum, Thomas

    2017-10-01

    Right ventricular (RV) remodelling is a lesser understood process of the chronic, progressive transformation of the RV structure leading to reduced functional capacity and subsequent failure. Besides conditions concerning whole hearts, some pathology selectively affects the RV, leading to a distinct RV-specific clinical phenotype. MicroRNAs have been identified as key regulators of biological processes that drive the progression of chronic diseases. The role of microRNAs in diseases affecting the left ventricle has been studied for many years, however there is still limited information on microRNAs specific to diseases in the right ventricle. Here, we review recently described details on the expression, regulation, and function of microRNAs in the pathological remodelling of the right heart. Recently identified strategies using microRNAs as pharmacological targets or biomarkers will be highlighted. Increasing knowledge of pathogenic microRNAs will finally help improve our understanding of underlying distinct mechanisms and help utilize novel targets or biomarkers to develop treatments for patients suffering from right heart diseases. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions, please email: journals.permissions@oup.com.

  19. MicroRNAs Promote Granule Cell Expansion in the Cerebellum Through Gli2.

    Science.gov (United States)

    Constantin, Lena; Wainwright, Brandon J

    2015-12-01

    MicroRNAs (miRNAs) are important regulators of cerebellar function and homeostasis. Their deregulation results in cerebellar neuronal degeneration and spinocerebellar ataxia type 1 and contributes to medulloblastoma. Canonical miRNA processing involves Dicer, which cleaves precursor miRNAs into mature double-stranded RNA duplexes. In order to address the role of miRNAs in cerebellar granule cell precursor development, loxP-flanked exons of Dicer1 were conditionally inactivated using the granule cell precursor-specific Atoh1-Cre recombinase. A reduction of 87% in Dicer1 transcript was achieved in this conditional Dicer knockdown model. Although knockdown resulted in normal survival, mice had disruptions to the cortical layering of the anterior cerebellum, which resulted from the premature differentiation of granule cell precursors in this region during neonatal development. This defect manifested as a thinner external granular layer with ectopic mature granule cells, and a depleted internal granular layer. We found that expression of the activator components of the Hedgehog-Patched pathway, the Gli family of transcription factors, was perturbed in conditional Dicer knockdown mice. We propose that loss of Gli2 mRNA mediated the anterior-restricted defect in conditional Dicer knockdown mice and, as proof of principle, were able to show that miR-106b positively regulated Gli2 mRNA expression. These findings confirm the importance of miRNAs as positive mediators of Hedgehog-Patched signalling during granule cell precursor development.

  20. Preparation of superconductor precursor powders

    Science.gov (United States)

    Bhattacharya, Raghunath

    1998-01-01

    A process for the preparation of a precursor metallic powder composition for use in the subsequent formation of a superconductor. The process comprises the steps of providing an electrodeposition bath comprising an electrolyte medium and a cathode substrate electrode, and providing to the bath one or more soluble salts of one or more respective metals which are capable of exhibiting superconductor properties upon subsequent appropriate treatment. The bath is continually energized to cause the metallic and/or reduced particles formed at the electrode to drop as a powder from the electrode into the bath, and this powder, which is a precursor powder for superconductor production, is recovered from the bath for subsequent treatment. The process permits direct inclusion of all metals in the preparation of the precursor powder, and yields an amorphous product mixed on an atomic scale to thereby impart inherent high reactivity. Superconductors which can be formed from the precursor powder include pellet and powder-in-tube products.

  1. Toward a theory of precursors

    International Nuclear Information System (INIS)

    Freivogel, Ben; Giddings, Steven B.; Lippert, Matthew

    2002-01-01

    To better understand the possible breakdown of locality in quantum gravitational systems, we pursue the identity of precursors in the context of the anti-de Sitter/conformal field theory correspondence. Holography implies a breakdown of standard bulk locality which we expect to occur only at extremely high energy. We consider precursors that encode bulk information causally disconnected from the boundary and whose measurement involves nonlocal bulk processes. We construct a toy model of holography which encapsulates the expected properties of precursors and compare it with previous such discussions. If these precursors can be identified in the gauge theory, they are almost certainly Wilson loops, perhaps with decorations, but the relevant information is encoded in the high-energy sector of the theory and should not be observable by low energy measurements. This would be in accord with the locality bound, which serves as a criterion for situations where breakdown of bulk locality is expected

  2. Epigenetic microRNA Regulation

    DEFF Research Database (Denmark)

    Wiklund, Erik Digman

    2011-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that negatively regulate gene expression post-transcriptionally by binding to complementary sequences in the 3’UTR of target mRNAs in the cytoplasm. However, recent evidence suggests that certain miRNAs are enriched in the nucleus, and their t......MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that negatively regulate gene expression post-transcriptionally by binding to complementary sequences in the 3’UTR of target mRNAs in the cytoplasm. However, recent evidence suggests that certain miRNAs are enriched in the nucleus...

  3. MicroRNAs and Presbycusis.

    Science.gov (United States)

    Hu, Weiming; Wu, Junwu; Jiang, Wenjing; Tang, Jianguo

    2018-02-01

    Presbycusis (age-related hearing loss) is the most universal sensory degenerative disease in elderly people caused by the degeneration of cochlear cells. Non-coding microRNAs (miRNAs) play a fundamental role in gene regulation in almost every multicellular organism, and control the aging processes. It has been identified that various miRNAs are up- or down-regulated during mammalian aging processes in tissue-specific manners. Most miRNAs bind to specific sites on their target messenger-RNAs (mRNAs) and decrease their expression. Germline mutation may lead to dysregulation of potential miRNAs expression, causing progressive hair cell degeneration and age-related hearing loss. Therapeutic innovations could emerge from a better understanding of diverse function of miRNAs in presbycusis. This review summarizes the relationship between miRNAs and presbycusis, and presents novel miRNAs-targeted strategies against presbycusis.

  4. Genomic Organization of Zebrafish microRNAs

    Directory of Open Access Journals (Sweden)

    Paydar Ima

    2008-05-01

    Full Text Available Abstract Background microRNAs (miRNAs are small (~22 nt non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. Results We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. Conclusion Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.

  5. Prevalence and risk factors for esophageal squamous cell cancer and precursor lesions in Anyang, China: a population-based endoscopic survey

    Science.gov (United States)

    He, Z; Zhao, Y; Guo, C; Liu, Y; Sun, M; Liu, F; Wang, X; Guo, F; Chen, K; Gao, L; Ning, T; Pan, Y; Li, Y; Zhang, S; Lu, C; Wang, Z; Cai, H; Ke, Y

    2010-01-01

    Background: The etiology of esophageal squamous cell cancer (ESCC) in high prevalence regions of China remains unclear. Methods: Endoscopic biopsies were conducted among 7381 inhabitants aged from 25 to 65 of Anyang, China. Results: In this study, 2.57, 0.20 and 0.16% of the participants had mild, moderate and severe squamous dysplasia, respectively; 0.19 and 0.08% showed squamous carcinoma in situ and invasive ESCC. Using deep well (depth >100 meters) as water source (odds ratio=0.72, 95% confidence interval: 0.54–0.96) was negatively associated with ESCC and its precursors, whereas tobacco and alcohol use were not significantly associated with ESCC. Conclusions: Water source and other factors in this region need further evaluation by longitudinal studies. PMID:20700119

  6. Effect of precursor and preparation method on manganese based activated carbon sorbents for removing H2S from hot coal gas.

    Science.gov (United States)

    Wang, Jiancheng; Qiu, Biao; Han, Lina; Feng, Gang; Hu, Yongfeng; Chang, Liping; Bao, Weiren

    2012-04-30

    Activated carbon (AC) supported manganese oxide sorbents were prepared by the supercritical water impregnation (SCWI) using two different precursor of Mn(NO(3))(2) (SCW(N)) and Mn(Ac)(2)·4H(2)O (SCW(A)). Their capacities of removing H(2)S from coal gas were evaluated and compared to the sorbents prepared by the pore volume impregnation (PVI) method. The structure and composition of different sorbents were characterized by XRD, SEM, TEM, XPS and XANES techniques. It is found that the precursor of active component plays the crucial role and SCW(N) sorbents show much better sulfidation performance than the SCW(A) sorbents. This is because the Mn(3)O(4) active phase of the SCW(N) sorbents are well dispersed on the AC support, while the Mn(2)SiO(4)-like species in the SCW(A) sorbent can be formed and seriously aggregated. The SCW(N) sorbents with 2.80% and 5.60% manganese are favorable for the sulfidation reaction, since the Mn species are better dispersed on the SCW(N) sorbents than those on the PV(N) sorbents and results in the better sulfidation performance of the SCW(N) sorbents. As the Mn content increases to 11.20%, the metal oxide particles on AC supports aggregate seriously, which leads to poorer sulfidation performance of the SCW(N)11.20% sorbents than that of the PV(N)11.20% sorbents. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Diagnostic and Prognostic MicroRNA Biomarkers for Prostate Cancer in Cell-free Urine

    DEFF Research Database (Denmark)

    Fredsøe, Jacob Christian; Rasmussen, Anne Karin; Thomsen, Anni Rønfeldt

    2017-01-01

    Background: Widespread use of prostate-specific antigen (PSA) testing for prostate cancer (PC) detection has led to extensive overdiagnosis and overtreatment. Urine-based microRNA (miRNA) biomarkers could be useful in PC diagnosis and prognosis. Objective: To train and validate urine-based micro......RNA (miRNA) biomarkers that may assist in PC diagnosis and prognosis. Design, setting, and participants: We profiled the expression levels of 92 miRNAs via reverse transcriptase–poymerase chain reaction in cell-free urine samples from 29 patients with benign prostatic hyperplasia (BPH) and 215 patients...... could help in primary diagnosis of PC and guide treatment decisions. Further validation studies are warranted. Patient summary: Using two large patient cohorts, we searched for novel prostate cancer biomarkers in urine. We found two new sets of microRNA biomarkers in urine that could accurately predict...

  8. Effects of pathogen reduction systems on platelet microRNAs, mRNAs, activation, and function.

    Science.gov (United States)

    Osman, Abdimajid; Hitzler, Walter E; Meyer, Claudius U; Landry, Patricia; Corduan, Aurélie; Laffont, Benoit; Boilard, Eric; Hellstern, Peter; Vamvakas, Eleftherios C; Provost, Patrick

    2015-01-01

    Pathogen reduction (PR) systems for platelets, based on chemically induced cross-linking and inactivation of nucleic acids, potentially prevent transfusion transmission of infectious agents, but can increase clinically significant bleeding in some clinical studies. Here, we documented the effects of PR systems on microRNA and mRNA levels of platelets stored in the blood bank, and assessed their impact on platelet activation and function. Unlike platelets subjected to gamma irradiation or stored in additive solution, platelets treated with Intercept (amotosalen+ ultraviolet-A [UVA] light) exhibited significantly reduced levels of 6 of the 11 microRNAs, and 2 of the 3 anti-apoptotic mRNAs (Bcl-xl and Clusterin) that we monitored, compared with platelets stored in plasma. Mirasol (riboflavin+ UVB light) treatment of platelets did not produce these effects. PR neither affected platelet microRNA synthesis or function nor induced cross-linking of microRNA-sized endogenous platelet RNA species. However, the reduction in the platelet microRNA levels induced by Intercept correlated with the platelet activation (p < 0.05) and an impaired platelet aggregation response to ADP (p < 0.05). These results suggest that Intercept treatment may induce platelet activation, resulting in the release of microRNAs and mRNAs from platelets. The clinical implications of this reduction in platelet nucleic acids secondary to Intercept remain to be established.

  9. MicroRNAs as regulatory elements in psoriasis

    Directory of Open Access Journals (Sweden)

    Liu Yuan

    2016-01-01

    Full Text Available Psoriasis is a chronic, autoimmune, and complex genetic disorder that affects 23% of the European population. The symptoms of Psoriatic skin are inflammation, raised and scaly lesions. microRNA, which is short, nonprotein-coding, regulatory RNAs, plays critical roles in psoriasis. microRNA participates in nearly all biological processes, such as cell differentiation, development and metabolism. Recent researches reveal that multitudinous novel microRNAs have been identified in skin. Some of these substantial novel microRNAs play as a class of posttranscriptional gene regulator in skin disease, such as psoriasis. In order to insight into microRNAs biological functions and verify microRNAs biomarker, we review diverse references about characterization, profiling and subtype of microRNAs. Here we will share our opinions about how and which microRNAs are as regulatory in psoriasis.

  10. MicroRNA delivery for regenerative medicine.

    Science.gov (United States)

    Peng, Bo; Chen, Yongming; Leong, Kam W

    2015-07-01

    MicroRNA (miRNA) directs post-transcriptional regulation of a network of genes by targeting mRNA. Although relatively recent in development, many miRNAs direct differentiation of various stem cells including induced pluripotent stem cells (iPSCs), a major player in regenerative medicine. An effective and safe delivery of miRNA holds the key to translating miRNA technologies. Both viral and nonviral delivery systems have seen success in miRNA delivery, and each approach possesses advantages and disadvantages. A number of studies have demonstrated success in augmenting osteogenesis, improving cardiogenesis, and reducing fibrosis among many other tissue engineering applications. A scaffold-based approach with the possibility of local and sustained delivery of miRNA is particularly attractive since the physical cues provided by the scaffold may synergize with the biochemical cues induced by miRNA therapy. Herein, we first briefly cover the application of miRNA to direct stem cell fate via replacement and inhibition therapies, followed by the discussion of the promising viral and nonviral delivery systems. Next we present the unique advantages of a scaffold-based delivery in achieving lineage-specific differentiation and tissue development. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. High-­Performance Carbon Molecular Sieve Gas Separation Membranes Based on a Carbon-­Rich Intrinsically Microporous Polyimide Precursor

    KAUST Repository

    Hazazi, Khalid

    2018-04-01

    The objective of this study was to investigate the transport properties and the microstructure of CMS membranes derived from a carbon-rich intrinsically microporous polyimide precursor. CMS membranes were prepared by a heat treatment of the polyimide precursor using a well-defined heating protocol in a horizontal tube furnace up to 1000 °C. A nitrogen purge was kept inside the furnace to remove all the evolved by-products as the precursor started to decompose and carbonize. The microstructures of the carbon molecular sieve membranes (CMSMs) were examined using wide-angle x-ray diffraction, Raman spectra, N2 adsorption and CO2 adsorption. The average interlayer spacing (d002) between the graphite plates was estimated using the data obtained by the WXRD. The average d002 decreased as a result of increasing the pyrolysis temperature; average d002 distances for CMS prepared at 700 and 1000 °C were estimated to be 0.40 to 0.38 nm, respectively. Raman spectra confirmed the progressive structural ordering as heat-treatment temperature increased. A substantial decrease in the intensity of the D band was observed as a function of pyrolysis temperature, indicating a decrease in the disordered structure. Graphitic structure and turbostratic carbon coexist in the as-prepared carbon membranes, of which the microcrystal size La and the stacking height Lc were increasing as a function of pyrolysis temperature. N2 adsorption showed a remarkable increase in the BET surface area as a function of pyrolysis temperature. BET surface areas for the pristine and CMSs prepared at 700 to 900 °C were in the range of 650 to 680 m2/g with a remarkable shift in the pore size distribution toward the ultra- microporous region. CO2 adsorption was used to estimate the surface area for pores with sizes of less than 1 nm. Surface areas were observed to increase from 350 m2/g at 500 °C to 857 m2/g at 800 °C, and then started dropping slightly from 857 to 650 m2/g at 800 to 1000 °C, respectively

  12. MicroRNAs of the mesothorax in Qinlingacris elaeodes, an alpine grasshopper showing a wing polymorphism with unilateral wing form.

    Science.gov (United States)

    Li, R; Jiang, G F; Ren, Q P; Wang, Y T; Zhou, X M; Zhou, C F; Qin, D Z

    2016-04-01

    MicroRNAs (miRNAs) are now recognized as key post-transcriptional regulators in regulation of phenotypic diversity. Qinlingacris elaeodes is a species of the alpine grasshopper, which is endemic to China. Adult individuals have three wing forms: wingless, unilateral-winged and short-winged. This is an ideal species to investigate the phenotypic plasticity, development and evolution of insect wings because of its case of unilateral wing form in both the sexes. We sequenced a small RNA library prepared from mesothoraxes of the adult grasshoppers using the Illumina deep sequencing technology. Approximately 12,792,458 raw reads were generated, of which the 854,580 high-quality reads were used only for miRNA identification. In this study, we identified 49 conserved miRNAs belonging to 41 families and 69 species-specific miRNAs. Moreover, seven miRNA*s were detected both for conserved miRNAs and species-specific miRNAs, which were supported by hairpin forming precursors based on polymerase chain reaction. This is the first description of miRNAs in alpine grasshoppers. The results provide a useful resource for further studies on molecular regulation and evolution of miRNAs in grasshoppers. These findings not only enrich the miRNAs for insects but also lay the groundwork for the study of post-transcriptional regulation of wing forms.

  13. MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    Directory of Open Access Journals (Sweden)

    Huynen Martijn A

    2011-06-01

    Full Text Available Abstract Background MicroRNAs (miRNAs play a fundamental role in the regulation of gene expression by translational repression or target mRNA degradation. Regulatory elements in miRNA promoters are less well studied, but may reveal a link between their expression and a specific cell type. Results To explore this link in myeloid cells, miRNA expression profiles were generated from monocytes and dendritic cells (DCs. Differences in miRNA expression among monocytes, DCs and their stimulated progeny were observed. Furthermore, putative promoter regions of miRNAs that are significantly up-regulated in DCs were screened for Transcription Factor Binding Sites (TFBSs based on TFBS motif matching score, the degree to which those TFBSs are over-represented in the promoters of the up-regulated miRNAs, and the extent of conservation of the TFBSs in mammals. Conclusions Analysis of evolutionarily conserved TFBSs in DC promoters revealed preferential clustering of sites within 500 bp upstream of the precursor miRNAs and that many mRNAs of cognate TFs of the conserved TFBSs were indeed expressed in the DCs. Taken together, our data provide evidence that selected miRNAs expressed in DCs have evolutionarily conserved TFBSs relevant to DC biology in their promoters.

  14. MicroRNA profiling of antler stem cells in potentiated and dormant states and their potential roles in antler regeneration.

    Science.gov (United States)

    Ba, Hengxing; Wang, Datao; Li, Chunyi

    2016-04-01

    MicroRNAs (miRNAs) can effectively regulate gene expression at the post-transcriptional level and play a critical role in tissue growth, development and regeneration. Our previous studies showed that antler regeneration is a stem cell-based process and antler stem cells reside in the periosteum of a pedicle, the permanent bony protuberance, from which antler regeneration takes place. Antlers are the only mammalian organ that can fully regenerate and hence provide a unique opportunity to identify miRNAs that are involved in organ regeneration. In the present study, we used next generation sequencing technology sequenced miRNAs of the stem cells derived from either the potentiated or the dormant pedicle periosteum. A population of both conserved and 20 deer-specific miRNAs was identified. These conserved miRNAs were derived from 453 homologous hairpin precursors across 88 animal species, and were further grouped into 167 miRNA families. Among them, the miR-296 is embryonic stem cell-specific. The potentiation process resulted in the significant regulation (>±2 Fold, q value cell potentiation process. This research has identified miRNAs that are associated either with the dormant or the potentiated antler stem cells and identified some target miRNAs for further research into their role played in mammalian organ regeneration.

  15. Electrical properties of GaN-based metal-insulator-semiconductor structures with Al2O3 deposited by atomic layer deposition using water and ozone as the oxygen precursors

    Science.gov (United States)

    Kubo, Toshiharu; Freedsman, Joseph J.; Iwata, Yasuhiro; Egawa, Takashi

    2014-04-01

    Al2O3 deposited by atomic layer deposition (ALD) was used as an insulator in metal-insulator-semiconductor (MIS) structures for GaN-based MIS-devices. As the oxygen precursors for the ALD process, water (H2O), ozone (O3), and both H2O and O3 were used. The chemical characteristics of the ALD-Al2O3 surfaces were investigated by x-ray photoelectron spectroscopy. After fabrication of MIS-diodes and MIS-high-electron-mobility transistors (MIS-HEMTs) with the ALD-Al2O3, their electrical properties were evaluated by current-voltage (I-V) and capacitance-voltage (C-V) measurements. The threshold voltage of the C-V curves for MIS-diodes indicated that the fixed charge in the Al2O3 layer is decreased when using both H2O and O3 as the oxygen precursors. Furthermore, MIS-HEMTs with the H2O + O3-based Al2O3 showed good dc I-V characteristics without post-deposition annealing of the ALD-Al2O3, and the drain leakage current in the off-state region was suppressed by seven orders of magnitude.

  16. MicroRNAs: role and therapeutic targets in viral hepatitis

    NARCIS (Netherlands)

    van der Ree, Meike H.; de Bruijne, Joep; Kootstra, Neeltje A.; Jansen, Peter Lm; Reesink, Hendrik W.

    2014-01-01

    MicroRNAs regulate gene expression by binding to the 3'-untranslated region (UTR) of target messenger RNAs (mRNAs). The importance of microRNAs has been shown for several liver diseases, for example, viral hepatitis. MicroRNA-122 is highly abundant in the liver and is involved in the regulation of

  17. The Drosophila nerfin-1 mRNA requires multiple microRNAs to regulate its spatial and temporal translation dynamics in the developing nervous system.

    Science.gov (United States)

    Kuzin, Alexander; Kundu, Mukta; Brody, Thomas; Odenwald, Ward F

    2007-10-01

    The mRNA encoding the Drosophila Zn-finger transcription factor Nerfin-1, required for CNS axon pathfinding events, is subject to post-transcriptional silencing. Although nerfin-1 mRNA is expressed in many neural precursor cells including all early delaminating CNS neuroblasts, the encoded Nerfin-1 protein is detected only in the nuclei of neural precursors that divide just once to generate neurons and then only transiently in nascent neurons. Using a nerfin-1 promoter-controlled reporter transgene, replacement of the nerfin-1 3' UTR with the viral SV-40 3' UTR releases the neuroblast translational block and prolongs reporter protein expression in neurons. Comparative genomics analysis reveals that the nerfin-1 mRNA 3' UTR contains multiple highly conserved sequence blocks that either harbor and/or overlap 21 predicted binding sites for 18 different microRNAs. To determine the functional significance of these microRNA-binding sites and less conserved microRNA target sites, we have studied their ability to block or limit the expression of reporter protein in nerfin-1-expressing cells during embryonic development. Our results indicate that no single microRNA is sufficient to fully inhibit protein expression but rather multiple microRNAs that target different binding sites are required to block ectopic protein expression in neural precursor cells and temporally restrict expression in neurons. Taken together, these results suggest that multiple microRNAs play a cooperative role in the post-transcriptional regulation of nerfin-1 mRNA, and the high degree of microRNA-binding site evolutionary conservation indicates that all members of the Drosophila genus employ a similar strategy to regulate the onset and extinction dynamics of Nerfin-1 expression.

  18. In Situ Detection of MicroRNA Expression with RNAscope Probes.

    Science.gov (United States)

    Yin, Viravuth P

    2018-01-01

    Elucidating the spatial resolution of gene transcripts provides important insight into potential gene function. MicroRNAs are short, singled-stranded noncoding RNAs that control gene expression through base-pair complementarity with target mRNAs in the 3' untranslated region (UTR) and inhibiting protein expression. However, given their small size of ~22- to 24-nt and low expression levels, standard in situ hybridization detection methods are not amendable for microRNA spatial resolution. Here, I describe a technique that employs RNAscope probe design and propriety amplification technology that provides simultaneous single molecule detection of individual microRNA and its target gene. This method allows for rapid and sensitive detection of noncoding RNA transcripts in frozen tissue sections.

  19. Precursor Mediated Synthesis of Nanostructured Silicas: From Precursor-Surfactant Ion Pairs to Structured Materials.

    Science.gov (United States)

    Hesemann, Peter; Nguyen, Thy Phung; Hankari, Samir El

    2014-04-11

    The synthesis of nanostructured anionic-surfactant-templated mesoporous silica (AMS) recently appeared as a new strategy for the formation of nanostructured silica based materials. This method is based on the use of anionic surfactants together with a co-structure-directing agent (CSDA), mostly a silylated ammonium precursor. The presence of this CSDA is necessary in order to create ionic interactions between template and silica forming phases and to ensure sufficient affinity between the two phases. This synthetic strategy was for the first time applied in view of the synthesis of surface functionalized silica bearing ammonium groups and was then extended on the formation of materials functionalized with anionic carboxylate and bifunctional amine-carboxylate groups. In the field of silica hybrid materials, the "anionic templating" strategy has recently been applied for the synthesis of silica hybrid materials from cationic precursors. Starting from di- or oligosilylated imidazolium and ammonium precursors, only template directed hydrolysis-polycondensation reactions involving complementary anionic surfactants allowed accessing structured ionosilica hybrid materials. The mechanistic particularity of this approach resides in the formation of precursor-surfactant ion pairs in the hydrolysis-polycondensation mixture. This review gives a systematic overview over the various types of materials accessed from this cooperative ionic templating approach and highlights the high potential of this original strategy for the formation of nanostructured silica based materials which appears as a complementary strategy to conventional soft templating approaches.

  20. Precursor Mediated Synthesis of Nanostructured Silicas: From Precursor-Surfactant Ion Pairs to Structured Materials

    Directory of Open Access Journals (Sweden)

    Peter Hesemann

    2014-04-01

    Full Text Available The synthesis of nanostructured anionic-surfactant-templated mesoporous silica (AMS recently appeared as a new strategy for the formation of nanostructured silica based materials. This method is based on the use of anionic surfactants together with a co-structure-directing agent (CSDA, mostly a silylated ammonium precursor. The presence of this CSDA is necessary in order to create ionic interactions between template and silica forming phases and to ensure sufficient affinity between the two phases. This synthetic strategy was for the first time applied in view of the synthesis of surface functionalized silica bearing ammonium groups and was then extended on the formation of materials functionalized with anionic carboxylate and bifunctional amine-carboxylate groups. In the field of silica hybrid materials, the “anionic templating” strategy has recently been applied for the synthesis of silica hybrid materials from cationic precursors. Starting from di- or oligosilylated imidazolium and ammonium precursors, only template directed hydrolysis-polycondensation reactions involving complementary anionic surfactants allowed accessing structured ionosilica hybrid materials. The mechanistic particularity of this approach resides in the formation of precursor-surfactant ion pairs in the hydrolysis-polycondensation mixture. This review gives a systematic overview over the various types of materials accessed from this cooperative ionic templating approach and highlights the high potential of this original strategy for the formation of nanostructured silica based materials which appears as a complementary strategy to conventional soft templating approaches.

  1. Identification and characteristics of microRNAs from Bombyx mori

    Directory of Open Access Journals (Sweden)

    Gao Xiaolian

    2008-05-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small RNA molecules that regulate gene expression by targeting messenger RNAs (mRNAs and causing mRNA cleavage or translation blockage. Of the 355 Arthropod miRNAs that have been identified, only 21 are B. mori miRNAs that were predicted computationally; of these, only let-7 has been confirmed by Northern blotting. Results Combining a computational method based on sequence homology searches with experimental identification based on microarray assays and Northern blotting, we identified 46 miRNAs, an additional 21 plausible miRNAs, and a novel small RNA in B. mori. The latter, bmo-miR-100-like, was identified using the known miRNA aga-miR-100 as a probe; bmo-miR-100-like was detected by microarray assay and Northern blotting, but its precursor sequences did not fold into a hairpin structure. Among these identified miRNAs, we found 12 pairs of miRNAs and miRNA*s. Northern blotting revealed that some B. mori miRNA genes were expressed only during specific stages, indicating that B. mori miRNA genes (e.g., bmo-miR-277 have developmentally regulated patterns of expression. We identified two miRNA gene clusters in the B. mori genome. bmo-miR-2b, which is found in the gene cluster bmo-miR-2a-1/bmo-miR-2a-1*/bmo-miR-2a-2/bmo-miR-2b/bmo-miR-13a*/bmo-miR-13b, encodes a newly identified member of the mir-2 family. Moreover, we found that methylation can increase the sensitivity of a DNA probe used to detect a miRNA by Northern blotting. Functional analysis revealed that 11 miRNAs may regulate 13 B. mori orthologs of the 25 known Drosophila miRNA-targeted genes according to the functional conservation. We predicted the binding sites on the 1671 3'UTR of B. mori genes; 547 targeted genes, including 986 target sites, were predicted. Of these target sites, 338 had perfect base pairing to the seed region of 43 miRNAs. From the predicted genes, 61 genes, each of them with multiple predicted target sites, should be

  2. Mechanical performance and thermal stability of glass fiber reinforced silica aerogel composites based on co-precursor method by freeze drying

    Science.gov (United States)

    Zhou, Ting; Cheng, Xudong; Pan, Yuelei; Li, Congcong; Gong, Lunlun; Zhang, Heping

    2018-04-01

    In order to maintain the integrity, glass fiber (GF) reinforced silica aerogel composites were synthesized using methltrimethoxysilane (MTMS) and water glass co-precursor by freeze drying method. The composites were characterized by scanning electron microscopy, Brunauer-Emmett-Teller analysis, uniaxial compressive test, three-point bending test, thermal conductivity analysis, contact angle test, TG-DSC analysis. It was found that the molar ratio of MTMS/water glass could significantly affect the properties of composites. The bulk density and thermal conductivity first decreased and then increased with the increasing molar ratio. The composites showed remarkable mechanical strength and flexibility compared with pure silica aerogel. Moreover, when the molar ratio is 1.8, the composites showed high specific surface area (870.9 m2/g), high contact angle (150°), great thermal stability (560 °C) and low thermal conductivity (0.0248 W/m·K). These outstanding properties indicate that GF/aerogels have broad prospects in the field of thermal insulation.

  3. Spirobisindane-based polyimide as efficient precursor of thermally-rearranged and carbon molecular sieve membranes for enhanced propylene/propane separation

    KAUST Repository

    Swaidan, Ramy Jawdat

    2016-09-02

    High performance thermally-rearranged (TR) and carbon molecular sieve (CMS) membranes made from an intrinsically microporous polymer precursor PIM-6FDA-OH are reported for the separation of propylene from propane. Thermal rearrangement of PIM-6FDA-OH to the corresponding polybenzoxazole (PBO) membrane resulted in a pure-gas C3H6/C3H8 selectivity of 15 and C3H6 permeability of 14 Barrer, positioning it above the polymeric C3H6/C3H8 upper bound. For the first time, the C3H6/C3H8 mixed-gas properties of a TR polymer were investigated and showed a C3H6 permeability of 11 Barrer and C3H6/ C3H8 selectivity of 11, essentially independent of feed pressure up to 5 bar. The CMS membrane made by treatment at 600 C showed further improvement in performance as demonstrated with a pure-gas C3H8/C3H8 selectivity of 33 and a C3H6 permeability of 45 Barrer. The mixed-gas C3H6/C3H8 selectivity dropped from 24 to 17 from 2 to 5 bar feed pressure due to a decrease in C3H6 permeability most likely caused by competitive sorption without any evidence of plasticization. (C) 2016 Elsevier B.V. All rights reserved.

  4. Nonlinear magnetohydrodynamics of edge localized mode precursors

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Z. B., E-mail: guozhipku@gmail.com [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing (China); WCI Center for Fusion Theory, NFRI, Gwahangno 113, Yusung-gu, Daejeon 305-333 (Korea, Republic of); Wang, Lu [SEEE, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Wang, X. G. [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing (China)

    2015-02-15

    A possible origin of edge-localized-mode (ELM) precursors based on nonlinear ideal peeling-ballooning mode is reported. Via nonlinear variational principle, a nonlinear evolution equation of the radial displacement is derived and solved, analytically. Besides an explosive growth in the initial nonlinear phase, it is found that the local displacement evolves into an oscillating state in the developed nonlinear phase. The nonlinear frequency of the ELM precursors scales as ω{sub pre}∼x{sup 1/3}ξ{sup ^}{sub ψ,in}{sup 2/3}n, with x position in radial direction, ξ{sup ^}{sub ψ,in} strength of initial perturbation, and n toroidal mode number.

  5. Role of microRNAs in sepsis.

    Science.gov (United States)

    Kingsley, S Manoj Kumar; Bhat, B Vishnu

    2017-07-01

    MicroRNAs have been found to be of high significance in the regulation of various genes and processes in the body. Sepsis is a serious clinical problem which arises due to the excessive host inflammatory response to infection. The non-specific clinical features and delayed diagnosis of sepsis has been a matter of concern for long time. MicroRNAs could enable better diagnosis of sepsis and help in the identification of the various stages of sepsis. Improved diagnosis may enable quicker and more effective treatment measures. The initial acute and transient phase of sepsis involves excessive secretion of pro-inflammatory cytokines which causes severe damage. MicroRNAs negatively regulate the toll-like receptor signaling pathway and regulate the production of inflammatory cytokines during sepsis. Likewise, microRNAs have shown to regulate the vascular barrier and endothelial function in sepsis. They are also involved in the regulation of the apoptosis, immunosuppression, and organ dysfunction in later stages of sepsis. Their importance at various levels of the pathophysiology of sepsis has been discussed along with the challenges and future perspectives. MicroRNAs could be key players in the diagnosis and staging of sepsis. Their regulation at various stages of sepsis suggests that they may have an important role in altering the outcome associated with sepsis.

  6. A Cancer-Indicative microRNA Pattern in Normal Prostate Tissue

    Directory of Open Access Journals (Sweden)

    Thorsten Schlomm

    2013-03-01

    Full Text Available We analyzed the levels of selected micro-RNAs in normal prostate tissue to assess their potential to indicate tumor foci elsewhere in the prostate. Histologically normal prostate tissue samples from 31 prostate cancer patients and two cancer negative control groups with either unsuspicious or elevated prostate specific antigen (PSA levels (14 and 17 individuals, respectively were analyzed. Based on the expression analysis of 157 microRNAs in a pool of prostate tissue samples and information from data bases/literature, we selected eight microRNAs for quantification by real-time polymerase chain reactions (RT-PCRs. Selected miRNAs were analyzed in histologically tumor-free biopsy samples from patients and healthy controls. We identified seven microRNAs (miR-124a, miR-146a & b, miR-185, miR-16 and let-7a & b, which displayed significant differential expression in normal prostate tissue from men with prostate cancer compared to both cancer negative control groups. Four microRNAs (miR-185, miR-16 and let-7a and let-7b remained to significantly discriminate normal tissues from prostate cancer patients from those of the cancer negative control group with elevated PSA levels. The transcript levels of these microRNAs were highly indicative for the presence of cancer in the prostates, independently of the PSA level. Our results suggest a microRNA-pattern in histologically normal prostate tissue, indicating prostate cancer elsewhere in the organ.

  7. Regulation of immune responses and tolerance: the microRNA perspective.

    Science.gov (United States)

    Chen, Chang-Zheng; Schaffert, Steven; Fragoso, Rita; Loh, Christina

    2013-05-01

    Much has been learned about the molecular and cellular components critical for the control of immune responses and tolerance. It remains a challenge, however, to control the immune response and tolerance at the system level without causing significant toxicity to normal tissues. Recent studies suggest that microRNA (miRNA) genes, an abundant class of non-coding RNA genes that produce characteristic approximately 22 nucleotides small RNAs, play important roles in immune cells. In this article, we discuss emerging knowledge regarding the functions of miRNA genes in the immune system. We delve into the roles of miRNAs in regulating signaling strength and threshold, homeostasis, and the dynamics of the immune response and tolerance during normal and pathogenic immunological conditions. We also present observations based on analyzes of miR-181 family genes that indicate the potential functions of primary and/or precursor miRNAs in target recognition and explore the impact of these findings on target identification. Finally, we illustrate that despite the subtle effects of miRNAs on gene expression, miRNAs have the potential to influence the outcomes of normal and pathogenic immune responses by controlling the quantitative and dynamic aspects of immune responses. Tuning miRNA functions in immune cells, through gain- and loss-of-function approaches in mice, may reveal novel approach to restore immune equilibrium from pathogenic conditions, such as autoimmune disease and leukemia, without significant toxicity. © 2013 John Wiley & Sons A/S. Published by Blackwell Publishing Ltd.

  8. A genome-wide characterization of microRNA genes in maize.

    Directory of Open Access Journals (Sweden)

    Lifang Zhang

    2009-11-01

    Full Text Available MicroRNAs (miRNAs are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.

  9. Use of different Zn precursors for the deposition of Zn(S,O) buffer layers by chemical bath for chalcopyrite based Cd-free thin-film solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Saez-Araoz, R.; Lux-Steiner, M.C. [Hahn Meitner Institut, Berlin (Germany); Freie Universitaet Berlin, Berlin (Germany); Ennaoui, A.; Kropp, T.; Veryaeva, E. [Hahn Meitner Institut, Berlin (Germany); Niesen, T.P. [AVANCIS GmbH and Co. KG, Munich (Germany)

    2008-10-15

    Progress in fabricating Cu(In,Ga)(S,Se){sub 2} (CIGSSe) solar cells with Zn(S,O) buffer layers prepared by chemical bath deposition (CBD) is discussed. The effect of different Zn salt precursors on solar cell device performance is investigated using production scale CIGSSe absorbers provided by AVANCIS GmbH and Co. KG. The CBD process has been developed at the Hahn-Meitner-Institut (HMI) using zinc nitrate, zinc sulphate or zinc chloride as zinc precursor. An average efficiency of 14.2{+-}0.8% is obtained by using one-layer CBD Zn(S,O) The dominant recombination path for well performing solar cells is discussed based on the results obtained from temperature dependent J(V) analysis. The structure and morphology of buffer layers deposited using zinc nitrate and zinc sulphate has been studied by means of transmission electron micrographs of glass/Mo/CIGSSe/Zn(S,O) structures. Results show a conformal coverage of the absorber by a Zn(S,O) layer of 15-25 nm consisting of nanocrystals with radii of {proportional_to}5 nm. XAES analysis of the buffer layer reveals a similar surface composition for buffer layers deposited with zinc nitrate and zinc sulphate. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  10. Solvothermal Synthesis of Three-Dimensional Hierarchical CuS Microspheres from a Cu-Based Ionic Liquid Precursor for High-Performance Asymmetric Supercapacitors.

    Science.gov (United States)

    Zhang, Jing; Feng, Huijie; Yang, Jiaqin; Qin, Qing; Fan, Hongmin; Wei, Caiying; Zheng, Wenjun

    2015-10-07

    It is meaningful to exploit copper sulfide materials with desired structure as well as potential application due to their cheapness and low toxicity. A low-temperature and facile solvothermal method for preparing three-dimensional (3D) hierarchical covellite (CuS) microspheres from an ionic liquid precursor [Bmim]2Cu2Cl6 (Bmim = 1-butyl-3-methylimidazolium) is reported. The formation of CuS nanostructures was achieved by decomposition of intermediate complex Cu(Tu)3Cl (thiourea = Tu), which produced CuS microspheres with diameters of 2.5-4 μm assembled by nanosheets with thicknesses of 10-15 nm. The ionic liquid, as an "all-in-one" medium, played a key role for the fabrication and self-assembly of CuS nanosheets. The alkylimidazolium rings ([Bmim](+)) were found to adsorb onto the (001) facets of CuS crystals, which inhibited the crystal growth along the [001] direction, while the alkyl chain had influence on the assembly of CuS nanosheets. The CuS microspheres showed enhanced electrochemical performance and high stability for the application in supercapacitors due to intriguing structural design and large specific surface area. When this well-defined CuS electrode was assembled into an asymmetric supercapacitor (ASC) with an activated carbon (AC) electrode, the CuS//AC-ASC demonstrated good cycle performance (∼88% capacitance after 4000 cycles) and high energy density (15.06 W h kg(-1) at a power density of 392.9 W kg(-1)). This work provides new insights into the use of copper sulfide electrode materials for asymmetric supercapacitors and other electrochemical devices.

  11. MicroRNAs, epigenetics and disease

    DEFF Research Database (Denmark)

    Silahtaroglu, Asli; Stenvang, Jan

    2010-01-01

    Epigenetics is defined as the heritable chances that affect gene expression without changing the DNA sequence. Epigenetic regulation of gene expression can be through different mechanisms such as DNA methylation, histone modifications and nucleosome positioning. MicroRNAs are short RNA molecules...... which do not code for a protein but have a role in post-transcriptional silencing of multiple target genes by binding to their 3' UTRs (untranslated regions). Both epigenetic mechanisms, such as DNA methylation and histone modifications, and the microRNAs are crucial for normal differentiation...... diseases. In the present chapter we will mainly focus on microRNAs and methylation and their implications in human disease, mainly in cancer....

  12. ELFN1-AS1: A Novel Primate Gene with Possible MicroRNA Function Expressed Predominantly in Human Tumors

    Directory of Open Access Journals (Sweden)

    Dmitrii E. Polev

    2014-01-01

    Full Text Available Human gene LOC100505644 uncharacterized LOC100505644 [Homo sapiens] (Entrez Gene ID 100505644 is abundantly expressed in tumors but weakly expressed in few normal tissues. Till now the function of this gene remains unknown. Here we identified the chromosomal borders of the transcribed region and the major splice form of the LOC100505644-specific transcript. We characterised the major regulatory motifs of the gene and its splice sites. Analysis of the secondary structure of the major transcript variant revealed a hairpin-like structure characteristic for precursor microRNAs. Comparative genomic analysis of the locus showed that it originated in primates de novo. Taken together, our data indicate that human gene LOC100505644 encodes some non-protein coding RNA, likely a microRNA. It was assigned a gene symbol ELFN1-AS1 (ELFN1 antisense RNA 1 (non-protein coding. This gene combines features of evolutionary novelty and predominant expression in tumors.

  13. Identification of microRNAs in the coral Stylophora pistillata.

    KAUST Repository

    Liew, Yi Jin

    2014-03-21

    Coral reefs are major contributors to marine biodiversity. However, they are in rapid decline due to global environmental changes such as rising sea surface temperatures, ocean acidification, and pollution. Genomic and transcriptomic analyses have broadened our understanding of coral biology, but a study of the microRNA (miRNA) repertoire of corals is missing. miRNAs constitute a class of small non-coding RNAs of ∼22 nt in size that play crucial roles in development, metabolism, and stress response in plants and animals alike. In this study, we examined the coral Stylophora pistillata for the presence of miRNAs and the corresponding core protein machinery required for their processing and function. Based on small RNA sequencing, we present evidence for 31 bona fide microRNAs, 5 of which (miR-100, miR-2022, miR-2023, miR-2030, and miR-2036) are conserved in other metazoans. Homologues of Argonaute, Piwi, Dicer, Drosha, Pasha, and HEN1 were identified in the transcriptome of S. pistillata based on strong sequence conservation with known RNAi proteins, with additional support derived from phylogenetic trees. Examination of putative miRNA gene targets indicates potential roles in development, metabolism, immunity, and biomineralisation for several of the microRNAs. Here, we present first evidence of a functional RNAi machinery and five conserved miRNAs in S. pistillata, implying that miRNAs play a role in organismal biology of scleractinian corals. Analysis of predicted miRNA target genes in S. pistillata suggests potential roles of miRNAs in symbiosis and coral calcification. Given the importance of miRNAs in regulating gene expression in other metazoans, further expression analyses of small non-coding RNAs in transcriptional studies of corals should be informative about miRNA-affected processes and pathways.

  14. Ionospheric precursors for crustal earthquakes in Italy

    Directory of Open Access Journals (Sweden)

    L. Perrone

    2010-04-01

    Full Text Available Crustal earthquakes with magnitude 6.0>M≥5.5 observed in Italy for the period 1979–2009 including the last one at L'Aquila on 6 April 2009 were considered to check if the earlier obtained relationships for ionospheric precursors for strong Japanese earthquakes are valid for the Italian moderate earthquakes. The ionospheric precursors are based on the observed variations of the sporadic E-layer parameters (h'Es, fbEs and foF2 at the ionospheric station Rome. Empirical dependencies for the seismo-ionospheric disturbances relating the earthquake magnitude and the epicenter distance are obtained and they have been shown to be similar to those obtained earlier for Japanese earthquakes. The dependences indicate the process of spreading the disturbance from the epicenter towards periphery during the earthquake preparation process. Large lead times for the precursor occurrence (up to 34 days for M=5.8–5.9 tells about a prolong preparation period. A possibility of using the obtained relationships for the earthquakes prediction is discussed.

  15. Cellular Kinetics of Perivascular MSC Precursors

    Directory of Open Access Journals (Sweden)

    William C. W. Chen

    2013-01-01

    Full Text Available Mesenchymal stem/stromal cells (MSCs and MSC-like multipotent stem/progenitor cells have been widely investigated for regenerative medicine and deemed promising in clinical applications. In order to further improve MSC-based stem cell therapeutics, it is important to understand the cellular kinetics and functional roles of MSCs in the dynamic regenerative processes. However, due to the heterogeneous nature of typical MSC cultures, their native identity and anatomical localization in the body have remained unclear, making it difficult to decipher the existence of distinct cell subsets within the MSC entity. Recent studies have shown that several blood-vessel-derived precursor cell populations, purified by flow cytometry from multiple human organs, give rise to bona fide MSCs, suggesting that the vasculature serves as a systemic reservoir of MSC-like stem/progenitor cells. Using individually purified MSC-like precursor cell subsets, we and other researchers have been able to investigate the differential phenotypes and regenerative capacities of these contributing cellular constituents in the MSC pool. In this review, we will discuss the identification and characterization of perivascular MSC precursors, including pericytes and adventitial cells, and focus on their cellular kinetics: cell adhesion, migration, engraftment, homing, and intercellular cross-talk during tissue repair and regeneration.

  16. Signatures of RNA binding proteins globally coupled to effective microRNA target sites

    DEFF Research Database (Denmark)

    Jacobsen, Anders; Wen, Jiayu; Marks, Debora S

    2010-01-01

    MicroRNAs (miRNAs) and small interfering RNAs (siRNAs), bound to Argonaute proteins (RISC), destabilize mRNAs through base-pairing with the mRNA. However, the gene expression changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting...

  17. Optomagnetic Detection of MicroRNA Based on Duplex-Specific Nuclease-Assisted Target Recycling and Multilayer Core-Satellite Magnetic Superstructures

    DEFF Research Database (Denmark)

    Tian, Bo; Ma, Jing; Qiu, Zhen

    2017-01-01

    -efficiency, and potential for bioresponsive multiplexing. Herein, we demonstrate a sensitive and rapid miRNA detection method based on optomagnetic read-out, duplex-specific nuclease (DSN)-assisted target recycling, and the use of multilayer core-satellite magnetic superstructures. Triggered by the presence of target mi...

  18. Variation within 3' UTRs of base excision repair genes and response to therapy in colorectal cancer patients: a potential modulation of microRNAs binding.

    Czech Academy of Sciences Publication Activity Database

    Pardini, B.; Rosa, F.; Barone, E.; Di Gaetano, C.; Slyšková, Jana; Novotný, J.; Levý, M.; Garritano, S.; Vodičková, Ludmila; Buchler, T.; Gemignani, F.; Landi, S.; Vodička, Pavel; Naccarati, Alessio

    2013-01-01

    Roč. 19, č. 21 (2013), s. 6044-6056 ISSN 1078-0432 R&D Projects: GA ČR GAP304/10/1286; GA ČR(CZ) GAP304/12/1585 Institutional support: RVO:68378041 Keywords : colorectal cancer * base excision repair * survival Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.193, year: 2013

  19. microRNAs in mycobacterial disease: friend or foe?

    Directory of Open Access Journals (Sweden)

    Manali D Mehta

    2014-07-01

    Full Text Available As the role of microRNA in all aspects of biology continues to be unraveled, the interplay between microRNAs and human disease is becoming clearer. It should come of no surprise that microRNAs play a major part in the outcome of infectious diseases, since early work has implicated microRNAs as regulators of the immune response. Here, we provide a review on how microRNAs influence the course of mycobacterial infections, which cause two of humanity’s most ancient infectious diseases: tuberculosis and leprosy. Evidence derived from profiling and functional experiments suggests that regulation of specific microRNAs during infection can either enhance the immune response or facilitate pathogen immune evasion. Now, it remains to be seen if the manipulation of host cell microRNA profiles can be an opportunity for therapeutic intervention for these difficult-to-treat diseases.

  20. Trending analysis of precursor events

    International Nuclear Information System (INIS)

    Watanabe, Norio

    1998-01-01

    The Accident Sequence Precursor (ASP) Program of United States Nuclear Regulatory Commission (U.S.NRC) identifies and categorizes operational events at nuclear power plants in terms of the potential for core damage. The ASP analysis has been performed on yearly basis and the results have been published in the annual reports. This paper describes the trends in initiating events and dominant sequences for 459 precursors identified in the ASP Program during the 1969-94 period and also discusses a comparison with dominant sequences predicted in the past Probabilistic Risk Assessment (PRA) studies. These trends were examined for three time periods, 1969-81, 1984-87 and 1988-94. Although the different models had been used in the ASP analyses for these three periods, the distribution of precursors by dominant sequences show similar trends to each other. For example, the sequences involving loss of both main and auxiliary feedwater were identified in many PWR events and those involving loss of both high and low coolant injection were found in many BWR events. Also, it was found that these dominant sequences were comparable to those determined to be dominant in the predictions by the past PRAs. As well, a list of the 459 precursors identified are provided in Appendix, indicating initiating event types, unavailable systems, dominant sequences, conditional core damage probabilities, and so on. (author)

  1. Synthesis of labelled ecdysone precursors

    International Nuclear Information System (INIS)

    Haag, T.; Hetru, C.; Nakatani, Y.; Luu, B.; Meister, M.; Pichat, L.; Audinot, M.

    1985-01-01

    High specific activity tritiated 3β,14α-dihydroxy-5β-cholest-7-en-6-one, has been prepared using a precursor which permits rapid and easy labelling. This compound is converted to ecdysone under in vitro conditions by insect prothoracic glands, a well known site of ecdysone biosynthesis. (author)

  2. MicroRNA Functions in Osteogenesis and Dysfunctions in Osteoporosis

    Science.gov (United States)

    van Wijnen, Andre J.; van de Peppel, Jeroen; van Leeuwen, Johannes P.; Lian, Jane B.; Stein, Gary S.; Westendorf, Jennifer J.; Oursler, Merry-Jo; Sampen, Hee-Jeong Im; Taipaleenmaki, Hanna; Hesse, Eric; Riester, Scott; Kakar, Sanjeev

    2013-01-01

    MicroRNAs (miRNAs) are critical post-transcriptional regulators of gene expression that control osteoblast mediated bone formation and osteoclast-related bone remodelling. Deregulation of miRNA mediated mechanisms is emerging as an important pathological factor in bone degeneration (e.g., osteoporosis) and other bone-related diseases. MiRNAs are intriguing regulatory molecules that are networked with cell signaling pathways and intricate transcriptional programs through ingenuous circuits with remarkably simple logic. This overview examines key principles by which miRNAs control differentiation of osteoblasts as they evolve from mesenchymal stromal cells during osteogenesis, or of osteoclasts as they originate from monocytic precursors in the hematopoietic lineage during osteoclastogenesis. Of particular note are miRNAs that are temporally up-regulated during osteoblastogenesis (e.g., miR-218) or osteoclastogenesis (e.g., miR-148a). Each miRNA stimulates differentiation by suppressing inhibitory signalling pathways (‘double-negative’ regulation). The excitement surrounding miRNAs in bone biology stems from the prominent effects that individual miRNAs can have on biological transitions during differentiation of skeletal cells and correlations of miRNA dysfunction with bone diseases. MiRNAs have significant clinical potential which is reflected by their versatility as disease-specific biomarkers and their promise as therapeutic agents to ameliorate or reverse bone tissue degeneration. PMID:23605904

  3. Development of potential selective and reversible pyrazoline based MAO-B inhibitors as MAO-B PET tracer precursors and reference substances for the early detection of Alzheimer's disease.

    Science.gov (United States)

    Neudorfer, Catharina; Shanab, Karem; Jurik, Andreas; Schreiber, Veronika; Neudorfer, Carolina; Vraka, Chrysoula; Schirmer, Eva; Holzer, Wolfgang; Ecker, Gerhard; Mitterhauser, Markus; Wadsak, Wolfgang; Spreitzer, Helmut

    2014-09-15

    Since high MAO-B levels are present in early stages of AD, the MAO-B system can be designated as an appropriate and prospective tracer target of molecular imaging biomarkers for the detection of early AD. According to the preceding investigations of Mishra et al. the aim of this work was the development of a compound library of selective and reversible MAO-B inhibitors by performing bioisosteric modifications of the core structure of 3-(anthracen-9-yl)-5-phenyl-4,5-dihydro-1H-pyrazoles. In conclusion, 13 new pyrazoline based derivatives have been prepared, which will serve as precursor substances for future radiolabeling as well as reference compounds for the investigation of increased MAO-B levels in AD. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. C. elegans microRNAs.

    Science.gov (United States)

    Vella, Monica C; Slack, Frank J

    2005-09-21

    MicroRNAs (miRNAs) are small, non-coding regulatory RNAs found in many phyla that control such diverse events as development, metabolism, cell fate and cell death. They have also been implicated in human cancers. The C. elegans genome encodes hundreds of miRNAs, including the founding members of the miRNA family lin-4 and let-7. Despite the abundance of C. elegans miRNAs, few miRNA targets are known and little is known about the mechanism by which they function. However, C. elegans research continues to push the boundaries of discovery in this area. lin-4 and let-7 are the best understood miRNAs. They control the timing of adult cell fate determination in hypodermal cells by binding to partially complementary sites in the mRNA of key developmental regulators to repress protein expression. For example, lin-4 is predicted to bind to seven sites in the lin-14 3' untranslated region (UTR) to repress LIN-14, while let-7 is predicted to bind two let-7 complementary sites in the lin-41 3' UTR to down-regulate LIN-41. Two other miRNAs, lsy-6 and mir-273, control left-right asymmetry in neural development, and also target key developmental regulators for repression. Approximately one third of the C. elegans miRNAs are differentially expressed during development indicating a major role for miRNAs in C. elegans development. Given the remarkable conservation of developmental mechanism across phylogeny, many of the principles of miRNAs discovered in C. elegans are likely to be applicable to higher animals.

  5. Frontotemporal Lobar Degeneration and microRNAs

    Directory of Open Access Journals (Sweden)

    Paola ePiscopo

    2016-02-01

    Full Text Available Frontotemporal lobar degeneration (FTLD includes a spectrum of disorders characterized by changes of personality and social behaviour and, often, a gradual and progressive language dysfunction. In the last years, several efforts have been fulfilled in identifying both genetic mutations and pathological proteins associated with FTLD. The molecular bases undergoing the onset and progression of the disease remain still unknown. Recent literature prompts an involvement of RNA metabolism in FTLD, particularly miRNAs. Dysregulation of miRNAs in several disorders, including neurodegenerative diseases, and increasing importance of circulating miRNAs in different pathologies has suggested to implement the study of their possible application as biological markers and new therapeutic targets; moreover, miRNA-based therapy is becoming a powerful tool to deepen the function of a gene, the mechanism of a disease, and validate therapeutic targets. Regarding FTLD, different studies showed that miRNAs are playing an important role. For example, several reports have evaluated miRNA regulation of the progranulin gene suggesting that it is under their control, as described for miR-29b, miR-107 and miR-659. More recently, it has been demonstrated that TMEM106B gene, which protein is elevated in FTLD-TDP brains, is repressed by miR-132/212 cluster; this post-transcriptional mechanism increases intracellular levels of progranulin, affecting its pathways. These findings if confirmed could suggest that these microRNAs have a role as potential targets for some related-FTLD genes. In this review, we focus on the emerging roles of the miRNAs in the pathogenesis of FTLD.

  6. Human amniotic epithelial cell feeder layers maintain human iPS cell pluripotency via inhibited endogenous microRNA-145 and increased Sox2 expression

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Te, E-mail: liute79@yahoo.com [School of Environmental Science and Engineering, Donghua University, Shanghai 201620 (China); Shanghai Geriatric Institute of Chinese Medicine, Shanghai 200031 (China); Cheng, Weiwei [International Peace Maternity and Child Health Hospital, Shanghai Jiaotong University, Shanghai 200030 (China); Huang, Yongyi [Laboratoire PROTEE, Batiment R, Universite du Sud Toulon-Var, 83957 LA GARDE Cedex (France); Huang, Qin; Jiang, Lizhen [Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Guo, Lihe, E-mail: liute79@yahoo.com [Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China)

    2012-02-15

    Currently, human induced pluripotent stem (iPS) cells were generated from patient or disease-specific sources and share the same key properties as embryonic stem cells. This makes them attractive for personalized medicine, drug screens or cellular therapy. Long-term cultivation and maintenance of normal iPS cells in an undifferentiated self-renewing state are a major challenge. Our previous studies have shown that human amniotic epithelial cells (HuAECs) could provide a good source of feeder cells for mouse and human embryonic stem cells, or spermatogonial stem cells, but the mechanism for this is unknown. Here, we examined the effect of endogenous microRNA-145 regulation on Sox2 expression in human iPS cells by HuAECs feeder cells regulation, and in turn on human iPS cells pluripotency. We found that human IPS cells transfected with a microRNA-145 mutant expressed Sox2 at high levels, allowing iPS to maintain a high level of AP activity in long-term culture and form teratomas in SCID mice. Expression of stem cell markers was increased in iPS transfected with the microRNA-145 mutant, compared with iPS was transfected with microRNA-145. Besides, the expression of Drosha proteins of the microRNA-processor complex, required for the generation of precursor pre-miRNA, was significantly increased in human iPS cells cultured on MEF but not on HuAECs. Taken together, these results suggest that endogenous Sox2 expression may be regulated by microRNA-145 in human iPS cells with HuAECs feeder cells, and Sox2 is a crucial component required for maintenance of them in an undifferentiated, proliferative state capable of self-renewal. Highlights: Black-Right-Pointing-Pointer microRNA-145 inhibits Sox2 expression in human iPS cells. Black-Right-Pointing-Pointer microRNA-145 suppresses the self-renewal and pluripotency of human iPS cells. Black-Right-Pointing-Pointer HuAECs regulate expression of microRNA-145 and Sox2 in human iPS cells. Black-Right-Pointing-Pointer HuAECs feeder

  7. Human amniotic epithelial cell feeder layers maintain human iPS cell pluripotency via inhibited endogenous microRNA-145 and increased Sox2 expression

    International Nuclear Information System (INIS)

    Liu, Te; Cheng, Weiwei; Huang, Yongyi; Huang, Qin; Jiang, Lizhen; Guo, Lihe

    2012-01-01

    Currently, human induced pluripotent stem (iPS) cells were generated from patient or disease-specific sources and share the same key properties as embryonic stem cells. This makes them attractive for personalized medicine, drug screens or cellular therapy. Long-term cultivation and maintenance of normal iPS cells in an undifferentiated self-renewing state are a major challenge. Our previous studies have shown that human amniotic epithelial cells (HuAECs) could provide a good source of feeder cells for mouse and human embryonic stem cells, or spermatogonial stem cells, but the mechanism for this is unknown. Here, we examined the effect of endogenous microRNA-145 regulation on Sox2 expression in human iPS cells by HuAECs feeder cells regulation, and in turn on human iPS cells pluripotency. We found that human IPS cells transfected with a microRNA-145 mutant expressed Sox2 at high levels, allowing iPS to maintain a high level of AP activity in long-term culture and form teratomas in SCID mice. Expression of stem cell markers was increased in iPS transfected with the microRNA-145 mutant, compared with iPS was transfected with microRNA-145. Besides, the expression of Drosha proteins of the microRNA-processor complex, required for the generation of precursor pre-miRNA, was significantly increased in human iPS cells cultured on MEF but not on HuAECs. Taken together, these results suggest that endogenous Sox2 expression may be regulated by microRNA-145 in human iPS cells with HuAECs feeder cells, and Sox2 is a crucial component required for maintenance of them in an undifferentiated, proliferative state capable of self-renewal. Highlights: ► microRNA-145 inhibits Sox2 expression in human iPS cells. ► microRNA-145 suppresses the self-renewal and pluripotency of human iPS cells. ► HuAECs regulate expression of microRNA-145 and Sox2 in human iPS cells. ► HuAECs feeder layers maintain human iPS cells pluripotency. ► HuAECs negatively regulates the synthesis of

  8. The proliferative human monocyte subpopulation contains osteoclast precursors

    Science.gov (United States)

    Lari, Roya; Kitchener, Peter D; Hamilton, John A

    2009-01-01

    Introduction Immediate precursors of bone-resorbing osteoclasts are cells of the monocyte/macrophage lineage. Particularly during clinical conditions showing bone loss, it would appear that osteoclast precursors are mobilized from bone marrow into the circulation prior to entering tissues undergoing such loss. The observed heterogeneity of peripheral blood monocytes has led to the notion that different monocyte subpopulations may have special or restricted functions, including as osteoclast precursors. Methods Human peripheral blood monocytes were sorted based upon their degree of proliferation and cultured in macrophage colony-stimulating factor (M-CSF or CSF-1) and receptor activator of nuclear factor-kappa-B ligand (RANKL). Results The monocyte subpopulation that is capable of proliferation gave rise to significantly more multinucleated, bone-resorbing osteoclasts than the bulk of the monocytes. Conclusions Human peripheral blood osteoclast precursors reside in the proliferative monocyte subpopulation. PMID:19222861

  9. MicroRNA mimicry blocks pulmonary fibrosis

    NARCIS (Netherlands)

    Montgomery, Rusty L; Yu, Guoying; Latimer, Paul A; Stack, Christianna; Robinson, Kathryn; Dalby, Christina M; Kaminski, Naftali; van Rooij, Eva

    2014-01-01

    Over the last decade, great enthusiasm has evolved for microRNA (miRNA) therapeutics. Part of the excitement stems from the fact that a miRNA often regulates numerous related mRNAs. As such, modulation of a single miRNA allows for parallel regulation of multiple genes involved in a particular

  10. MicroRNAs in skin tissue engineering.

    Science.gov (United States)

    Miller, Kyle J; Brown, David A; Ibrahim, Mohamed M; Ramchal, Talisha D; Levinson, Howard

    2015-07-01

    35.2 million annual cases in the U.S. require clinical intervention for major skin loss. To meet this demand, the field of skin tissue engineering has grown rapidly over the past 40 years. Traditionally, skin tissue engineering relies on the "cell-scaffold-signal" approach, whereby isolated cells are formulated into a three-dimensional substrate matrix, or scaffold, and exposed to the proper molecular, physical, and/or electrical signals to encourage growth and differentiation. However, clinically available bioengineered skin equivalents (BSEs) suffer from a number of drawbacks, including time required to generate autologous BSEs, poor allogeneic BSE survival, and physical limitations such as mass transfer issues. Additionally, different types of skin wounds require different BSE designs. MicroRNA has recently emerged as a new and exciting field of RNA interference that can overcome the barriers of BSE design. MicroRNA can regulate cellular behavior, change the bioactive milieu of the skin, and be delivered to skin tissue in a number of ways. While it is still in its infancy, the use of microRNAs in skin tissue engineering offers the opportunity to both enhance and expand a field for which there is still a vast unmet clinical need. Here we give a review of skin tissue engineering, focusing on the important cellular processes, bioactive mediators, and scaffolds. We further discuss potential microRNA targets for each individual component, and we conclude with possible future applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. MicroRNAs, Regulatory Networks, and Comorbidities

    DEFF Research Database (Denmark)

    Russo, Francesco; Belling, Kirstine; Jensen, Anders Boeck

    2017-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of messenger RNAs (mRNAs). Each miRNA targets a specific set of mRNAs. Upon binding the miRNA inhibits mRNA translation or facilitate mRNA degradation. miRNAs are frequently deregulated in several pathologies...

  12. The Innate Lymphoid Cell Precursor.

    Science.gov (United States)

    Ishizuka, Isabel E; Constantinides, Michael G; Gudjonson, Herman; Bendelac, Albert

    2016-05-20

    The discovery of tissue-resident innate lymphoid cell populations effecting different forms of type 1, 2, and 3 immunity; tissue repair; and immune regulation has transformed our understanding of mucosal immunity and allergy. The emerging complexity of these populations along with compounding issues of redundancy and plasticity raise intriguing questions about their precise lineage relationship. Here we review advances in mapping the emergence of these lineages from early lymphoid precursors. We discuss the identification of a common innate lymphoid cell precursor characterized by transient expression of the transcription factor PLZF, and the lineage relationships of innate lymphoid cells with conventional natural killer cells and lymphoid tissue inducer cells. We also review the rapidly growing understanding of the network of transcription factors that direct the development of these lineages.

  13. Precursor polymer compositions comprising polybenzimidazole

    Science.gov (United States)

    Klaehn, John R.; Peterson, Eric S.; Orme, Christopher J.

    2015-07-14

    Stable, high performance polymer compositions including polybenzimidazole (PBI) and a melamine-formaldehyde polymer, such as methylated, poly(melamine-co-formaldehyde), for forming structures such as films, fibers and bulky structures. The polymer compositions may be formed by combining polybenzimidazole with the melamine-formaldehyde polymer to form a precursor. The polybenzimidazole may be reacted and/or intertwined with the melamine-formaldehyde polymer to form the polymer composition. For example, a stable, free-standing film having a thickness of, for example, between about 5 .mu.m and about 30 .mu.m may be formed from the polymer composition. Such films may be used as gas separation membranes and may be submerged into water for extended periods without crazing and cracking. The polymer composition may also be used as a coating on substrates, such as metal and ceramics, or may be used for spinning fibers. Precursors for forming such polymer compositions are also disclosed.

  14. Characterization and Profiling of Liver microRNAs by RNA-sequencing in Cattle Divergently Selected for Residual Feed Intake

    Directory of Open Access Journals (Sweden)

    Wijdan Al-Husseini

    2016-10-01

    Full Text Available MicroRNAs (miRNAs are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Liver plays an important role in the feed efficiency of animals and high and low efficient cattle demonstrated different gene expression profiles by microarray. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI and identify miRNAs related to feed efficiency in beef cattle. Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1. We identified 305 known bovine miRNAs. Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378, and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (v. 21. We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle. Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI

  15. Smart detection of microRNAs through fluorescence enhancement on a photonic crystal.

    Science.gov (United States)

    Pasquardini, L; Potrich, C; Vaghi, V; Lunelli, L; Frascella, F; Descrovi, E; Pirri, C F; Pederzolli, C

    2016-04-01

    The detection of low abundant biomarkers, such as circulating microRNAs, demands innovative detection methods with increased resolution, sensitivity and specificity. Here, a biofunctional surface was implemented for the selective capture of microRNAs, which were detected through fluorescence enhancement directly on a photonic crystal. To set up the optimal biofunctional surface, epoxy-coated commercially available microscope slides were spotted with specific anti-microRNA probes. The optimal concentration of probe as well as of passivating agent were selected and employed for titrating the microRNA hybridization. Cross-hybridization of different microRNAs was also tested, resulting negligible. Once optimized, the protocol was adapted to the photonic crystal surface, where fluorescent synthetic miR-16 was hybridized and imaged with a dedicated equipment. The photonic crystal consists of a dielectric multilayer patterned with a grating structure. In this way, it is possible to take advantage from both a resonant excitation of fluorophores and an angularly redirection of the emitted radiation. As a result, a significant fluorescence enhancement due to the resonant structure is collected from the patterned photonic crystal with respect to the outer non-structured surface. The dedicated read-out system is compact and based on a wide-field imaging detection, with little or no optical alignment issues, which makes this approach particularly interesting for further development such as for example in microarray-type bioassays. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. A cytometry microparticle platform approach for screening tobacco microRNA changes after agrobacterium delivery

    Energy Technology Data Exchange (ETDEWEB)

    Powell, Joshua D.; Chen, Qiang; Mason, Hugh S.

    2016-08-01

    Abstract Key message nta-miR-398 is significantly up-regulated while nta-miR-428d is significantly down-regulated in tobacco after agroinfiltration AbstractMicroRNAs are a class of non-coding regulatory RNAs that can modulate development as well as alter innate antiviral defenses in plants. In this study we explored host changes at the microRNA level within tobacco (Nicotiana benthamiana) after expression of a recombinant anti-Ebola GP1 antibody through Agrobacterium tumefaciens agroinfiltration delivery. A multiplex nanoparticle-based cytometry assay tracked the host expression changes of 53 tobacco microRNAs. Our results revealed that the most abundant microRNAs in actively growing leaves corresponded to nanoparticle probes specific to nta-mir-6149 and nta-miR-168b. After agroinfiltration, probes targeting nta-mir-398 and nta-mir-482d were significantly altered in their respective expression levels and were further verified through RT-qPCR analysis. To our knowledge this study is the first to profile microRNA expression in tobacco after agroinfiltration using a multiplex nanoparticle approach.

  17. 2-Chloro-2,2-difluoroacetophenone: a non-ODS-based difluorocarbene precursor and its use in the difluoromethylation of phenol derivatives.

    Science.gov (United States)

    Zhang, Laijun; Zheng, Ji; Hu, Jinbo

    2006-12-22

    A novel and non-ODS-based (ODS = ozone-depleting substance) preparation of 2-chloro-2,2-difluoroacetophenone (1) was achieved in high yield by using 2,2,2-trifluoroacetophenone as the starting material. Compound 1 was found to act as a good difluorocarbene reagent, which readily reacts with a variety of structurally diverse phenol derivatives 4 in the presence of potassium hydroxide or potassium carbonate to produce aryl difluoromethyl ethers 5 in good yields. This new and easy-to-handle synthetic methodology offers an environmentally friendly alternative to other Freon- or Halon-based difluoromethylating approaches.

  18. Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress.

    Science.gov (United States)

    Zhu, Jianfeng; Li, Wanfeng; Yang, Wenhua; Qi, Liwang; Han, Suying

    2013-09-01

    142 miRNAs were identified and 38 miRNA targets were predicted, 4 of which were validated, in C. intermedia . The expression of 12 miRNAs in salt-stressed leaves was assessed by qRT-PCR. MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs and analysis of transcriptome data were performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. Furthermore, 36 potential target genes of 17 known miRNA families and 2 potential target genes of 1 novel miRNA were predicted; 4 of these were validated by 5' RACE. The expression of 12 miRNAs was validated in different tissues, and these and five target mRNAs were assessed by qRT-PCR after salt treatment. The expression levels of seven miRNAs (cin-miR157a, cin-miR159a, cin-miR165a, cin-miR167b, cin-miR172b, cin-miR390a and cin-miR396a) were upregulated, while cin-miR398a expression was downregulated after salt treatment. The targets of cin-miR157a, cin-miR165a, cin-miR172b and cin-miR396a were downregulated and showed an approximately negative correlation with their corresponding miRNAs under salt treatment. These results would help further understanding of miRNA regulation in response to abiotic stress in C. intermedia.

  19. Non radioactive precursor import into chloroplasts

    International Nuclear Information System (INIS)

    Lombardo, V.A.; Ottado, J.

    2003-01-01

    Full text: Eukaryotic cells have a subcellular organization based on organelles. Protein transport to these organelles is quantitatively important because the majority of cellular proteins are codified in nuclear genes and then delivered to their final destination. Most of the chloroplast proteins are translated on cytoplasmic ribosomes as larger precursors with an amino terminal transit peptide that is necessary and sufficient to direct the precursor to the chloroplast. Once inside the organelle the transit peptide is cleaved and the mature protein adopts its folded form. In this work we developed a system for the expression and purification of the pea ferredoxin-NADP + reductase precursor (preFNR) for its import into chloroplasts in non radioactive conditions. We constructed a preFNR fused in its carboxy terminus to a 6 histidines peptide (preFNR-6xHis) that allows its identification using a commercial specific antibody. The construction was expressed, purified, processed and precipitated, rendering a soluble and active preFNR-6xHis that was used in binding and import into chloroplasts experiments. The reisolated chloroplasts were analyzed by SDS-PAGE, electro-blotting and revealed by immuno-detection using either colorimetric or chemiluminescent reactive. We performed also import experiments labeling preFNR and preFNR-6xHis with radioactive methionine as controls. We conclude that preFNR-6xHis is bound and imported into chloroplasts as the wild type preFNR and that both colorimetric or chemiluminescent detection methods are useful to avoid the manipulation of radioactive material. (author)

  20. Precursor systems analyses of automated highway systems. Knowledge based systems and learning methods for AHS. Volume 10. Final report, September 1993-February 1995

    Energy Technology Data Exchange (ETDEWEB)

    Schmoltz, J.; Blumer, A.; Noonan, J.; Shedd, D.; Twarog, J.

    1995-06-01

    Managing each AHS vehicle and the AHS system as a whole is an extremely complex yndertaking. The authors have investigated and now report on Artificial Intelligence (AI) approaches that can help. In particular, we focus on AI technologies known as Knowledge Based Systems (KBSs) and Learning Methods (LMs). Our primary purpose is to identify opportunities: we identify several problems in AHS and AI technologies that can solve them. Our secondary purpose is to examine in some detail a subset of these opportunities: we examine how KBSs and LMs can help in controlling the high level movements--e.g., keep in lane, change lanes, speed up, slow down--of an automated vehicle. This detailed examination includes the implementation of a prototype system having three primary components. The Tufts Automated Highway System Kit(TAHSK) discrete time micro-level traffic simulator is a generic AHS simulator. TAHSK interfaces with the Knowledge Based Controller (KBCon) knowledge based high level controller, which controls the high level actions of individual AHS vehicles. Finally, TAHSK also interfaces with a Reinforcement learning (RL) module that was used to explore the possibilities of RL techniques in an AHS environment.

  1. Fluid Mechanics of Lean Blowout Precursors in Gas Turbine Combustors

    Directory of Open Access Journals (Sweden)

    T. M. Muruganandam

    2012-03-01

    Full Text Available Understanding of lean blowout (LBO phenomenon, along with the sensing and control strategies could enable the gas turbine combustor designers to design combustors with wider operability regimes. Sensing of precursor events (temporary extinction-reignition events based on chemiluminescence emissions from the combustor, assessing the proximity to LBO and using that data for control of LBO has already been achieved. This work describes the fluid mechanic details of the precursor dynamics and the blowout process based on detailed analysis of near blowout flame behavior, using simultaneous chemiluminescence and droplet scatter observations. The droplet scatter method represents the regions of cold reactants and thus help track unburnt mixtures. During a precursor event, it was observed that the flow pattern changes significantly with a large region of unburnt mixture in the combustor, which subsequently vanishes when a double/single helical vortex structure brings back the hot products back to the inlet of the combustor. This helical pattern is shown to be the characteristic of the next stable mode of flame in the longer combustor, stabilized by double helical vortex breakdown (VBD mode. It is proposed that random heat release fluctuations near blowout causes VBD based stabilization to shift VBD modes, causing the observed precursor dynamics in the combustor. A complete description of the evolution of flame near the blowout limit is presented. The description is consistent with all the earlier observations by the authors about precursor and blowout events.

  2. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  3. MicroRNA expression profiling of the porcine developing brain

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Busk, Peter Kamp

    2011-01-01

    MicroRNAs are small, non-coding RNA molecules that regulate gene expression at the post-transcriptional level and play an important role in the control of developmental and physiological processes. In particular, the developing brain contains an impressive diversity of microRNAs. Most micro...... and the growth curve when compared to humans. Considering these similarities, studies examining microRNA expression during porcine brain development could potentially be used to predict the expression profile and role of microRNAs in the human brain....

  4. Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

    DEFF Research Database (Denmark)

    Kruhøffer, Mogens; Andersen, Lars Dyrskjøt; Voss, Thorsten

    2007-01-01

    We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood...... and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated micro......RNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis....

  5. Radon as an earthquake precursor

    International Nuclear Information System (INIS)

    Planinic, J.; Radolic, V.; Vukovic, B.

    2004-01-01

    Radon concentrations in soil gas were continuously measured by the LR-115 nuclear track detectors during a four-year period. Seismic activities, as well as barometric pressure, rainfall and air temperature were also observed. The influence of meteorological parameters on temporal radon variations was investigated, and a respective equation of the multiple regression was derived. The earthquakes with magnitude ≥3 at epicentral distances ≤200 km were recognized by means of radon anomaly. Empirical equations between earthquake magnitude, epicentral distance and precursor time were examined, and respective constants were determined

  6. Radon as an earthquake precursor

    Energy Technology Data Exchange (ETDEWEB)

    Planinic, J. E-mail: planinic@pedos.hr; Radolic, V.; Vukovic, B

    2004-09-11

    Radon concentrations in soil gas were continuously measured by the LR-115 nuclear track detectors during a four-year period. Seismic activities, as well as barometric pressure, rainfall and air temperature were also observed. The influence of meteorological parameters on temporal radon variations was investigated, and a respective equation of the multiple regression was derived. The earthquakes with magnitude {>=}3 at epicentral distances {<=}200 km were recognized by means of radon anomaly. Empirical equations between earthquake magnitude, epicentral distance and precursor time were examined, and respective constants were determined.

  7. Carbon molecular sieve membrane from a microporous spirobisindane-based polyimide precursor with enhanced ethylene/ethane mixed-gas selectivity

    KAUST Repository

    Salinas, Octavio

    2017-01-13

    Ethylene is typically produced by steam cracking of various hydrocarbon feedstocks. The gaseous products are then separated in a demethanizer followed by a deethanizer unit and finally sent to a C splitter for the final purification step. Cryogenic distillation of ethylene from ethane is the most energy-intensive unit operation process in the chemical industry. Therefore, the development of more energy-efficient processes for ethylene purification is highly desirable. Membrane-based separation has been proposed as an alternative option for replacement or debottlenecking of C splitters but current polymer membrane materials exhibit insufficient mixed-gas CH/CH selectivity (<7) to be technically and economically attractive. In this work, a highly selective carbon molecular sieve (CMS) membrane derived from a novel spirobisindane-based polyimide of intrinsic microporosity (PIM-6FDA) was developed and characterized. PIM-6FDA showed a single-stage degradation process under an inert nitrogen atmosphere which commenced at ∼480 °C. The CMS formed by pyrolysis at 800 °C had a diffusion/size-sieving-controlled morphology with a mixed-gas (50% CH/50% CH) ethylene/ethane selectivity of 15.6 at 20 bar feed pressure at 35 °C. The mixed-gas ethylene/ethane selectivity is the highest reported value for CMS-type membranes to date.

  8. MicroRNA Expression Profiling by Bead Array Technology in Human Tumor Cell Lines Treated with Interferon-Alpha-2a

    Directory of Open Access Journals (Sweden)

    Siegrist Fredy

    2009-01-01

    Full Text Available Abstract MicroRNAs are positive and negative regulators of eukaryotic gene expression that modulate transcript abundance by specific binding to sequence motifs located prevalently in the 3' untranslated regions of target messenger RNAs (mRNA. Interferon-alpha-2a (IFNα induces a large set of protein coding genes mediating antiproliferative and antiviral responses. Here we use a global microarray-based microRNA detection platform to identify genes that are induced by IFNα in hepatoma- or melanoma-derived human tumor cell lines. Despite the enormous differences in expression levels between these models, we were able to identify microRNAs that are upregulated by IFNα in both lines suggesting the possibility that interferon-regulated microRNAs are involved in the transcriptional repression of mRNA relevant to cytokine responses.

  9. Expression profiling of microRNAs in human bone tissue from postmenopausal women.

    Science.gov (United States)

    De-Ugarte, Laura; Serra-Vinardell, Jenny; Nonell, Lara; Balcells, Susana; Arnal, Magdalena; Nogues, Xavier; Mellibovsky, Leonardo; Grinberg, Daniel; Diez-Perez, Adolfo; Garcia-Giralt, Natalia

    2018-01-01

    Bone tissue is composed of several cell types, which express their own microRNAs (miRNAs) that will play a role in cell function. The set of total miRNAs expressed in all cell types configures the specific signature of the bone tissue in one physiological condition. The aim of this study was to explore the miRNA expression profile of bone tissue from postmenopausal women. Tissue was obtained from trabecular bone and was analyzed in fresh conditions (n = 6). Primary osteoblasts were also obtained from trabecular bone (n = 4) and human osteoclasts were obtained from monocyte precursors after in vitro differentiation (n = 5). MicroRNA expression profiling was obtained for each sample by microarray and a global miRNA analysis was performed combining the data acquired in all the microarray experiments. From the 641 miRNAs detected in bone tissue samples, 346 (54%) were present in osteoblasts and/or osteoclasts. The other 46% were not identified in any of the bone cells analyzed. Intersection of osteoblast and osteoclast arrays identified 101 miRNAs shared by both cell types, which accounts for 30-40% of miRNAs detected in these cells. In osteoblasts, 266 miRNAs were detected, of which 243 (91%) were also present in the total bone array, representing 38% of all bone miRNAs. In osteoclasts, 340 miRNAs were detected, of which 196 (58%) were also present in the bone tissue array, representing 31% of all miRNAs detected in total bone. These analyses provide an overview of miRNAs expressed in bone tissue, broadening our knowledge in the microRNA field.

  10. Regulation of Plant Microprocessor Function in Shaping microRNA Landscape

    Directory of Open Access Journals (Sweden)

    Jakub Dolata

    2018-06-01

    Full Text Available MicroRNAs are small molecules (∼21 nucleotides long that are key regulators of gene expression. They originate from long stem–loop RNAs as a product of cleavage by a protein complex called Microprocessor. The core components of the plant Microprocessor are the RNase type III enzyme Dicer-Like 1 (DCL1, the zinc finger protein Serrate (SE, and the double-stranded RNA binding protein Hyponastic Leaves 1 (HYL1. Microprocessor assembly and its processing of microRNA precursors have been reported to occur in discrete nuclear bodies called Dicing bodies. The accessibility of and modifications to Microprocessor components affect microRNA levels and may have dramatic consequences in plant development. Currently, numerous lines of evidence indicate that plant Microprocessor activity is tightly regulated. The cellular localization of HYL1 is dependent on a specific KETCH1 importin, and the E3 ubiquitin ligase COP1 indirectly protects HYL1 from degradation in a light-dependent manner. Furthermore, proper localization of HYL1 in Dicing bodies is regulated by MOS2. On the other hand, the Dicing body localization of DCL1 is regulated by NOT2b, which also interacts with SE in the nucleus. Post-translational modifications are substantial factors that contribute to protein functional diversity and provide a fine-tuning system for the regulation of protein activity. The phosphorylation status of HYL1 is crucial for its activity/stability and is a result of the interplay between kinases (MPK3 and SnRK2 and phosphatases (CPL1 and PP4. Additionally, MPK3 and SnRK2 are known to phosphorylate SE. Several other proteins (e.g., TGH, CDF2, SIC, and RCF3 that interact with Microprocessor have been found to influence its RNA-binding and processing activities. In this minireview, recent findings on the various modes of Microprocessor activity regulation are discussed.

  11. Fluorescing macerals from wood precursors

    Energy Technology Data Exchange (ETDEWEB)

    Stout, S A; Bensley, D F

    1987-01-01

    A preliminary investigation into the origin of wood-derived macerals has established the existence of autofluorescent maceral precursors in the secondary xylem of swamp-inhabiting plant species. The optical character and fluorescent properties of microtomed thin-sections of modern woods from the Florida Everglades and Okefenokee Swamp, Georgia are compared to the character and properties of their peatified equivalents from various Everglades and Okefenokee peat horizons and their lignitic equivalents from the Brandon lignite of Vermont and the Trail Ridge lignitic peat from northern Florida. The inherent fluorescence of woody cell walls is believed to be caused by lignin though other cell wall components may contribute. The fluorescence spectra for several wood and cell types had a ..gamma../sub m//sub a//sub x/ of 452 nm and Q value of 0.00. The color as observed in blue light and the spectral geometry as measured in UV light of peatified and lignitic woody cell walls (potential textinites) may change progressively during early coalification. Cell wall-derived maceral material is shown to maintain its fluorescing properties after being converted to a structureless material, perhaps a corpohuminite or humodetrinite precursor. Fluorescing xylem cell contents, such as condensed tannins or essential oils, can maintain the fluorescent character through early coalification. Xylem cell walls and xylem cell contents are shown to provide fluorescing progenitor materials which would not require subsequent infusion with 'lipid' materials to account for their fluorescence as phytoclast material or as macerals in coal. 35 references.

  12. Structure-Based Design of an Iminoheterocyclic β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central Aβ in Nonhuman Primates

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Mihirbaran; Wu, Yusheng; Misiaszek, Jeffrey; Li, Guoqing; Buevich, Alexei; Caldwell, John P.; Liu, Xiaoxiang; Mazzola, Robert D.; Orth, Peter; Strickland, Corey; Voigt, Johannes; Wang, Hongwu; Zhu, Zhaoning; Chen, Xia; Grzelak, Michael; Hyde, Lynn A.; Kuvelkar, Reshma; Leach, Prescott T.; Terracina, Giuseppe; Zhang, Lili; Zhang, Qi; Michener, Maria S.; Smith, Brad; Cox, Kathleen; Grotz, Diane; Favreau, Leonard; Mitra, Kaushik; Kazakevich, Irina; McKittrick, Brian A.; Greenlee, William; Kennedy, Matthew E.; Parker, Eric M.; Cumming, Jared N.; Stamford, Andrew W. (Merck)

    2016-04-14

    We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued. Optimization of the pyrimidine substituent that binds in the S2'–S2'' pocket of BACE1 remediated time-dependent CYP3A4 inhibition of earlier analogues in this series and imparted high BACE1 affinity. These efforts resulted in the discovery of difluorophenyl analogue 9 (MBi-4), which robustly lowered CSF and cortex Aβ40 in both rats and cynomolgus monkeys following a single oral dose. Compound 9 represents a unique molecular shape among BACE inhibitors reported to potently lower central Aβ in nonrodent preclinical species.

  13. Ultrasound-assisted synthesis of nano-structured Zinc(II)-based metal-organic frameworks as precursors for the synthesis of ZnO nano-structures.

    Science.gov (United States)

    Bigdeli, Fahime; Ghasempour, Hosein; Azhdari Tehrani, Alireza; Morsali, Ali; Hosseini-Monfared, Hassan

    2017-07-01

    A 3D, porous Zn(II)-based metal-organic framework {[Zn 2 (oba) 2 (4-bpmn)]·(DMF) 1.5 } n (TMU-21), (4-bpmn=N,N'-Bis-pyridin-4-ylmethylene-naphtalene-1,5-diamine, H 2 oba=4,4'-oxybis(benzoic acid)) with nano-rods morphology under ultrasonic irradiation at ambient temperature and atmospheric pressure was prepared and characterized by scanning electron microscopy. Sonication time and concentration of initial reagents effects on the size and morphology of nano-structured MOFs were studied. Also {[Zn 2 (oba) 2 (4-bpmn)] (TMU-21) and {[Zn 2 (oba) 2 (4-bpmb)] (TMU-6), 4-bpmb=N,N'-(1,4-phenylene)bis(1-(pyridin-4-yl)methanimine) were easily prepared by mechanochemical synthesis. Nanostructures of Zinc(II) oxide were obtained by calcination of these compounds and their de-solvated analogue as activated MOFs, at 550°C under air atmosphere. As a result of that, different Nanostructures of Zinc(II) oxide were obtained. The ZnO nanoparticles were characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM) and FT-IR spectroscopy. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Application of precursor methodology in initiating frequency estimates

    International Nuclear Information System (INIS)

    Kohut, P.; Fitzpatrick, R.G.

    1991-01-01

    The precursor methodology developed in recent years provides a consistent technique to identify important accident sequence precursors. It relies on operational events (extracting information from actual experience) and infers core damage scenarios based on expected safety system responses. The ranking or categorization of each precursor is determined by considering the full spectrum of potential core damage sequences. The methodology estimates the frequency of severe core damage based on the approach suggested by Apostolakis and Mosleh, which may lead to a potential overestimation of the severe-accident sequence frequency due to the inherent dependencies between the safety systems and the initiating events. The methodology is an encompassing attempt to incorporate most of the operating information available from nuclear power plants and is an attractive tool from the point of view of risk management. In this paper, a further extension of this methodology is discussed with regard to the treatment of initiating frequency of the accident sequences

  15. Phenoxo bridged dinuclear Zn(II) Schiff base complex as new precursor for preparation zinc oxide nanoparticles: Synthesis, characterization, crystal structures and photoluminescence studies

    Energy Technology Data Exchange (ETDEWEB)

    Saeednia, S., E-mail: sami_saeednia@yahoo.com [Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of); Iranmanesh, P. [Department of physics, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of); Ardakani, M. Hatefi; Mohammadi, M.; Norouzi, Gh. [Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of)

    2016-06-15

    Highlights: • A novel nano-scale Zn(II) complex was synthesized by solvothermal method. • Chemical structure of the nanostructures was characterized as well as bulk complex. • The photoluminescence property of the complex was investigated at room temperature. • The thermogravimetry and differential thermal analysis were carried out. • Thermal decomposition of the nanostructures was prepared zinc oxide nanoparticles. - Abstract: Nanoparticles of a novel Zn(II) Schiff base complex, [Zn(HL)NO{sub 3}]{sub 2} (1), (H{sub 2}L = 2-[(2-hydroxy-propylimino) methyl] phenol), was synthesized by using solvothermal method. Shape, morphology and chemical structure of the synthesized nanoparticles were characterized by scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier Transform Infrared Spectoscopy (FT-IR) and UV–vis spectroscopy. Structural determination of compound 1 was determined by single-crystal X-ray diffraction. The results were revealed that the zinc complex is a centrosymmetric dimer in which deprotonated phenolates bridge the two five-coordinate metal atoms and link the two halves of the dimer. The thermal stability of compound 1 was analyzed by thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). The effect of the initial substrates concentration and reaction time on size and morphology of compound 1 nanostructure was investigated as well. Furthermore, the luminescent properties of the complex 1 were examined. ZnO nanoparticles with diameter between 15 and 20 nm were simply synthesized by solid-state transformation of compound 1 at 700 °C.

  16. The Role of Exportin-5 in MicroRNA Biogenesis and Cancer

    Directory of Open Access Journals (Sweden)

    Ke Wu

    2018-04-01

    Full Text Available MicroRNAs (miRNAs are conserved small non-coding RNAs that play an important role in the regulation of gene expression and participate in a variety of biological processes. The biogenesis of miRNAs is tightly controlled at multiple steps, such as transcription of miRNA genes, processing by Drosha and Dicer, and transportation of precursor miRNAs (pre-miRNAs from the nucleus to the cytoplasm by exportin-5 (XPO5. Given the critical role of nuclear export of pre-miRNAs in miRNA biogenesis, any alterations of XPO5, resulting from either genetic mutation, epigenetic change, abnormal expression level or posttranslational modification, could affect miRNA expression and thus have profound effects on tumorigenesis. Importantly, XPO5 phosphorylation by ERK kinase and its cis/trans isomerization by the prolyl isomerase Pin1 impair XPO5′s nucleo-to-cytoplasmic transport ability of pre-miRNAs, leading to downregulation of mature miRNAs in hepatocellular carcinoma. In this review, we focus on how XPO5 transports pre-miRNAs in the cells and summarize the dysregulation of XPO5 in human tumors. Keywords: Exportin-5, MicroRNA, Biogenesis, Dysregulation, Cancer

  17. An update on the microRNAs and their targets in unicellular red alga porphyridium cruentum

    International Nuclear Information System (INIS)

    Barozai, M.Y.K.

    2018-01-01

    MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about approx 21 nucleotides in length. The miRNAs are reported in large number of higher eukaryotic plant species. But very little data of miRNAs in algae is available. Porphyridium cruentum is unicellular red alga famous as a source for polyunsaturated fatty acids, proteins and polysaccharide contents. The present study is aimed to update the microRNAs and their targets in this important algal species. A comparative genomics approach was applied to update the miRNAs in P. cruentum. This effort resulted in a total of 49 miRNAs belonging to 46 families in P. cruentum. Their precursor-miRNAs were observed with a range of 40 to 351 nucleotides (nt). The mature miRNA sequences showed a range of 17-24 nts. The minimum free energies by stem loop structures of these miRNAs are found with an average of -32 Kcalmol-1. A total of 13 targets, including important proteins like; Ribulose-1,5-bisphosphate carboxylase oxygenase, Light-harvesting complex I, Oxygen-evolving enhancer protein, Phycobiliproteins, Granule-bound starch synthase and Carbonic anhydrase were also predicted for these miRNAs. (author)

  18. Enzyme-free electrochemical detection of microRNA-21 using immobilized hairpin probes and a target-triggered hybridization chain reaction amplification strategy

    International Nuclear Information System (INIS)

    Liu, Hongying; Bei, Xiaoqiong; Xia, Qiuting; Fu, Yan; Zhang, Shi; Liu, Maochuan; Fan, Kai; Zhang, Mingzhen; Yang, Yong

    2016-01-01

    We describe a sensitive enzyme-free bioassay for the determination of microRNA-21. It is based on a combination of target-triggered hybridization chain reaction, tagging with CdTe quantum dots (QDs), and anodic stripping voltammetry. Firstly, a thiolated capture hairpin probe SH-HP1 was immobilized on the surface of a gold electrode. HP1 unfolds in the presence of microRNA-21. If hairpin probe 2 (HP2) is present, a HP1-HP2 complex will be formed which possesses an exposed stem of HP2, and microRNA is released in parallel. The released microRNA-21 triggers a hybridization chain reaction and this leads to form an exposed DNA segment of HP2 and cycle use microRNA-21. With the aid of assistant DNA A1 and A2, the exposed DNA segment of HP2 progressed to a long double strand. The strand is rich in CdTe QDs with the help of QDs-A1. Then, the attached QDs were dissolved with HNO 3 to give dissolved Cd(II) ions. Finally, the corresponding electrochemical current response of Cd(II) is monitored by anodic stripping voltammetry and used to quantify the concentration of microRNA-21. More microRNA-21 participated in this reaction increases the number of CdTe QDs, which results in increased electrochemical current. Thus, an ultrasensitive detection of microRNA-21 is accomplished by anodic stripping voltammetry. This gene assay displays a detection limit as low as 33 aM. It can discriminate between complementary DNA sequence and single-base mismatched DNA, indicating its high specificity. (author)

  19. Unique Preservation of Neural Cells in Hutchinson- Gilford Progeria Syndrome Is Due to the Expression of the Neural-Specific miR-9 MicroRNA

    Directory of Open Access Journals (Sweden)

    Xavier Nissan

    2012-07-01

    Full Text Available One puzzling observation in patients affected with Hutchinson-Gilford progeria syndrome (HGPS, who overall exhibit systemic and dramatic premature aging, is the absence of any conspicuous cognitive impairment. Recent studies based on induced pluripotent stem cells derived from HGPS patient cells have revealed a lack of expression in neural derivatives of lamin A, a major isoform of LMNA that is initially produced as a precursor called prelamin A. In HGPS, defective maturation of a mutated prelamin A induces the accumulation of toxic progerin in patient cells. Here, we show that a microRNA, miR-9, negatively controls lamin A and progerin expression in neural cells. This may bear major functional correlates, as alleviation of nuclear blebbing is observed in nonneural cells after miR-9 overexpression. Our results support the hypothesis, recently proposed from analyses in mice, that protection of neural cells from progerin accumulation in HGPS is due to the physiologically restricted expression of miR-9 to that cell lineage.

  20. Preparation of YBa2Cu3O7-x superconducting solutions and films from alkoxide-based precursors using sol-gel method and investigation of their chemical reaction mechanisms

    International Nuclear Information System (INIS)

    Mutlu, Ibrahim Halil; Acun, Hediye; Celik, Erdal; Turkmen, Hasan

    2007-01-01

    In the development of coated superconductors sol-gel technique has been widely used as an effective processing method, especially in making long-length wires and tapes. However, one drawback associated with the deposition of YBa 2 Cu 3 O 7-x and Gd 2 O 3 buffer layer on Ni tape is the adhesion characteristic at interfaces YBCO-Gd 2 O 3 and Gd 2 O 3 -NiO and NiO-Ni substrate. In this paper, two strategies for adhesion enhancement of multilayered ceramic oxide coatings on Ni substrate were proposed: (1) formation of chemical bonds through surface condensation reactions, and development of ceramic networks through diffusion of alkoxide precursors. The current research has focused on the fabrication and adhesion of YBCO coatings on buffered Ni substrate using nine solutions prepared from Y, Ba and Cu alkoxides, solvent and chelating agent. Only two of YBCO solutions were successfully obtained while the rest of them were unsuccessful. Among these solutions we scrutinized chemical reaction mechanisms of a successful and an unsuccessful solution for comparison. How the chemical bonds and solubility were affected by the acids, base and solvents used in the solutions was demonstrated. It was shown that pH of the solution, homogeneity of the solution and gelation, steric affect of the chemicals in sol-gel solutions are significant issues to obtain high quality superconducting YBCO thin films. In addition, X-ray diffraction (XRD) was used to analyze phase structure of YBCO and compare results of chemical reactions obtained by a chemdraw programme. Scanning electron microscope (SEM) studies was carried out to examine microstructures of YBCO films produced from alkoxide precursors, solvent, chelating agent and modifying liquid chemical materials such as triethanolamine or ammonium hydroxide. It was found to be YBCO, Gd 2 O 3 , NiO and Ni phases in YBCO/Gd 2 O 3 /Ni sample from XRD analysis. That the solution prepared by using triethanolamine provided the best film quality and

  1. Oligo- and Polymetastatic Progression in Lung Metastasis(es) Patients Is Associated with Specific MicroRNAs

    Science.gov (United States)

    Lussier, Yves A.; Ganai, Sabha; Khan, Sajid A.; Gnerlich, Jennifer; Darga, Thomas E.; Fan, Hanli; Karpenko, Oleksiy; Paty, Philip B.; Posner, Mitchell C.; Chmura, Steven J.; Hellman, Samuel; Ferguson, Mark K.; Weichselbaum, Ralph R.

    2012-01-01

    Rationale Strategies to stage and treat cancer rely on a presumption of either localized or widespread metastatic disease. An intermediate state of metastasis termed oligometastasis(es) characterized by limited progression has been proposed. Oligometastases are amenable to treatment by surgical resection or radiotherapy. Methods We analyzed microRNA expression patterns from lung metastasis samples of patients with ≤5 initial metastases resected with curative intent. Results Patients were stratified into subgroups based on their rate of metastatic progression. We prioritized microRNAs between patients with the highest and lowest rates of recurrence. We designated these as high rate of progression (HRP) and low rate of progression (LRP); the latter group included patients with no recurrences. The prioritized microRNAs distinguished HRP from LRP and were associated with rate of metastatic progression and survival in an independent validation dataset. Conclusion Oligo- and poly- metastasis are distinct entities at the clinical and molecular level. PMID:23251360

  2. Oligo- and polymetastatic progression in lung metastasis(es patients is associated with specific microRNAs.

    Directory of Open Access Journals (Sweden)

    Yves A Lussier

    Full Text Available RATIONALE: Strategies to stage and treat cancer rely on a presumption of either localized or widespread metastatic disease. An intermediate state of metastasis termed oligometastasis(es characterized by limited progression has been proposed. Oligometastases are amenable to treatment by surgical resection or radiotherapy. METHODS: We analyzed microRNA expression patterns from lung metastasis samples of patients with ≤ 5 initial metastases resected with curative intent. RESULTS: Patients were stratified into subgroups based on their rate of metastatic progression. We prioritized microRNAs between patients with the highest and lowest rates of recurrence. We designated these as high rate of progression (HRP and low rate of progression (LRP; the latter group included patients with no recurrences. The prioritized microRNAs distinguished HRP from LRP and were associated with rate of metastatic progression and survival in an independent validation dataset. CONCLUSION: Oligo- and poly- metastasis are distinct entities at the clinical and molecular level.

  3. Oligo- and polymetastatic progression in lung metastasis(es) patients is associated with specific microRNAs.

    Science.gov (United States)

    Lussier, Yves A; Khodarev, Nikolai N; Regan, Kelly; Corbin, Kimberly; Li, Haiquan; Ganai, Sabha; Khan, Sajid A; Gnerlich, Jennifer L; Gnerlich, Jennifer; Darga, Thomas E; Fan, Hanli; Karpenko, Oleksiy; Paty, Philip B; Posner, Mitchell C; Chmura, Steven J; Hellman, Samuel; Ferguson, Mark K; Weichselbaum, Ralph R

    2012-01-01

    Strategies to stage and treat cancer rely on a presumption of either localized or widespread metastatic disease. An intermediate state of metastasis termed oligometastasis(es) characterized by limited progression has been proposed. Oligometastases are amenable to treatment by surgical resection or radiotherapy. We analyzed microRNA expression patterns from lung metastasis samples of patients with ≤ 5 initial metastases resected with curative intent. Patients were stratified into subgroups based on their rate of metastatic progression. We prioritized microRNAs between patients with the highest and lowest rates of recurrence. We designated these as high rate of progression (HRP) and low rate of progression (LRP); the latter group included patients with no recurrences. The prioritized microRNAs distinguished HRP from LRP and were associated with rate of metastatic progression and survival in an independent validation dataset. Oligo- and poly- metastasis are distinct entities at the clinical and molecular level.

  4. smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

    Science.gov (United States)

    2012-01-01

    Background MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. Results To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. Conclusions This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to

  5. Bulk modulus of basic sodalite, Na8[AlSiO4]6(OH)2·2H2O, a possible zeolitic precursor in coal-fly-ash-based geopolymers

    KAUST Repository

    Oh, Jae Eun

    2011-01-01

    Synthetic basic sodalite, Na8[AlSiO4] 6(OH)2•2H2O, cubic, P43n, (also known as hydroxysodalite hydrate) was prepared by the alkaline activation of amorphous aluminosilicate glass, obtained from the phase separation of Class F fly ash. The sample was subjected to a process similar to geopolymerization, using high concentrations of a NaOH solution at 90 °C for 24 hours. Basic sodalite was chosen as a representative analogue of the zeolite precursor existing in Na-based Class F fly ash geopolymers. To determine its bulk modulus, high-pressure synchrotron X-ray powder diffraction was applied using a diamond anvil cell (DAC) up to a pressure of 4.5 GPa. A curve-fit with a truncated third-order Birch-Murnaghan equation of state with a fixed K\\'o = 4 to pressure-normalized volume data yielded the isothermal bulk modulus, K o = 43 ± 4 GPa, indicating that basic sodalite is more compressible than sodalite, possibly due to a difference in interactions between the framework host and the guest molecules. © 2010 Elsevier Ltd.

  6. The MicroRNA-200 Family Is Upregulated in Endometrial Carcinoma

    Science.gov (United States)

    Snowdon, Jaime; Zhang, Xiao; Childs, Tim; Tron, Victor A.; Feilotter, Harriet

    2011-01-01

    Background MicroRNAs (miRNAs, miRs) are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. MicroRNAs are dysregulated in cancer and may play essential roles in tumorigenesis. Additionally, miRNAs have been shown to have prognostic and diagnostic value in certain types of cancer. The objective of this study was to identify dysregulated miRNAs in endometrioid endometrial adenocarcinoma (EEC) and the precursor lesion, complex atypical hyperplasia (CAH). Methodology We compared the expression profiles of 723 human miRNAs from 14 cases of EEC, 10 cases of CAH, and 10 normal proliferative endometria controls using Agilent Human miRNA arrays following RNA extraction from formalin-fixed paraffin-embedded (FFPE) tissues. The expression of 4 dysregulated miRNAs was validated using real time reverse transcription-PCR. Results Forty-three miRNAs were dysregulated in EEC and CAH compared to normal controls (p<0.05). The entire miR-200 family (miR-200a/b/c, miR-141, and miR-429) was up-regulated in cases of EEC. Conclusions This information contributes to the candidate miRNA expression profile that has been generated for EEC and shows that certain miRNAs are dysregulated in the precursor lesion, CAH. These miRNAs in particular may play important roles in tumorigenesis. Examination of miRNAs that are consistently dysregulated in various studies of EEC, like the miR-200 family, will aid in the understanding of the role that miRNAs play in tumorigenesis in this tumour type. PMID:21897839

  7. The microRNA-200 family is upregulated in endometrial carcinoma.

    Directory of Open Access Journals (Sweden)

    Jaime Snowdon

    Full Text Available BACKGROUND: MicroRNAs (miRNAs, miRs are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. MicroRNAs are dysregulated in cancer and may play essential roles in tumorigenesis. Additionally, miRNAs have been shown to have prognostic and diagnostic value in certain types of cancer. The objective of this study was to identify dysregulated miRNAs in endometrioid endometrial adenocarcinoma (EEC and the precursor lesion, complex atypical hyperplasia (CAH. METHODOLOGY: We compared the expression profiles of 723 human miRNAs from 14 cases of EEC, 10 cases of CAH, and 10 normal proliferative endometria controls using Agilent Human miRNA arrays following RNA extraction from formalin-fixed paraffin-embedded (FFPE tissues. The expression of 4 dysregulated miRNAs was validated using real time reverse transcription-PCR. RESULTS: Forty-three miRNAs were dysregulated in EEC and CAH compared to normal controls (p<0.05. The entire miR-200 family (miR-200a/b/c, miR-141, and miR-429 was up-regulated in cases of EEC. CONCLUSIONS: This information contributes to the candidate miRNA expression profile that has been generated for EEC and shows that certain miRNAs are dysregulated in the precursor lesion, CAH. These miRNAs in particular may play important roles in tumorigenesis. Examination of miRNAs that are consistently dysregulated in various studies of EEC, like the miR-200 family, will aid in the understanding of the role that miRNAs play in tumorigenesis in this tumour type.

  8. MicroRNA and gene signature of severe cutaneous drug ...

    African Journals Online (AJOL)

    Purpose: To build a microRNA and gene signature of severe cutaneous adverse drug reactions (SCAR), including Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Methods: MicroRNA expression profiles were downloaded from miRNA expression profile of patients' skin suffering from TEN using an ...

  9. Diet-responsive microRNAs are likely exogenous

    Science.gov (United States)

    In a recent report Title "et al". fostered miRNA-375 and miR-200c knock-out pups to wild-type dams and arrived at the conclusion that milk microRNAs are bioavailable in trace amounts at best and that postprandial concentrations of microRNAs are too low to elicit biological effects. Their take home m...

  10. MicroRNA and gene signature of severe cutaneous drug ...

    African Journals Online (AJOL)

    greater than 30 % of the same patients [5]. Nevertheless, the mechanisms of SJS and TEN are not fully elucidated. MicroRNAs or miRs are single stranded RNAs that are capable of posttranscriptional gene regulation via targeting their Mrna [6]. MicroRNAs are very important regulators in many human diseases, for instance,.

  11. MicroRNA-608 and microRNA-34a regulate chordoma malignancy by targeting EGFR, Bcl-xL and MET.

    Directory of Open Access Journals (Sweden)

    Ying Zhang

    Full Text Available Chordomas are rare malignant tumors that originate from the notochord remnants and occur in the skull base, spine and sacrum. Due to a very limited understanding of the molecular pathogenesis of chordoma, there are no adjuvant and molecular therapies besides surgical resection and radiation therapy. microRNAs (miRNAs are small noncoding regulatory RNA molecules with critical roles in cancer. The role of miRNAs in chordomas is mostly unknown. We uncover microRNA-608 (miR-608 and microRNA-34a (miR-34a as novel tumor suppressive microRNAs that regulate malignancy in chordoma. We find that miR-608 and miR-34a expressions are downregulated in human chordoma cell lines and primary cells at least partially via alteration of their genes' copy numbers. We identify the commonly deregulated oncogenes EGFR and Bcl-xL as direct targets of miR-608 and the receptor tyrosine kinase MET as direct target of miR-34a. We show that EGFR and MET activations promote chordoma cell proliferation and invasion and that pharmacological inhibition of EGFR and MET inhibits chordoma cell proliferation and survival. We demonstrate that restoration of miR-608 and miR-34a inhibits cell proliferation and invasion and induces apoptosis in chordoma cells. We find that miR-34a inversely correlates with MET expression and miR-608 inversely correlates with EGFR expression in chordoma cells. These findings demonstrate for the first time that miR-608 and miR-34a regulate chordoma malignancy by regulating EGFR, MET and Bcl-xL.

  12. Perfluoroalkyl Acids (PFAAs) and Selected Precursors in the Baltic Sea Environment: Do Precursors Play a Role in Food Web Accumulation of PFAAs?

    Science.gov (United States)

    Gebbink, Wouter A; Bignert, Anders; Berger, Urs

    2016-06-21

    The present study examined the presence of perfluoroalkyl acids (PFAAs) and selected precursors in the Baltic Sea abiotic environment and guillemot food web, and investigated the relative importance of precursors in food web accumulation of PFAAs. Sediment, water, zooplankton, herring, sprat, and guillemot eggs were analyzed for perfluoroalkane sulfonic acids (PFSAs; C4,6,8,10) and perfluoroalkyl carboxylic acids (PFCAs; C6-15) along with six perfluoro-octane sulfonic acid (PFOS) precursors and 11 polyfluoroalkyl phosphoric acid diesters (diPAPs). FOSA, FOSAA and its methyl and ethyl derivatives (Me- and EtFOSAA), and 6:2/6:2 diPAP were detected in sediment and water. While FOSA and the three FOSAAs were detected in all biota, a total of nine diPAPs were only detected in zooplankton. Concentrations of PFOS precursors and diPAPs exceeded PFOS and PFCA concentrations, respectively, in zooplankton, but not in fish and guillemot eggs. Although PFOS precursors were present at all trophic levels, they appear to play a minor role in food web accumulation of PFOS based on PFOS precursor/PFOS ratios and PFOS and FOSA isomer patterns. The PFCA pattern in fish could not be explained by the intake pattern based on PFCAs and analyzed precursors, that is, diPAPs. Exposure to additional precursors might therefore be a dominant exposure pathway compared to direct PFCA exposure for fish.

  13. Non-canonical microRNAs miR-320 and miR-702 promote proliferation in Dgcr8-deficient embryonic stem cells

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Byeong-Moo [Department of Medicine/GI Unit, Massachusetts General Hospital, Boston, MA 02114 (United States); Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States); Choi, Michael Y., E-mail: mchoi@partners.org [Department of Medicine/GI Unit, Massachusetts General Hospital, Boston, MA 02114 (United States); Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States); Harvard Stem Cell Institute, Boston, MA 02114 (United States)

    2012-09-21

    Highlights: Black-Right-Pointing-Pointer Embryonic stem cells (ESCs) lacking non-canonical miRNAs proliferate slower. Black-Right-Pointing-Pointer miR-320 and miR-702 are two non-canonical miRNAs expressed in ESCs. Black-Right-Pointing-Pointer miR-320 and miR-702 promote proliferation of Dgcr8-deficient ESCs. Black-Right-Pointing-Pointer miR-320 targets p57 and helps to release Dgcr8-deficient ESCs from G1 arrest. Black-Right-Pointing-Pointer miR-702 targets p21 and helps to release Dgcr8-deficient ESCs from G1 arrest. -- Abstract: MicroRNAs are known to contribute significantly to stem cell phenotype by post-transcriptionally regulating gene expression. Most of our knowledge of microRNAs comes from the study of canonical microRNAs that require two sequential cleavages by the Drosha/Dgcr8 heterodimer and Dicer to generate mature products. In contrast, non-canonical microRNAs bypass the cleavage by the Drosha/Dgcr8 heterodimer within the nucleus but still require cytoplasmic cleavage by Dicer. The function of non-canonical microRNAs in embryonic stem cells (ESCs) remains obscure. It has been hypothesized that non-canonical microRNAs have important roles in ESCs based upon the phenotypes of ESC lines that lack these specific classes of microRNAs; Dicer-deficient ESCs lacking both canonical and non-canonical microRNAs have much more severe proliferation defect than Dgcr8-deficient ESCs lacking only canonical microRNAs. Using these cell lines, we identified two non-canonical microRNAs, miR-320 and miR-702, that promote proliferation of Dgcr8-deficient ESCs by releasing them from G1 arrest. This is accomplished by targeting the 3 Prime -untranslated regions of the cell cycle inhibitors p57 and p21 and thereby inhibiting their expression. This is the first report of the crucial role of non-canonical microRNAs in ESCs.

  14. Non-canonical microRNAs miR-320 and miR-702 promote proliferation in Dgcr8-deficient embryonic stem cells

    International Nuclear Information System (INIS)

    Kim, Byeong-Moo; Choi, Michael Y.

    2012-01-01

    Highlights: ► Embryonic stem cells (ESCs) lacking non-canonical miRNAs proliferate slower. ► miR-320 and miR-702 are two non-canonical miRNAs expressed in ESCs. ► miR-320 and miR-702 promote proliferation of Dgcr8-deficient ESCs. ► miR-320 targets p57 and helps to release Dgcr8-deficient ESCs from G1 arrest. ► miR-702 targets p21 and helps to release Dgcr8-deficient ESCs from G1 arrest. -- Abstract: MicroRNAs are known to contribute significantly to stem cell phenotype by post-transcriptionally regulating gene expression. Most of our knowledge of microRNAs comes from the study of canonical microRNAs that require two sequential cleavages by the Drosha/Dgcr8 heterodimer and Dicer to generate mature products. In contrast, non-canonical microRNAs bypass the cleavage by the Drosha/Dgcr8 heterodimer within the nucleus but still require cytoplasmic cleavage by Dicer. The function of non-canonical microRNAs in embryonic stem cells (ESCs) remains obscure. It has been hypothesized that non-canonical microRNAs have important roles in ESCs based upon the phenotypes of ESC lines that lack these specific classes of microRNAs; Dicer-deficient ESCs lacking both canonical and non-canonical microRNAs have much more severe proliferation defect than Dgcr8-deficient ESCs lacking only canonical microRNAs. Using these cell lines, we identified two non-canonical microRNAs, miR-320 and miR-702, that promote proliferation of Dgcr8-deficient ESCs by releasing them from G1 arrest. This is accomplished by targeting the 3′-untranslated regions of the cell cycle inhibitors p57 and p21 and thereby inhibiting their expression. This is the first report of the crucial role of non-canonical microRNAs in ESCs.

  15. MicroRNAs in large herpesvirus DNA genomes: recent advances.

    Science.gov (United States)

    Sorel, Océane; Dewals, Benjamin G

    2016-08-01

    MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that regulate gene expression. They alter mRNA translation through base-pair complementarity, leading to regulation of genes during both physiological and pathological processes. Viruses have evolved mechanisms to take advantage of the host cells to multiply and/or persist over the lifetime of the host. Herpesviridae are a large family of double-stranded DNA viruses that are associated with a number of important diseases, including lymphoproliferative diseases. Herpesviruses establish lifelong latent infections through modulation of the interface between the virus and its host. A number of reports have identified miRNAs in a very large number of human and animal herpesviruses suggesting that these short non-coding transcripts could play essential roles in herpesvirus biology. This review will specifically focus on the recent advances on the functions of herpesvirus miRNAs in infection and pathogenesis.

  16. Multilayer checkpoints for microRNA authenticity during RISC assembly.

    Science.gov (United States)

    Kawamata, Tomoko; Yoda, Mayuko; Tomari, Yukihide

    2011-09-01

    MicroRNAs (miRNAs) function through the RNA-induced silencing complex (RISC), which contains an Argonaute (Ago) protein at the core. RISC assembly follows a two-step pathway: miRNA/miRNA* duplex loading into Ago, and separation of the two strands within Ago. Here we show that the 5' phosphate of the miRNA strand is essential for duplex loading into Ago, whereas the preferred 5' nucleotide of the miRNA strand and the base-pairing status in the seed region and the middle of the 3' region function as additive anchors to Ago. Consequently, the miRNA authenticity is inspected at multiple steps during RISC assembly.

  17. Can microRNAs act as biomarkers of aging?

    Science.gov (United States)

    Kashyap, Luv

    2011-02-07

    Aging can be defined as a progressive decline in physiological efficiency regulated by an extremely complex multifactorial process. The genetic makeup of an individual appears to dictate this rate of aging in a species specific manner. For decades now, scientists have tried to look for tiny signatures or signs which might help us predict this rate of aging. MicroRNAs (miRNAs) are a unique class of short, non-coding RNAs that mediate the post-transcriptional regulation of gene expression ranging from developmental processes to disease induction or amelioration. Recently, they have also been implicated to have a role in aging in C.elegans. Based on the fact that there is a considerable similarity between aging in C.elegans and humans, these recent findings might suggest a possible role of miRNAs as bio-markers of aging. This mini-review brushes through the possibilities towards this direction.

  18. MicroRNA-29 facilitates transplantation of bone marrow-derived mesenchymal stem cells to alleviate pelvic floor dysfunction by repressing elastin.

    Science.gov (United States)

    Jin, Minfei; Wu, Yuelin; Wang, Jun; Ye, Weiping; Wang, Lei; Yin, Peipei; Liu, Wei; Pan, Chenhao; Hua, Xiaolin

    2016-11-17

    Pelvic floor dysfunction (PFD) is a condition affecting many women worldwide, with symptoms including stress urinary incontinence (SUI) and pelvic organ prolapse (POP). We have previously demonstrated stable elastin-expressing bone marrow-derived mesenchymal stem cells (BMSCs) attenuated PFD in rats, and aim to further study the effect of microRNA-29a-3p regulation on elastin expression and efficacy of BMSC transplantation therapy. We inhibited endogenous microRNA-29a-3p in BMSCs and investigated its effect on elastin expression by RT-PCR and Western blot. MicroRNA-29-inhibited BMSCs were then transplanted into PFD rats, accompanied by sustained release of bFGF using formulated bFGF in poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NP), followed by evaluation of urodynamic tests. MicroRNA-29a-3p inhibition resulted in upregulated expression and secretion of elastin in in vitro culture of BMSCs. After co-injection with PLGA-loaded bFGF NP into the PFD rats in vivo, microRNA-29a-3p-inhibited BMSCs significantly improved the urodynamic test results. Our multidisciplinary study, combining microRNA biology, genetically engineered BMSCs, and nanoparticle technology, provides an excellent stem cell-based therapy for repairing connective tissues and treating PFD.

  19. Mars MetNet Precursor Mission Status

    Science.gov (United States)

    Harri, A.-M.; Aleksashkin, S.; Guerrero, H.; Schmidt, W.; Genzer, M.; Vazquez, L.; Haukka, H.

    2013-09-01

    We are developing a new kind of planetary exploration mission for Mars in collaboration between the Finnish Meteorological Institute (FMI), Lavochkin Association (LA), Space Research Institute (IKI) and Institutio Nacional de Tecnica Aerospacial (INTA). The Mars MetNet mission is based on a new semi-hard landing vehicle called MetNet Lander (MNL). The scientific payload of the Mars MetNet Precursor [1] mission is divided into three categories: Atmospheric instruments, Optical devices and Composition and structure devices. Each of the payload instruments will provide significant insights in to the Martian atmospheric behavior. The key technologies of the MetNet Lander have been qualified and the electrical qualification model (EQM) of the payload bay has been built and successfully tested.

  20. MicroRNA-31 Regulates Chemosensitivity in Malignant Pleural Mesothelioma

    Directory of Open Access Journals (Sweden)

    Hannah L. Moody

    2017-09-01

    Full Text Available Malignant pleural mesothelioma (MPM is associated with an extremely poor prognosis, and most patients initially are or rapidly become unresponsive to platinum-based chemotherapy. MicroRNA-31 (miR-31 is encoded on a genomic fragile site, 9p21.3, which is reportedly lost in many MPM tumors. Based on previous findings in a variety of other cancers, we hypothesized that miR-31 alters chemosensitivity and that miR-31 reconstitution may influence sensitivity to chemotherapeutics in MPM. Reintroduction of miR-31 into miR-31 null NCI-H2452 cells significantly enhanced clonogenic resistance to cisplatin and carboplatin. Although miR-31 re-expression increased chemoresistance, paradoxically, a higher relative intracellular accumulation of platinum was detected. This was coupled to a significantly decreased intranuclear concentration of platinum. Linked with a downregulation of OCT1, a bipotential transcriptional regulator with multiple miR-31 target binding sites, we subsequently identified an indirect miR-31-mediated upregulation of ABCB9, a transporter associated with drug accumulation in lysosomes, and increased uptake of platinum to lysosomes. However, when overexpressed directly, ABCB9 promoted cellular chemosensitivity, suggesting that miR-31 promotes chemoresistance largely via an ABCB9-independent mechanism. Overall, our data suggest that miR-31 loss from MPM tumors promotes chemosensitivity and may be prognostically beneficial in the context of therapeutic sensitivity. Keywords: malignant pleural mesothelioma, microRNA-31, chemoresistance, cisplatin, ABCB9

  1. Developmental Dyslexia: Early Precursors, Neurobehavioral Markers, and Biological Substrates

    Science.gov (United States)

    Benasich, April A., Ed.; Fitch, R. Holly, Ed.

    2012-01-01

    Understanding the precursors and early indicators of dyslexia is key to early identification and effective intervention. Now there's a single research volume that brings together the very latest knowledge on the earliest stages of dyslexia and the diverse genetic, neurobiological, and cognitive factors that may contribute to it. Based on findings…

  2. Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

    NARCIS (Netherlands)

    Kluiver, Joost; Gibcus, Johan H.; Hettinga, Chris; Adema, Annelies; Richter, Mareike K. S.; Halsema, Nancy; Slezak-Prochazka, Izabella; Ding, Ye; Kroesen, Bart-Jan; van den Berg, Anke

    2012-01-01

    MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and

  3. Regulation of cardiac microRNAs by serum response factor

    Directory of Open Access Journals (Sweden)

    Wei Jeanne Y

    2011-02-01

    Full Text Available Abstract Serum response factor (SRF regulates certain microRNAs that play a role in cardiac and skeletal muscle development. However, the role of SRF in the regulation of microRNA expression and microRNA biogenesis in cardiac hypertrophy has not been well established. In this report, we employed two distinct transgenic mouse models to study the impact of SRF on cardiac microRNA expression and microRNA biogenesis. Cardiac-specific overexpression of SRF (SRF-Tg led to altered expression of a number of microRNAs. Interestingly, downregulation of miR-1, miR-133a and upregulation of miR-21 occurred by 7 days of age in these mice, long before the onset of cardiac hypertrophy, suggesting that SRF overexpression impacted the expression of microRNAs which contribute to cardiac hypertrophy. Reducing cardiac SRF level using the antisense-SRF transgenic approach (Anti-SRF-Tg resulted in the expression of miR-1, miR-133a and miR-21 in the opposite direction. Furthermore, we observed that SRF regulates microRNA biogenesis, specifically the transcription of pri-microRNA, thereby affecting the mature microRNA level. The mir-21 promoter sequence is conserved among mouse, rat and human; one SRF binding site was found to be in the mir-21 proximal promoter region of all three species. The mir-21 gene is regulated by SRF and its cofactors, including myocardin and p49/Strap. Our study demonstrates that the downregulation of miR-1, miR-133a, and upregulation of miR-21 can be reversed by one single upstream regulator, SRF. These results may help to develop novel therapeutic interventions targeting microRNA biogenesis.

  4. MicroRNA discovery and analysis of pinewood nematode Bursaphelenchus xylophilus by deep sequencing.

    Directory of Open Access Journals (Sweden)

    Qi-Xing Huang

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are considered to be very important in regulating the growth, development, behavior and stress response in animals and plants in post-transcriptional gene regulation. Pinewood nematode, Bursaphelenchus xylophilus, is an important invasive plant parasitic nematode in Asia. To have a comprehensive knowledge about miRNAs of the nematode is necessary for further in-depth study on roles of miRNAs in the ecological adaptation of the invasive species. METHODS AND FINDINGS: Five small RNA libraries were constructed and sequenced by Illumina/Solexa deep-sequencing technology. A total of 810 miRNA candidates (49 conserved and 761 novel were predicted by a computational pipeline, of which 57 miRNAs (20 conserved and 37 novel encoded by 53 miRNA precursors were identified by experimental methods. Ten novel miRNAs were considered to be species-specific miRNAs of B. xylophilus. Comparison of expression profiles of miRNAs in the five small RNA libraries showed that many miRNAs exhibited obviously different expression levels in the third-stage dispersal juvenile and at a cold-stressed status. Most of the miRNAs exhibited obviously down-regulated expression in the dispersal stage. But differences among the three geographic libraries were not prominent. A total of 979 genes were predicted to be targets of these authentic miRNAs. Among them, seven heat shock protein genes were targeted by 14 miRNAs, and six FMRFamide-like neuropeptides genes were targeted by 17 miRNAs. A real-time quantitative polymerase chain reaction was used to quantify the mRNA expression levels of target genes. CONCLUSIONS: Basing on the fact that a negative correlation existed between the expression profiles of miRNAs and the mRNA expression profiles of their target genes (hsp, flp by comparing those of the nematodes at a cold stressed status and a normal status, we suggested that miRNAs might participate in ecological adaptation and behavior regulation of the

  5. A Universal Aptamer Chimera for the Delivery of Functional microRNA-126.

    Science.gov (United States)

    Rohde, Jan-H; Weigand, Julia E; Suess, Beatrix; Dimmeler, Stefanie

    2015-06-01

    microRNAs (miRs) regulate vascular diseases such as atherosclerosis and cancer. miR-126 is important for endothelial cell signaling and promotes angiogenesis, protects against atherosclerosis, and reduces breast cancer cell growth and metastasis. The overexpression of miR-126, therefore, may be an attractive therapeutic strategy for the treatment of cardiovascular disease or cancer. Here we report a novel strategy to deliver miR-126 to endothelial and breast cancer cells. We tested three different strategies to deliver miR-126 by linking the miR to an aptamer for the ubiquitously expressed transferrin receptor (transferrin receptor aptamer, TRA). Linking the precursor of miR-126 (pre-miR-126) to the TRA by annealing of a complementary stick led to efficient uptake and processing of miR-126, resulting in the delivery of 1.6×10(6)±0.3×10(6) copies miR-126-3p per ng RNA in human endothelial cells and 7.4×10(5)±2×10(5) copies miR-126-3p per ng in MCF7 breast cancer cells. The functionality of the active TRA-miR-126 chimera was further demonstrated by showing that the chimera represses the known miR-126 target VCAM-1 and improved endothelial cell sprouting in a spheroid assay. Moreover, the TRA-miR-126 chimera reduced proliferation and paracrine endothelial cell recruitment of breast cancer cells to a similar extent as miR-126-3p mimics introduced by conventional liposome-based transfection. Together, this data demonstrates that pre-miR-126 can be delivered by a non-specific aptamer to exert biological functions in two different cell models. The use of the TRA-miR-126 chimera or the combination of the delivery strategy with other endothelial or tumor specific aptamers may provide an interesting therapeutic option to treat vascular disease or cancers.

  6. MicroRNA profile changes in human immunodeficiency virus type 1 (HIV-1 seropositive individuals

    Directory of Open Access Journals (Sweden)

    Smith Stephen M

    2008-12-01

    Full Text Available Abstract MicroRNAs (miRNAs play diverse roles in regulating cellular and developmental functions. We have profiled the miRNA expression in peripheral blood mononuclear cells from 36 HIV-1 seropositive individuals and 12 normal controls. The HIV-1-positive individuals were categorized operationally into four classes based on their CD4+ T-cell counts and their viral loads. We report that specific miRNA signatures can be observed for each of the four classes.

  7. Identification of tissue microRNAs predictive of sunitinib activity in patients with metastatic renal cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Celia Prior

    Full Text Available To identify tissue microRNAs predictive of sunitinib activity in patients with metastatic renal-cell-carcinoma (MRCC and to evaluate in vitro their mechanism of action in sunitinib resistance.We screened 673 microRNAs using TaqMan Low-density-Arrays (TLDAs in tumors from MRCC patients with extreme phenotypes of marked efficacy and resistance to sunitinib, selected from an identification cohort (n = 41. The most relevant differentially expressed microRNAs were selected using bioinformatics-based target prediction analysis and quantified by qRT-PCR in tumors from patients presenting similar phenotypes selected from an independent cohort (n = 101. In vitro experiments were conducted to study the role of miR-942 in sunitinib resistance.TLDAs identified 64 microRNAs differentially expressed in the identification cohort. Seven candidates were quantified by qRT-PCR in the independent series. MiR-942 was the most accurate predictor of sunitinib efficacy (p = 0.0074. High expression of miR-942, miR-628-5p, miR-133a, and miR-484 was significantly associated with decreased time to progression and overall survival. These microRNAs were also overexpressed in the sunitinib resistant cell line Caki-2 in comparison with the sensitive cell line. MiR-942 overexpression in Caki-2 up-regulates MMP-9 and VEGF secretion which, in turn, promote HBMEC endothelial migration and sunitinib resistance.We identified differentially expressed microRNAs in MRCC patients presenting marked sensitivity or resistance to sunitinib. MiR-942 was the best predictor of efficacy. We describe a novel paracrine mechanism through which high miR-942 levels in MRCC cells up-regulates MMP-9 and VEGF secretion to enhance endothelial migration and sunitinib resistance. Our results support further validation of these miRNA in clinical confirmatory studies.

  8. MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma

    DEFF Research Database (Denmark)

    Larsen, Ann-Cathrine; Holst, Line; Kaczkowski, Bogumil

    2014-01-01

    Purpose: To determine the association of microRNA expression and chromosomal changes with metastasis and survival in uveal melanoma (UM). Methods: Thirty-six patients with UM were selected based on the metastatic status, and clinicopathological data were collected. Multiplex ligation-dependent pr...

  9. Rapid synthesis of macrocycles from diol precursors

    DEFF Research Database (Denmark)

    Wingstrand, Magnus; Madsen, Charlotte Marie; Clausen, Mads Hartvig

    2009-01-01

    A method for the formation of synthetic macrocycles with different ring sizes from diols is presented. Reacting a simple diol precursor with electrophilic reagents leads to a cyclic carbonate, sulfite or phosphate in a single step in 25-60% yield. Converting the cyclization precursor to a bis-ele...

  10. Precursors in photonic crystals - art. no. 618218

    NARCIS (Netherlands)

    Uitham, R.; Hoenders, B. J.; DeLaRue, RM; Viktorovitch, P; Lopez, C; Midrio, M

    2006-01-01

    We derive the Sommerfeld precursor and present the first calculations for the Brillouin precursor that result from the transmission of a pulse through a photonic crystal. The photonic crystal is modelled by a one-dimensional N-layer medium and the pulse is a generic electromagnetic plane wave packet

  11. The Sommerfeld precursor in photonic crystals

    NARCIS (Netherlands)

    Uitham, R; Hoenders, BJ

    2006-01-01

    We calculate the Sommerfeld precursor that results after transmission of a generic electromagnetic plane wave pulse with transverse electric polarization, through a one-dimensional rectangular N-layer photonic crystal with two slabs per layer. The shape of this precursor equals the shape of the

  12. Rare Drosha Splice Variants Are Deficient in MicroRNA Processing but Do Not Affect General MicroRNA Expression in Cancer Cells

    Directory of Open Access Journals (Sweden)

    Stefanie E. Grund

    2012-03-01

    Full Text Available Drosha is a key enzyme in microRNA biogenesis, generating the precursor miRNA (pre-miRNA by excising the stem-loop embedded in the primary transcripts (pri-miRNA. The specificity for the pri-miRNAs and determination of the cleavage site are provided by its binding partner DGCR8, which is necessary for efficient processing. The crucial Drosha domains for pri-miRNA cleavage are the middle part, the two enzymatic RNase III domains (RIIID, and the dsRNA binding domain (dsRBD in the C-terminus. Here, we identify alternatively spliced transcripts in human melanoma and NT2 cell lines, encoding C-terminally truncated Drosha proteins lacking part of the RIIIDb and the entire dsRBD. Proteins generated from these alternative splice variants fail to bind to DGCR8 but still interact with Ewing sarcoma protein (EWS. In vitro as well as in vivo, the Drosha splice variants are deficient in pri-miRNA processing. However, the aberrant transcripts in melanoma cells do not consistently reduce mature miRNA levels compared with melanoma cell lines lacking those splice variants, possibly owing to their limited abundance. Our findings show that alternative processing-deficient Drosha splice variants exist in melanoma cells. In elevated amounts, these alternatively spliced transcripts could provide one potential mechanism accounting for the deregulation of miRNAs in cancer cells. On the basis of our results, the search for alternative inactive splice variants might be fruitful in different tumor entities to unravel the molecular basis of the previously observed decreased microRNA processing efficiency in cancer.

  13. Progressing from Identification and Functional Analysis of Precursor Behavior to Treatment of Self-Injurious Behavior

    Science.gov (United States)

    Dracobly, Joseph D.; Smith, Richard G.

    2012-01-01

    This multiple-study experiment evaluated the utility of assessing and treating severe self-injurious behavior (SIB) based on the outcomes of a functional analysis of precursor behavior. In Study 1, a precursor to SIB was identified using descriptive assessment and conditional probability analyses. In Study 2, a functional analysis of precursor…

  14. MicroRNAs in mantle cell lymphoma

    DEFF Research Database (Denmark)

    Husby, Simon; Geisler, Christian; Grønbæk, Kirsten

    2013-01-01

    Mantle cell lymphoma (MCL) is a rare and aggressive subtype of non-Hodgkin lymphoma. New treatment modalities, including intensive induction regimens with immunochemotherapy and autologous stem cell transplant, have improved survival. However, many patients still relapse, and there is a need...... for novel therapeutic strategies. Recent progress has been made in the understanding of the role of microRNAs (miRNAs) in MCL. Comparisons of tumor samples from patients with MCL with their normal counterparts (naive B-cells) have identified differentially expressed miRNAs with roles in cellular growth...

  15. MicroRNA regulation of Autophagy

    DEFF Research Database (Denmark)

    Frankel, Lisa B; Lund, Anders H

    2012-01-01

    recently contributed to our understanding of the molecular mechanisms of the autophagy machinery, yet several gaps remain in our knowledge of this process. The discovery of microRNAs (miRNAs) established a new paradigm of post-transcriptional gene regulation and during the past decade these small non......RNAs to regulation of the autophagy pathway. This regulation occurs both through specific core pathway components as well as through less well-defined mechanisms. Although this field is still in its infancy, we are beginning to understand the potential implications of these initial findings, both from a pathological...

  16. MicroRNA Delivery for Regenerative Medicine

    OpenAIRE

    Peng, Bo; Chen, Yongming; Leong, Kam W.

    2015-01-01

    MicroRNA (miRNA) directs post-transcriptional regulation of a network of genes by targeting mRNA. Although relatively recent in development, many miRNAs direct differentiation of various stem cells including induced pluripotent stem cells (iPSCs), a major player in regenerative medicine. An effective and safe delivery of miRNA holds the key to translating miRNA technologies. Both viral and nonviral delivery systems have seen success in miRNA delivery, and each approach possesses advantages an...

  17. The interrelationships of mathematical precursors in kindergarten.

    Science.gov (United States)

    Cirino, Paul T

    2011-04-01

    This study evaluated the interrelations among cognitive precursors across quantitative, linguistic, and spatial attention domains that have been implicated for math achievement in young children. The dimensionality of the quantity precursors was evaluated in 286 kindergarteners via latent variable techniques, and the contribution of precursors from each domain was established for small sums addition. Results showed a five-factor structure for the quantity precursors, with the major distinction being between nonsymbolic and symbolic tasks. The overall model demonstrated good fit and strong predictive power (R(2)=55%) for addition number combinations. Linguistic and spatial attention domains showed indirect relationships with outcomes, with their effects mediated by symbolic quantity measures. These results have implications for the measurement of mathematical precursors and yield promise for predicting future math performance. Copyright © 2010 Elsevier Inc. All rights reserved.

  18. MicroRNAs in Coronary Heart Disease: Ready to Enter the Clinical Arena?

    Directory of Open Access Journals (Sweden)

    Elena Cavarretta

    2016-01-01

    Full Text Available Coronary artery disease (CAD and its complication remain the leading cause of mortality in industrialized countries despite great advances in terms of diagnosis, prognosis, and treatment options. MicroRNAs (miRNAs, small noncoding RNAs, act as posttranscriptional gene expression modulators and have been implicated as key regulators in several physiological and pathological processes linked to CAD. Circulating miRNAs have been evaluated as promising novel biomarkers of CAD, acute coronary syndromes, and acute myocardial infarction, with prognostic implications. Several challenges related to technical aspects, miRNAs normalization, drugs interaction, and quality reporting of statistical multivariable analysis of the miRNAs observational studies remain unresolved. MicroRNA-based therapies in cardiovascular diseases are not ready yet for human trials but definitely appealing. Through this review we will provide clinicians with a concise overview of the pros and cons of microRNAs.

  19. microRNA expression in the neural retina: Focus on Müller glia.

    Science.gov (United States)

    Quintero, Heberto; Lamas, Mónica

    2018-03-01

    The neural retina hosts a unique specialized type of macroglial cell that not only preserves retinal homeostasis, function, and integrity but also may serve as a source of new neurons during regenerative processes: the Müller cell. Precise microRNA-driven mechanisms of gene regulation impel and direct the processes of Müller glia lineage acquisition from retinal progenitors during development, the triggering of their response to retinal degeneration and, in some cases, Müller cell reprogramming and regenerative events. In this review we survey the recent reports describing, through functional assays, the regulatory role of microRNAs in Müller cell physiology, differentiation potential, and retinal pathology. We discuss also the evidence based on expression analysis that points out the relevance of a Müller glia-specific microRNA signature that would orchestrate these processes. © 2017 Wiley Periodicals, Inc.

  20. Identification of conserved microRNAs and their targets in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Hu, Jihong; Sun, Lulu; Ding, Yi

    2013-04-01

    The microRNAs (miRNAs) are a new class of non-protein coding small RNAs that regulate gene expression at the post-transcriptional level in plants. Although thousands of miRNAs have been identified in many plant species, little studies have been reported about chickpea microRNAs. In this study, 28 potential miRNA candidates belonging to 20 families were identified from 16 ESTs and 12 GSSs in chickpea using a comparative genome-based computational analysis. A total of 664 miRNA targets were predicted and some of them encoded transcription factors as well as genes that function in stress response, signal transduction, methylation and a variety of other metabolic processes. These findings lay the foundation for further understanding of miRNA function in the development of chickpea.

  1. MicroRNAs in sensorineural diseases of the ear

    Directory of Open Access Journals (Sweden)

    Kathy eUshakov

    2013-12-01

    Full Text Available Non-coding microRNAs have a fundamental role in gene regulation and expression in almost every multicellular organism. Only discovered in the last decade, microRNAs are already known to play a leading role in many aspects of disease. In the vertebrate inner ear, microRNAs are essential for controlling development and survival of hair cells. Moreover, dysregulation of microRNAs has been implicated in sensorineural hearing impairment, as well as in other ear diseases such as cholesteatomas, vestibular schwannomas and otitis media. Due to the inaccessibility of the ear in humans, animal models have provided the optimal tools to study microRNA expression and function, in particular mice and zebrafish. A major focus of current research has been to discover the targets of the microRNAs expressed in the inner ear, in order to determine the regulatory pathways of the auditory and vestibular systems. The potential for microRNA manipulation in development of therapeutic tools for hearing impairment is as yet unexplored, paving the way for future work in the field.

  2. Boron nitride ceramics from molecular precursors: synthesis, properties and applications.

    Science.gov (United States)

    Bernard, Samuel; Salameh, Chrystelle; Miele, Philippe

    2016-01-21

    Hexagonal boron nitride (h-BN) attracts considerable interest because its structure is similar to that of carbon graphite while it displays different properties which are of interest for environmental and green technologies. The polar nature of the B-N bond in sp(2)-bonded BN makes it a wide band gap insulator with different chemistry on its surface and particular physical and chemical properties such as a high thermal conductivity, a high temperature stability, a high resistance to corrosion and oxidation and a strong UV emission. It is chemically inert and nontoxic and has good environmental compatibility. h-BN also has enhanced physisorption properties due to the dipolar fields near its surface. Such properties are closely dependent on the processing method. Bottom-up approaches consist of transforming molecular precursors into non-oxide ceramics with retention of the structural units inherent to the precursor molecule. The purpose of the present review is to give an up-to-date overview on the most recent achievements in the preparation of h-BN from borazine-based molecular single-source precursors including borazine and 2,4,6-trichloroborazine through both vapor phase syntheses and methods in the liquid/solid state involving polymeric intermediates, called the Polymer-Derived Ceramics (PDCs) route. In particular, the effect of the chemistry, composition and architecture of the borazine-based precursors and derived polymers on the shaping ability as well as the properties of h-BN is particularly highlighted.

  3. RNAi therapeutics and applications of microRNAs in cancer treatment.

    Science.gov (United States)

    Uchino, Keita; Ochiya, Takahiro; Takeshita, Fumitaka

    2013-06-01

    RNA interference-based therapies are proving to be powerful tools for combating various diseases, including cancer. Scientists are researching the development of safe and efficient systems for the delivery of small RNA molecules, which are extremely fragile in serum, to target organs and cells in the human body. A dozen pre-clinical and clinical trials have been under way over the past few years involving biodegradable nanoparticles, lipids, chemical modification and conjugation. On the other hand, microRNAs, which control the balance of cellular biological processes, have been studied as attractive therapeutic targets in cancer treatment. In this review, we provide an overview of RNA interference-based therapeutics in clinical trials and discuss the latest technology for the systemic delivery of nucleic acid drugs. Furthermore, we focus on dysregulated microRNAs in human cancer, which have progressed in pre-clinical trials as therapeutic targets, and describe a wide range of strategies to control the expression levels of endogenous microRNAs. Further development of RNA interference technologies and progression of clinical trials will contribute to the achievement of practical applications of nucleic acid drugs.

  4. Environmental contaminants and microRNA regulation: Transcription factors as regulators of toxicant-altered microRNA expression

    Energy Technology Data Exchange (ETDEWEB)

    Sollome, James; Martin, Elizabeth [Department of Environmental Science & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill (United States); Sethupathy, Praveen [Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC (United States); Fry, Rebecca C., E-mail: rfry@unc.edu [Department of Environmental Science & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill (United States); Curriculum in Toxicology, School of Medicine, University of North Carolina, Chapel Hill, NC (United States)

    2016-12-01

    MicroRNAs (miRNAs) regulate gene expression by binding mRNA and inhibiting translation and/or inducing degradation of the associated transcripts. Expression levels of miRNAs have been shown to be altered in response to environmental toxicants, thus impacting cellular function and influencing disease risk. Transcription factors (TFs) are known to be altered in response to environmental toxicants and play a critical role in the regulation of miRNA expression. To date, environmentally-responsive TFs that are important for regulating miRNAs remain understudied. In a state-of-the-art analysis, we utilized an in silico bioinformatic approach to characterize potential transcriptional regulators of environmentally-responsive miRNAs. Using the miRStart database, genomic sequences of promoter regions for all available human miRNAs (n = 847) were identified and promoter regions were defined as − 1000/+500 base pairs from the transcription start site. Subsequently, the promoter region sequences of environmentally-responsive miRNAs (n = 128) were analyzed using enrichment analysis to determine overrepresented TF binding sites (TFBS). While most (56/73) TFs differed across environmental contaminants, a set of 17 TFs was enriched for promoter binding among miRNAs responsive to numerous environmental contaminants. Of these, one TF was common to miRNAs altered by the majority of environmental contaminants, namely SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 3 (SMARCA3). These identified TFs represent candidate common transcriptional regulators of miRNAs perturbed by environmental toxicants. - Highlights: • Transcription factors that regulate environmentally-modulated miRNA expression are understudied • Transcription factor binding sites (TFBS) located within DNA promoter regions of miRNAs were identified. • Specific transcription factors may serve as master regulators of environmentally-mediated microRNA expression.

  5. Environmental contaminants and microRNA regulation: Transcription factors as regulators of toxicant-altered microRNA expression

    International Nuclear Information System (INIS)

    Sollome, James; Martin, Elizabeth; Sethupathy, Praveen; Fry, Rebecca C.

    2016-01-01

    MicroRNAs (miRNAs) regulate gene expression by binding mRNA and inhibiting translation and/or inducing degradation of the associated transcripts. Expression levels of miRNAs have been shown to be altered in response to environmental toxicants, thus impacting cellular function and influencing disease risk. Transcription factors (TFs) are known to be altered in response to environmental toxicants and play a critical role in the regulation of miRNA expression. To date, environmentally-responsive TFs that are important for regulating miRNAs remain understudied. In a state-of-the-art analysis, we utilized an in silico bioinformatic approach to characterize potential transcriptional regulators of environmentally-responsive miRNAs. Using the miRStart database, genomic sequences of promoter regions for all available human miRNAs (n = 847) were identified and promoter regions were defined as − 1000/+500 base pairs from the transcription start site. Subsequently, the promoter region sequences of environmentally-responsive miRNAs (n = 128) were analyzed using enrichment analysis to determine overrepresented TF binding sites (TFBS). While most (56/73) TFs differed across environmental contaminants, a set of 17 TFs was enriched for promoter binding among miRNAs responsive to numerous environmental contaminants. Of these, one TF was common to miRNAs altered by the majority of environmental contaminants, namely SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 3 (SMARCA3). These identified TFs represent candidate common transcriptional regulators of miRNAs perturbed by environmental toxicants. - Highlights: • Transcription factors that regulate environmentally-modulated miRNA expression are understudied • Transcription factor binding sites (TFBS) located within DNA promoter regions of miRNAs were identified. • Specific transcription factors may serve as master regulators of environmentally-mediated microRNA expression

  6. Selected microRNAs define cell fate determination of murine central memory CD8 T cells.

    Directory of Open Access Journals (Sweden)

    Gonzalo Almanza

    2010-06-01

    Full Text Available During an immune response T cells enter memory fate determination, a program that divides them into two main populations: effector memory and central memory T cells. Since in many systems protection appears to be preferentially mediated by T cells of the central memory it is important to understand when and how fate determination takes place. To date, cell intrinsic molecular events that determine their differentiation remains unclear. MicroRNAs are a class of small, evolutionarily conserved RNA molecules that negatively regulate gene expression, causing translational repression and/or messenger RNA degradation. Here, using an in vitro system where activated CD8 T cells driven by IL-2 or IL-15 become either effector memory or central memory cells, we assessed the role of microRNAs in memory T cell fate determination. We found that fate determination to central memory T cells is under the balancing effects of a discrete number of microRNAs including miR-150, miR-155 and the let-7 family. Based on miR-150 a new target, KChIP.1 (K (+ channel interacting protein 1, was uncovered, which is specifically upregulated in developing central memory CD8 T cells. Our studies indicate that cell fate determination such as surface phenotype and self-renewal may be decided at the pre-effector stage on the basis of the balancing effects of a discrete number of microRNAs. These results may have implications for the development of T cell vaccines and T cell-based adoptive therapies.

  7. New research progress of microRNAs in retinoblastoma

    Directory of Open Access Journals (Sweden)

    Jing Zeng

    2014-11-01

    Full Text Available Retinoblastoma(RBis the most common intraocular malignancy of children with extremely poor prognosis. MicroRNAs are small non-coding single-stranded RNAs in eukaryotic cells, which regulate the expression of gene by mRNA degradation or translation inhibition. MicroRNAs, acting as oncogenes or tumor suppressor genes, are associated with the occurrence and development of RB directly, which is vital for the early diagnosis and clinical targeted therapy of RB. This review summarized the expression of microRNAs in RB and the related mechanism.

  8. Computational identification of 18 micrornas and their targets in three species of rose

    International Nuclear Information System (INIS)

    Baloch, I.A.; Barozai, M.Y.K.; Achakzai, A.K.K.

    2015-01-01

    MicroRNAs (miRNAs) are non-protein coding, small endogenous RNAs. Their length ranges from 18-26 nucleotides (nt). The miRNAs convergence property becomes a rational approach for the hunt of novel miRNAs in other organisms by homology search. As presently very little miRNAs are reported for rose species, so this study deals with the identification of miRNAs in different species of rose. Consequently 18 miRNA belonging to 17 miRNA families were identified in 3 species of rose (Rosa hybrid, Rosa chinensis and Rosa virginiana). All of the identified miRNA families (miR156, 160, 164, 166, 398, 482, 831, 837, 838, 841, 847, 3436, 3627, 6135, 6285, 6287 and 6288) are being reported for the first time in rose. Precursors of the identified miRNAs form stable minimum free energy (MFE) stem-loop structures and the mature miRNAs are found in the stem portions of their corresponding precursors. 11 putative targets of the miRNAs have also been identified. The identified targets are various proteins including transcription factors. Identification of 18 miRNAs will be supportive to explore the gene regulation phenomenon in various species of roses and it will be a good contribution for understanding the post transcriptional gene regulation in various stages of the life cycles of roses. (author)

  9. Small Molecule Targeting of a MicroRNA Associated with Hepatocellular Carcinoma.

    Science.gov (United States)

    Childs-Disney, Jessica L; Disney, Matthew D

    2016-02-19

    Development of precision therapeutics is of immense interest, particularly as applied to the treatment of cancer. By analyzing the preferred cellular RNA targets of small molecules, we discovered that 5"-azido neomycin B binds the Drosha processing site in the microRNA (miR)-525 precursor. MiR-525 confers invasive properties to hepatocellular carcinoma (HCC) cells. Although HCC is one of the most common cancers, treatment options are limited, making the disease often fatal. Herein, we find that addition of 5"-azido neomycin B and its FDA-approved precursor, neomycin B, to an HCC cell line selectively inhibits production of the mature miRNA, boosts a downstream protein, and inhibits invasion. Interestingly, neomycin B is a second-line agent for hepatic encephalopathy (HE) and bacterial infections due to cirrhosis. Our results provocatively suggest that neomycin B, or second-generation derivatives, may be dual functioning molecules to treat both HE and HCC. Collectively, these studies show that rational design approaches can be tailored to disease-associated RNAs to afford potential lead therapeutics.

  10. Evaluation of microRNA alignment techniques

    Science.gov (United States)

    Kaspi, Antony; El-Osta, Assam

    2016-01-01

    Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

  11. Immunomodulating microRNAs of mycobacterial infections.

    Science.gov (United States)

    Bettencourt, Paulo; Pires, David; Anes, Elsa

    2016-03-01

    MicroRNAs are a class of small non-coding RNAs that have emerged as key regulators of gene expression at the post-transcriptional level by sequence-specific binding to target mRNAs. Some microRNAs block translation, while others promote mRNA degradation, leading to a reduction in protein availability. A single miRNA can potentially regulate the expression of multiple genes and their encoded proteins. Therefore, miRNAs can influence molecular signalling pathways and regulate many biological processes in health and disease. Upon infection, host cells rapidly change their transcriptional programs, including miRNA expression, as a response against the invading microorganism. Not surprisingly, pathogens can also alter the host miRNA profile to their own benefit, which is of major importance to scientists addressing high morbidity and mortality infectious diseases such as tuberculosis. In this review, we present recent findings on the miRNAs regulation of the host response against mycobacterial infections, providing new insights into host-pathogen interactions. Understanding these findings and its implications could reveal new opportunities for designing better diagnostic tools, therapies and more effective vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Customization of Artificial MicroRNA Design.

    Science.gov (United States)

    Van Vu, Tien; Do, Vinh Nang

    2017-01-01

    RNAi approaches, including microRNA (miRNA) regulatory pathway, offer great tools for functional characterization of unknown genes. Moreover, the applications of artificial microRNA (amiRNA) in the field of plant transgenesis have also been advanced to engineer pathogen-resistant or trait-improved transgenic plants. Until now, despite the high potency of amiRNA approach, no commercial plant cultivar expressing amiRNAs with improved traits has been released yet. Beside the issues of biosafety policies, the specificity and efficacy of amiRNAs are of major concerns. Sufficient cares should be taken for the specificity and efficacy of amiRNAs due to their potential off-target effects and other issues relating to in vivo expression of pre-amiRNAs. For these reasons, the proper design of amiRNAs with the lowest off-target possibility is very important for successful applications of the approach in plant. Therefore, there are many studies with the aim to improve the amiRNA design and amiRNA expressing backbones for obtaining better specificity and efficacy. However, the requirement for an efficient reference for the design is still needed. In the present chapter, we attempt to summarize and discuss all the major concerns relating to amiRNA design with the hope to provide a significant guideline for this approach.

  13. Operational experience feedback with precursor analysis

    International Nuclear Information System (INIS)

    Koncar, M.; Ferjancic, M.; Muehleisen, A.; Vojnovic, D.

    2003-01-01

    Experience of practical operation is a valuable source of information for improving the safety and reliability of nuclear power plants. Operational experience feedback (Olef) system manages this aspect of NPP operation. The traditional ways of investigating operational events, such as the root cause analysis (RCA), are predominantly qualitative. RCA as a part of the Olef system provides technical guidance and management expectations in the conduct of assessing the root cause to prevent recurrence, covering the following areas: conditions preceding the event, sequence of events, equipment performance and system response, human performance considerations, equipment failures, precursors to the event, plant response and follow-up, radiological considerations, regulatory process considerations and safety significance. The root cause of event is recognized when there is no known answer on question 'why has it happened?' regarding relevant condition that may have affected the event. At that point the Olef is proceeding by actions taken in response to events, utilization, dissemination and exchange of operating experience information and at the end reviewing the effectiveness of the Olef. Analysis of the event and the selection of recommended corrective/preventive actions for implementation and prioritization can be enhanced by taking into account the information and insights derived from Pasa-based analysis. A Pasa based method, called probabilistic precursor event analysis (PPE A) provides a complement to the RCA approach by focusing on how an event might have developed adversely, and implies the mapping of an operational event on a probabilistic risk model of the plant in order to obtain a quantitative assessment of the safety significance of the event PSA based event analysis provides, due to its quantitative nature, appropriate prioritization of corrective actions. PPEA defines requirements for PSA model and code, identifies input requirements and elaborates following

  14. Laser microdissection of sensory organ precursor cells of Drosophila microchaetes.

    Directory of Open Access Journals (Sweden)

    Eulalie Buffin

    Full Text Available BACKGROUND: In Drosophila, each external sensory organ originates from the division of a unique precursor cell (the sensory organ precursor cell or SOP. Each SOP is specified from a cluster of equivalent cells, called a proneural cluster, all of them competent to become SOP. Although, it is well known how SOP cells are selected from proneural clusters, little is known about the downstream genes that are regulated during SOP fate specification. METHODOLOGY/PRINCIPAL FINDINGS: In order to better understand the mechanism involved in the specification of these precursor cells, we combined laser microdissection, toisolate SOP cells, with transcriptome analysis, to study their RNA profile. Using this procedure, we found that genes that exhibit a 2-fold or greater expression in SOPs versus epithelial cells were mainly associated with Gene Ontology (GO terms related with cell fate determination and sensory organ specification. Furthermore, we found that several genes such as pebbled/hindsight, scabrous, miranda, senseless, or cut, known to be expressed in SOP cells by independent procedures, are particularly detected in laser microdissected SOP cells rather than in epithelial cells. CONCLUSIONS/SIGNIFICANCE: These results confirm the feasibility and the specificity of our laser microdissection based procedure. We anticipate that this analysis will give new insight into the selection and specification of neural precursor cells.

  15. MicroRNA-22 impairs anti-tumor ability of dendritic cells by targeting p38.

    Directory of Open Access Journals (Sweden)

    Xue Liang

    Full Text Available Dendritic cells (DCs play a critical role in triggering anti-tumor immune responses. Their intracellular p38 signaling is of great importance in controlling DC activity. In this study, we identified microRNA-22 (miR-22 as a microRNA inhibiting p38 protein expression by directly binding to the 3' untranslated region (3'UTR of its mRNA. The p38 down-regulation further interfered with the synthesis of DC-derived IL-6 and the differentiation of DC-driven Th17 cells. Moreover, overexpression of miR-22 in DCs impaired their tumor-suppressing ability while miR-22 inhibitor could reverse this phenomenon and improve the curative effect of DC-based immunotherapy. Thus, our results highlight a suppressive role for miR-22 in the process of DC-invoked anti-tumor immunity and that blocking this microRNA provides a new strategy for generating potent DC vaccines for patients with cancer.

  16. Effects of MicroRNA on Regulatory T Cells and Implications for Adoptive Cellular Therapy to Ameliorate Graft-versus-Host Disease

    Directory of Open Access Journals (Sweden)

    Keli L. Hippen

    2018-01-01

    Full Text Available Regulatory T cells (Tregs are key mediators of the immune system. MicroRNAs (miRNAs are a family of ~22 nucleotide non-coding RNAs that are processed from longer precursors by the RNases Drosha and Dicer. miRNA regulates protein expression posttranscriptionally through mRNA destabilization or translational silencing. A critical role for miRNA in Treg function was initially discovered when both Dicer and Drosha knockout (KO mice were found to develop a fatal autoimmune disease phenotypically similar to Foxp3 KO mice.

  17. Roles of microRNA-15 family in normal and pathological late lung development

    OpenAIRE

    Sakkas, Elpidoforos

    2016-01-01

    MicroRNAs are key regulators of organogenesis and during the last years many studies focused on microRNA expression during embryonic development. To date, there is no study to report possible roles of microRNAs in late lung development and especially during the alveolarization process. The objective of this study was to identify microRNAs that are deregulated under hyperoxic conditions and to assess whether microRNA expression can be modulated in vivo. Lung microRNA expression screening wa...

  18. Biochemical Removal of HAP Precursors From Coal

    International Nuclear Information System (INIS)

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE's interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals

  19. Progress in molecular precursors for electronic materials

    Energy Technology Data Exchange (ETDEWEB)

    Buhro, W.E. [Washington Univ., St. Louis, MO (United States)

    1996-09-01

    Molecular-precursor chemistry provides an essential underpinning to all electronic-materials technologies, including photovoltaics and related areas of direct interest to the DOE. Materials synthesis and processing is a rapidly developing field in which advances in molecular precursors are playing a major role. This article surveys selected recent research examples that define the exciting current directions in molecular-precursor science. These directions include growth of increasingly complex structures and stoichiometries, surface-selective growth, kinetic growth of metastable materials, growth of size-controlled quantum dots and quantum-dot arrays, and growth at progressively lower temperatures. Continued progress in molecular-precursor chemistry will afford precise control over the crystal structures, nanostructures, and microstructures of electronic materials.

  20. Biochemical Removal of HAP Precursors From Coal

    Energy Technology Data Exchange (ETDEWEB)

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE`s interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals.

  1. Probabilistic precursor analysis - an application of PSA

    International Nuclear Information System (INIS)

    Hari Prasad, M.; Gopika, V.; Sanyasi Rao, V.V.S.; Vaze, K.K.

    2011-01-01

    Incidents are inevitably part of the operational life of any complex industrial facility, and it is hard to predict how various contributing factors combine to cause the outcome. However, it should be possible to detect the existence of latent conditions that, together with the triggering failure(s), result in abnormal events. These incidents are called precursors. Precursor study, by definition, focuses on how a particular event might have adversely developed. This paper focuses on the events which can be analyzed to assess their potential to develop into core damage situation and looks into extending Probabilistic Safety Assessment techniques to precursor studies and explains the benefits through a typical case study. A preliminary probabilistic precursor analysis has been carried out for a typical NPP. The major advantages of this approach are the strong potential for augmenting event analysis which is currently carried out purely on deterministic basis. (author)

  2. nanoparticles synthesized by citrate precursor m

    African Journals Online (AJOL)

    user

    (M=Co, Cu) nanoparticles synthesized by citrate precursor method ... The structural characterization was carried out using an X-ray Diffractometer (Rikagu Miniflex, Japan) ..... His current area of interest includes magnetic nanomaterials.

  3. Identification and validation of human papillomavirus encoded microRNAs.

    Directory of Open Access Journals (Sweden)

    Kui Qian

    Full Text Available We report here identification and validation of the first papillomavirus encoded microRNAs expressed in human cervical lesions and cell lines. We established small RNA libraries from ten human papillomavirus associated cervical lesions including cancer and two human papillomavirus harboring cell lines. These libraries were sequenced using SOLiD 4 technology. We used the sequencing data to predict putative viral microRNAs and discovered nine putative papillomavirus encoded microRNAs. Validation was performed for five candidates, four of which were successfully validated by qPCR from cervical tissue samples and cell lines: two were encoded by HPV 16, one by HPV 38 and one by HPV 68. The expression of HPV 16 microRNAs was further confirmed by in situ hybridization, and colocalization with p16INK4A was established. Prediction of cellular target genes of HPV 16 encoded microRNAs suggests that they may play a role in cell cycle, immune functions, cell adhesion and migration, development, and cancer. Two putative viral target sites for the two validated HPV 16 miRNAs were mapped to the E5 gene, one in the E1 gene, two in the L1 gene and one in the LCR region. This is the first report to show that papillomaviruses encode their own microRNA species. Importantly, microRNAs were found in libraries established from human cervical disease and carcinoma cell lines, and their expression was confirmed in additional tissue samples. To our knowledge, this is also the first paper to use in situ hybridization to show the expression of a viral microRNA in human tissue.

  4. The Role of MicroRNAs in Pancreatitis

    Science.gov (United States)

    2015-10-01

    AD______________ AWARD NUMBER: W81XWH-14-1-0469 TITLE: The Role of microRNAs in Pancreatitis PRINCIPAL INVESTIGATOR: Li, Yong RECIPIENT...The Role of MicroRNAs in Pancreatitis 5b. GRANT NUMBER W81XWH-14-1-0469 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Li, Yong 5e...AVAILABILITY STATEMENT Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Pancreatitis (inflammation of the

  5. Regulation of Corticosteroidogenic Genes by MicroRNAs

    Directory of Open Access Journals (Sweden)

    Stacy Robertson

    2017-01-01

    Full Text Available The loss of normal regulation of corticosteroid secretion is important in the development of cardiovascular disease. We previously showed that microRNAs regulate the terminal stages of corticosteroid biosynthesis. Here, we assess microRNA regulation across the whole corticosteroid pathway. Knockdown of microRNA using Dicer1 siRNA in H295R adrenocortical cells increased levels of CYP11A1, CYP21A1, and CYP17A1 mRNA and the secretion of cortisol, corticosterone, 11-deoxycorticosterone, 18-hydroxycorticosterone, and aldosterone. Bioinformatic analysis of genes involved in corticosteroid biosynthesis or metabolism identified many putative microRNA-binding sites, and some were selected for further study. Manipulation of individual microRNA levels demonstrated a direct effect of miR-125a-5p and miR-125b-5p on CYP11B2 and of miR-320a-3p levels on CYP11A1 and CYP17A1 mRNA. Finally, comparison of microRNA expression profiles from human aldosterone-producing adenoma and normal adrenal tissue showed levels of various microRNAs, including miR-125a-5p to be significantly different. This study demonstrates that corticosteroidogenesis is regulated at multiple points by several microRNAs and that certain of these microRNAs are differentially expressed in tumorous adrenal tissue, which may contribute to dysregulation of corticosteroid secretion. These findings provide new insights into the regulation of corticosteroid production and have implications for understanding the pathology of disease states where abnormal hormone secretion is a feature.

  6. Planar half-cell shaped precursor body

    DEFF Research Database (Denmark)

    2015-01-01

    The invention relates to a half-cell shaped precursor body of either anode type or cathode type, the half-cell shaped precursor body being prepared to be free sintered to form a sintered or pre-sintered half-cell being adapted to be stacked in a solid oxide fuel cell stack. The obtained half......-cell has an improved planar shape, which remains planar also after a sintering process and during temperature fluctuations....

  7. A methodology for analyzing precursors to earthquake-initiated and fire-initiated accident sequences

    International Nuclear Information System (INIS)

    Budnitz, R.J.; Lambert, H.E.; Apostolakis, G.

    1998-04-01

    This report covers work to develop a methodology for analyzing precursors to both earthquake-initiated and fire-initiated accidents at commercial nuclear power plants. Currently, the U.S. Nuclear Regulatory Commission sponsors a large ongoing project, the Accident Sequence Precursor project, to analyze the safety significance of other types of accident precursors, such as those arising from internally-initiated transients and pipe breaks, but earthquakes and fires are not within the current scope. The results of this project are that: (1) an overall step-by-step methodology has been developed for precursors to both fire-initiated and seismic-initiated potential accidents; (2) some stylized case-study examples are provided to demonstrate how the fully-developed methodology works in practice, and (3) a generic seismic-fragility date base for equipment is provided for use in seismic-precursors analyses. 44 refs., 23 figs., 16 tabs

  8. MicroRNA expression characterizes oligometastasis(es).

    Science.gov (United States)

    Lussier, Yves A; Xing, H Rosie; Salama, Joseph K; Khodarev, Nikolai N; Huang, Yong; Zhang, Qingbei; Khan, Sajid A; Yang, Xinan; Hasselle, Michael D; Darga, Thomas E; Malik, Renuka; Fan, Hanli; Perakis, Samantha; Filippo, Matthew; Corbin, Kimberly; Lee, Younghee; Posner, Mitchell C; Chmura, Steven J; Hellman, Samuel; Weichselbaum, Ralph R

    2011-01-01

    Cancer staging and treatment presumes a division into localized or metastatic disease. We proposed an intermediate state defined by ≤ 5 cumulative metastasis(es), termed oligometastases. In contrast to widespread polymetastases, oligometastatic patients may benefit from metastasis-directed local treatments. However, many patients who initially present with oligometastases progress to polymetastases. Predictors of progression could improve patient selection for metastasis-directed therapy. Here, we identified patterns of microRNA expression of tumor samples from oligometastatic patients treated with high-dose radiotherapy. Patients who failed to develop polymetastases are characterized by unique prioritized features of a microRNA classifier that includes the microRNA-200 family. We created an oligometastatic-polymetastatic xenograft model in which the patient-derived microRNAs discriminated between the two metastatic outcomes. MicroRNA-200c enhancement in an oligometastatic cell line resulted in polymetastatic progression. These results demonstrate a biological basis for oligometastases and a potential for using microRNA expression to identify patients most likely to remain oligometastatic after metastasis-directed treatment.

  9. MicroRNA expression characterizes oligometastasis(es.

    Directory of Open Access Journals (Sweden)

    Yves A Lussier

    Full Text Available Cancer staging and treatment presumes a division into localized or metastatic disease. We proposed an intermediate state defined by ≤ 5 cumulative metastasis(es, termed oligometastases. In contrast to widespread polymetastases, oligometastatic patients may benefit from metastasis-directed local treatments. However, many patients who initially present with oligometastases progress to polymetastases. Predictors of progression could improve patient selection for metastasis-directed therapy.Here, we identified patterns of microRNA expression of tumor samples from oligometastatic patients treated with high-dose radiotherapy.Patients who failed to develop polymetastases are characterized by unique prioritized features of a microRNA classifier that includes the microRNA-200 family. We created an oligometastatic-polymetastatic xenograft model in which the patient-derived microRNAs discriminated between the two metastatic outcomes. MicroRNA-200c enhancement in an oligometastatic cell line resulted in polymetastatic progression.These results demonstrate a biological basis for oligometastases and a potential for using microRNA expression to identify patients most likely to remain oligometastatic after metastasis-directed treatment.

  10. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

    Science.gov (United States)

    2014-01-01

    Background Non-coding sequences such as microRNAs have important roles in disease processes. Computational microRNA target identification (CMTI) is becoming increasingly important since traditional experimental methods for target identification pose many difficulties. These methods are time-consuming, costly, and often need guidance from computational methods to narrow down candidate genes anyway. However, most CMTI methods are computationally demanding, since they need to handle not only several million query microRNA and reference RNA pairs, but also several million nucleotide comparisons within each given pair. Thus, the need to perform microRNA identification at such large scale has increased the demand for parallel computing. Methods Although most CMTI programs (e.g., the miRanda algorithm) are based on a modified Smith-Waterman (SW) algorithm, the existing parallel SW implementations (e.g., CUDASW++ 2.0/3.0, SWIPE) are unable to meet this demand in CMTI tasks. We present CUDA-miRanda, a fast microRNA target identification algorithm that takes advantage of massively parallel computing on Graphics Processing Units (GPU) using NVIDIA's Compute Unified Device Architecture (CUDA). CUDA-miRanda specifically focuses on the local alignment of short (i.e., ≤ 32 nucleotides) sequences against longer reference sequences (e.g., 20K nucleotides). Moreover, the proposed algorithm is able to report multiple alignments (up to 191 top scores) and the corresponding traceback sequences for any given (query sequence, reference sequence) pair. Results Speeds over 5.36 Giga Cell Updates Per Second (GCUPs) are achieved on a server with 4 NVIDIA Tesla M2090 GPUs. Compared to the original miRanda algorithm, which is evaluated on an Intel Xeon E5620@2.4 GHz CPU, the experimental results show up to 166 times performance gains in terms of execution time. In addition, we have verified that the exact same targets were predicted in both CUDA-miRanda and the original mi

  11. TargetSpy: a supervised machine learning approach for microRNA target prediction.

    Science.gov (United States)

    Sturm, Martin; Hackenberg, Michael; Langenberger, David; Frishman, Dmitrij

    2010-05-28

    Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved) seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences.In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I) no seed match requirement, II) seed match requirement, and III) conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed) predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on mouse and performs well in human and drosophila

  12. TargetSpy: a supervised machine learning approach for microRNA target prediction

    Directory of Open Access Journals (Sweden)

    Langenberger David

    2010-05-01

    Full Text Available Abstract Background Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. Results We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences. In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I no seed match requirement, II seed match requirement, and III conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Conclusion Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on

  13. Hydrodeoxygenation of coal using organometallic catalyst precursors

    Science.gov (United States)

    Kirby, Stephen R.

    2002-04-01

    coals. Trends within the data were similar to those reported by other authors. Based on the conclusions from both the model compound studies and the coal analysis, predictions were made of the catalyst precursors' performance in the HDO of the three selected coals. It was concluded that CoMo-T2 is a desirable catalyst precursor for the HDO of coals (particularly low-rank coals), but that an optimum set of conditions must be determined to take full advantage of its HDO ability. (Abstract shortened by UMI.)

  14. MicroRNAs in the Hypothalamus

    DEFF Research Database (Denmark)

    Meister, Björn; Herzer, Silke; Silahtaroglu, Asli

    2013-01-01

    MicroRNAs (miRNAs) are short (∼22 nucleotides) non-coding ribonucleic acid (RNA) molecules that negatively regulate the expression of protein-coding genes. Posttranscriptional silencing of target genes by miRNA is initiated by binding to the 3'-untranslated regions of target mRNAs, resulting...... of the hypothalamus and miRNAs have recently been shown to be important regulators of hypothalamic control functions. The aim of this review is to summarize some of the current knowledge regarding the expression and role of miRNAs in the hypothalamus.......RNA molecules are abundantly expressed in tissue-specific and regional patterns and have been suggested as potential biomarkers, disease modulators and drug targets. The central nervous system is a prominent site of miRNA expression. Within the brain, several miRNAs are expressed and/or enriched in the region...

  15. MicroRNA Implication in Cancer

    Directory of Open Access Journals (Sweden)

    Iker BADIOLA

    2010-03-01

    Full Text Available MicroRNAs (miRNA are a new class of posttranscriptional regulators. These small non-coding RNAs regulate the expression of target mRNA transcripts and are linked to several human disease such as Alzheimer, cancer or heart disease. But it has been the cancer disease which has experimented the major number of studies of miRNA linked to the disease progression. In the last years it has been reported the deregulation pattern of the miRNAs in malignant cells which have disrupted the control of the proliferation, differentiation or apoptosis. The evidence of the presence of specific miRNA deregulated in concrete cancer types has become the miRNAs like possible biomarkers and therapeutic targets. The specific miRNA patterns deregulated in concrete cancer cell types open new opportunities to the diagnosis and therapy.

  16. Neurodegenerative Disorders Treatment: The MicroRNA Role.

    Science.gov (United States)

    Ridolfi, Barbara; Abdel-Haq, Hanin

    2017-01-01

    Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, Huntington's disease and prion disease are not timely and effectively treated using conventional therapies. This emphasizes the need for alternative therapeutic approaches. In this respect, gene-based therapies have been adopted as potentially feasible alternative therapies, where the microRNA (miRNA) approach has experienced a great explosion in recent years. Because miRNAs have been shown to be implicated in the pathogenesis of several diseases including neurodegenerative diseases, they are intensely studied as candidates for diagnostic and prognostic biomarkers, as predictors of drug response and as therapeutic agents. In this review, we evaluate the feasibility of both direct and indirect miRNA mimics and inhibitors toward the regulation of neurodegenerative-related genes both in vivo and in vitro models, highlight the advantages and drawbacks associated with miRNA-based therapy, and summarize the relevant techniques and approaches attempted to deliver miRNAs to the central nervous system for therapeutic purposes, with particular regard to the exosomes. Additionally, we describe a new approach that holds great promise for the treatment of a wide range of diseases including neurodegenerative disorders. This approach is based on addressing the incorporation of miRNAs into exosomes to increase the quantity and quality of miRNA packed and delivered to the central nervous system and other sites of action. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. MicroRNAs and drug addiction

    Directory of Open Access Journals (Sweden)

    Paul J Kenny

    2013-05-01

    Full Text Available Drug addiction is considered a disorder of neuroplasticity in brain reward and cognition systems resulting from aberrant activation of gene expression programs in response to prolonged drug consumption. Noncoding RNAs are key regulators of almost all aspects of cellular physiology. MicroRNAs (miRNAs are small (~21–23 nucleotides noncoding RNA transcripts that regulate gene expression at the post-transcriptional level. Recently, microRNAs were shown to play key roles in the drug-induced remodeling of brain reward systems that likely drives the emergence of addiction. Here, we review evidence suggesting that one particular miRNA, miR-212, plays a particularly prominent role in vulnerability to cocaine addiction. We review evidence showing that miR-212 expression is increased in the dorsal striatum of rats that show compulsive-like cocaine-taking behaviors. Increases in miR-212 expression appear to protect against cocaine addiction, as virus-mediated striatal miR-212 over-expression decreases cocaine consumption in rats. Conversely, disruption of striatal miR-212 signaling using an antisense oligonucleotide increases cocaine intake. We also review data that identify two mechanisms by which miR-212 may regulate cocaine intake. First, miR-212 has been shown to amplify striatal CREB signaling through a mechanism involving activation of Raf1 kinase. Second, miR-212 was also shown to regulate cocaine intake by repressing striatal expression of methyl CpG binding protein 2 (MeCP2, consequently decreasing protein levels of brain-derived neurotrophic factor (BDNF. The concerted actions of miR-212 on striatal CREB and MeCP2/BDNF activity greatly attenuate the motivational effects of cocaine. These findings highlight the unique role for miRNAs in simultaneously controlling multiple signaling cascades implicated in addiction.

  18. microRNAs and lipid metabolism

    Science.gov (United States)

    Aryal, Binod; Singh, Abhishek K.; Rotllan, Noemi; Price, Nathan; Fernández-Hernando, Carlos

    2017-01-01

    Purpose of review Work over the last decade has identified the important role of microRNAs (miRNAS) in regulating lipoprotein metabolism and associated disorders including metabolic syndrome, obesity and atherosclerosis. This review summarizes the most recent findings in the field, highlighting the contribution of miRNAs in controlling low-density lipoprotein (LDL) and high-density lipoprotein (HDL) metabolism. Recent findings A number of miRNAs have emerged as important regulators of lipid metabolism, including miR-122 and miR-33. Work over the last two years has identified additional functions of miR-33 including the regulation of macrophage activation and mitochondrial metabolism. Moreover, it has recently been shown that miR-33 regulates vascular homeostasis and cardiac adaptation in response to pressure overload. In addition to miR-33 and miR-122, recent GWAS have identified single nucleotide polymorphisms (SNP) in the proximity of miRNAs genes associated with abnormal levels of circulating lipids in humans. Several of these miRNA, such as miR-148a and miR-128-1, target important proteins that regulate cellular cholesterol metabolism, including the low-density lipoprotein receptor (LDLR) and the ATP-binding cassette A1 (ABCA1). Summary microRNAs have emerged as critical regulators of cholesterol metabolism and promising therapeutic targets for treating cardiometabolic disorders including atherosclerosis. Here, we discuss the recent findings in the field highlighting the novel mechanisms by which miR-33 controls lipid metabolism and atherogenesis and the identification of novel miRNAs that regulate LDL metabolism. Finally, we summarize the recent findings that identified miR-33 as an important non-coding RNA that controls cardiovascular homeostasis independent of its role in regulating lipid metabolism. PMID:28333713

  19. Modelling earth current precursors in earthquake prediction

    Directory of Open Access Journals (Sweden)

    R. Di Maio

    1997-06-01

    Full Text Available This paper deals with the theory of earth current precursors of earthquake. A dilatancy-diffusion-polarization model is proposed to explain the anomalies of the electric potential, which are observed on the ground surface prior to some earthquakes. The electric polarization is believed to be the electrokinetic effect due to the invasion of fluids into new pores, which are opened inside a stressed-dilated rock body. The time and space variation of the distribution of the electric potential in a layered earth as well as in a faulted half-space is studied in detail. It results that the surface response depends on the underground conductivity distribution and on the relative disposition of the measuring dipole with respect to the buried bipole source. A field procedure based on the use of an areal layout of the recording sites is proposed, in order to obtain the most complete information on the time and space evolution of the precursory phenomena in any given seismic region.

  20. microRNAs Associated with Drought Response in the Bioenergy Crop Sugarcane (Saccharum spp.)

    Science.gov (United States)

    Vilela, Romel Duarte; Costa, Gustavo Gilson Lacerda; Dias, Lara Isys; Endres, Laurício; Menossi, Marcelo

    2012-01-01

    Sugarcane (Saccharum spp.) is one of the most important crops in the world. Drought stress is a major abiotic stress factor that significantly reduces sugarcane yields. However the gene network that mediates plant responses to water stress remains largely unknown in several crop species. Although several microRNAs that mediate post-transcriptional regulation during water stress have been described in other species, the role of the sugarcane microRNAs during drought stress has not been studied. The objective of this work was to identify sugarcane miRNAs that are differentially expressed under drought stress and to correlate this expression with the behavior of two sugarcane cultivars with different drought tolerances. The sugarcane cultivars RB867515 (higher drought tolerance) and RB855536 (lower drought tolerance) were cultivated in a greenhouse for three months and then subjected to drought for 2, 4, 6 or 8 days. By deep sequencing of small RNAs, we were able to identify 18 miRNA families. Among all of the miRNAs thus identified, seven were differentially expressed during drought. Six of these miRNAs were differentially expressed at two days of stress, and five miRNAs were differentially expressed at four days. The expression levels of five miRNAs (ssp-miR164, ssp-miR394, ssp-miR397, ssp-miR399-seq 1 and miR528) were validated by RT-qPCR (quantitative reverse transcriptase PCR). Six precursors and the targets of the differentially expressed miRNA were predicted using an in silico approach and validated by RT-qPCR; many of these targets may play important roles in drought tolerance. These findings constitute a significant increase in the number of identified miRNAs in sugarcane and contribute to the elucidation of the complex regulatory network that is activated by drought stress. PMID:23071617

  1. Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies

    Directory of Open Access Journals (Sweden)

    Fedele Vita

    2006-06-01

    Full Text Available Abstract Background Recent studies indicate that microRNAs (miRNAs are mechanistically involved in the development of various human malignancies, suggesting that they represent a promising new class of cancer biomarkers. However, previously reported methods for measuring miRNA expression consume large amounts of tissue, prohibiting high-throughput miRNA profiling from typically small clinical samples such as excision or core needle biopsies of breast or prostate cancer. Here we describe a novel combination of linear amplification and labeling of miRNA for highly sensitive expression microarray profiling requiring only picogram quantities of purified microRNA. Results Comparison of microarray and qRT-PCR measured miRNA levels from two different prostate cancer cell lines showed concordance between the two platforms (Pearson correlation R2 = 0.81; and extension of the amplification, labeling and microarray platform was successfully demonstrated using clinical core and excision biopsy samples from breast and prostate cancer patients. Unsupervised clustering analysis of the prostate biopsy microarrays separated advanced and metastatic prostate cancers from pooled normal prostatic samples and from a non-malignant precursor lesion. Unsupervised clustering of the breast cancer microarrays significantly distinguished ErbB2-positive/ER-negative, ErbB2-positive/ER-positive, and ErbB2-negative/ER-positive breast cancer phenotypes (Fisher exact test, p = 0.03; as well, supervised analysis of these microarray profiles identified distinct miRNA subsets distinguishing ErbB2-positive from ErbB2-negative and ER-positive from ER-negative breast cancers, independent of other clinically important parameters (patient age; tumor size, node status and proliferation index. Conclusion In sum, these findings demonstrate that optimized high-throughput microRNA expression profiling offers novel biomarker identification from typically small clinical samples such as breast

  2. MicroRNAs and Target Genes As Biomarkers for the Diagnosis of Early Onset of Parkinson Disease

    Directory of Open Access Journals (Sweden)

    Ahmad R. Arshad

    2017-10-01

    Full Text Available Among the neurodegenerative disorders, Parkinson's disease (PD ranks as the second most common disorder with a higher prevalence in individuals aged over 60 years old. Younger individuals may also be affected with PD which is known as early onset PD (EOPD. Despite similarities between the characteristics of EOPD and late onset PD (LODP, EOPD patients experience much longer disease manifestations and poorer quality of life. Although some individuals are more prone to have EOPD due to certain genetic alterations, the molecular mechanisms that differentiate between EOPD and LOPD remains unclear. Recent findings in PD patients revealed that there were differences in the genetic profiles of PD patients compared to healthy controls, as well as between EOPD and LOPD patients. There were variants identified that correlated with the decline of cognitive and motor symptoms as well as non-motor symptoms in PD. There were also specific microRNAs that correlated with PD progression, and since microRNAs have been shown to be involved in the maintenance of neuronal development, mitochondrial dysfunction and oxidative stress, there is a strong possibility that these microRNAs can be potentially used to differentiate between subsets of PD patients. PD is mainly diagnosed at the late stage, when almost majority of the dopaminergic neurons are lost. Therefore, identification of molecular biomarkers for early detection of PD is important. Given that miRNAs are crucial in controlling the gene expression, these regulatory microRNAs and their target genes could be used as biomarkers for early diagnosis of PD. In this article, we discussed the genes involved and their regulatory miRNAs, regarding their roles in PD progression, based on the findings of significantly altered microRNAs in EOPD studies. We also discussed the potential of these miRNAs as molecular biomarkers for early diagnosis.

  3. MicroRNA-29b modulates innate and antigen-specific immune responses in mouse models of autoimmunity.

    Directory of Open Access Journals (Sweden)

    Apolline Salama

    Full Text Available In addition to important regulatory roles in gene expression through RNA interference, it has recently been shown that microRNAs display immune stimulatory effects through direct interaction with receptors of innate immunity of the Toll-like receptor family, aggravating neuronal damage and tumour growth. Yet no evidence exists on consequences of microRNA immune stimulatory actions in the context of an autoimmune disease. Using microRNA analogues, we here show that pancreatic beta cell-derived microRNA sequences induce pro-inflammatory (TNFa, IFNa, IL-12, IL-6 or suppressive (IL-10 cytokine secretion by primary mouse dendritic cells in a sequence-dependent manner. For miR-29b, immune stimulation in RAW264.7 macrophages involved the endosomal Toll-like receptor-7, independently of the canonical RNA interference pathway. In vivo, the systemic delivery of miR-29b activates CD11b+B220- myeloid and CD11b-B220+ plasmacytoid dendritic cells and induces IFNa, TNFa and IL-6 production in the serum of recipient mice. Strikingly, in a murine model of adoptive transfer of autoimmune diabetes, miR-29b reduces the cytolytic activity of transferred effector CD8+ T-cells, insulitis and disease incidence in a single standalone intervention. Endogenous miR-29b, spontaneously released from beta-cells within exosomes, stimulates TNFa secretion from spleen cells isolated from diabetes-prone NOD mice in vitro. Hence, microRNA sequences modulate innate and ongoing adaptive immune responses raising the question of their potential role in the breakdown of tolerance and opening up new applications for microRNA-based immune therapy.

  4. A circulating microrna profile is associated with late-stage neovascular age-related macular degeneration.

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    Felix Grassmann

    Full Text Available Age-related macular degeneration (AMD is the leading cause of severe vision impairment in Western populations over 55 years. A growing number of gene variants have been identified which are strongly associated with an altered risk to develop AMD. Nevertheless, gene-based biomarkers which could be dysregulated at defined stages of AMD may point toward key processes in disease mechanism and thus may support efforts to design novel treatment regimens for this blinding disorder. Circulating microRNAs (cmiRNAs which are carried by nanosized exosomes or microvesicles in blood plasma or serum, have been recognized as valuable indicators for various age-related diseases. We therefore aimed to elucidate the role of cmiRNAs in AMD by genome-wide miRNA expression profiling and replication analyses in 147 controls and 129 neovascular AMD patients. We identified three microRNAs differentially secreted in neovascular (NV AMD (hsa-mir-301-3p, pcorrected = 5.6*10-5, hsa-mir-361-5p, pcorrected = 8.0*10-4 and hsa-mir-424-5p, pcorrected = 9.6*10-3. A combined profile of the three miRNAs revealed an area under the curve (AUC value of 0.727 and was highly associated with NV AMD (p = 1.2*10-8. To evaluate subtype-specificity, an additional 59 AMD cases with pure unilateral or bilateral geographic atrophy (GA were analyzed for microRNAs hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p. While we found no significant differences between GA AMD and controls neither individually nor for a combined microRNAs profile, hsa-mir-424-5p levels remained significantly higher in GA AMD when compared to NV (pcorrected<0.005. Pathway enrichment analysis on genes predicted to be regulated by microRNAs hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p, suggests canonical TGFβ, mTOR and related pathways to be involved in NV AMD. In addition, knockdown of hsa-mir-361-5p resulted in increased neovascularization in an in vitro angiogenesis assay.

  5. Natural RNA circles function as efficient microRNA sponges

    DEFF Research Database (Denmark)

    Hansen, Thomas Birkballe; Jensen, Trine I; Clausen, Bettina Hjelm

    2013-01-01

    MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called comp......MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so......-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more...... sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA....

  6. Clinical implications of microRNAs in human glioblastoma

    Directory of Open Access Journals (Sweden)

    Masahiro eMizoguchi

    2013-02-01

    Full Text Available Glioblastoma (GBM is one of the most common and dismal brain tumors in adults. Further elucidation of the molecular pathogenesis of GBM is mandatory to improve the overall survival of patients. A novel small non-coding RNA molecule, microRNA (miRNA, appears to represent one of the most attractive target molecules contributing to the pathogenesis of various types of tumors. Recent global analyses have revealed that several miRNAs are clinically implicated in GBM, with some reports indicating the association of miRNA dysregulation with acquired temozolomide (TMZ resistance. More recent studies have revealed that miRNAs could play a role in cancer stem cell (CSC properties, contributing to treatment resistance. In addition, greater impact might be expected from miRNA-targeted therapies based on tumor-derived exosomes that contain numerous functional miRNAs, which could be transferred between tumor cells and surrounding structures. Tumor-derived miRNAs are now considered to be a novel molecular mechanism promoting the progression of GBM. Establishment of miRNA-targeted therapies based on miRNA dysregulation of CSCs could provide effective therapeutic strategies for TMZ-resistant GBM. Recent progress has revealed that miRNAs are not only putative biological markers for diagnosis, but also one of the most promising targets for GBM treatment. Herein, we summarize the translational aspects of miRNAs in the diagnosis and treatment of GBM.

  7. MicroRNA-671-3p inhibits the development of breast cancer: A study based on in vitro experiments, in-house quantitative polymerase chain reaction and bioinformatics analysis

    Science.gov (United States)

    He, Rong-Quan; Lan, Ai-Hua; Zhong, Jin-Cai; Chen, Gang; Feng, Zhen-Bo; Wei, Kang-Lai

    2018-01-01

    MicroRNAs (miRNAs or miRs) are highly conserved small noncoding RNA molecules involved in gene regulation. An increasing number of studies have demonstrated that miRNAs act as oncogenes or antioncogenes in various types of cancer, including breast cancer (BC). However, the exact role of miR-671-3p in BC has not yet been reported. In the present study, in vitro experiments were implemented to explore the effects of miR-671-3p on the proliferation and apoptosis of BC cells, and reverse transcription-quantitative polymerase chain reaction was conducted using in-house clinical BC samples to address the expression level and clinical value of miR-671-3p in BC. Simultaneously, miR-671-3p target genes were collected, and subsequent bioinformatics analyses were executed to probe the potential signaling pathway through which miR-671-3p influenced the occurrence and progression of BC. According to the results, the expression level of miR-671-3p was lower in BC tissues compared with that in adjacent non-tumorous tissues (P=0.048), and the area under the curve was 0.697 (95% confidence interval=0.538-0.856), with a sensitivity and specificity of 0.818 and 0.579, respectively. Forced miR-671-3p expression in the BC cell line MDA-MB-231 evidently arrested cell proliferation and induced cell apoptosis. Furthermore, in silico enrichment analyses suggested that miR-671-3p may be involved in the initiation and progression of BC through the targeting of genes associated with the Wnt signaling pathway. In conclusion, the present study findings suggested that miR-671-3p may function as a tumor suppressor in BC by influencing the Wnt signaling cascade, which provides a prospective molecular target for the therapy of BC. PMID:29620195

  8. Regulation of neutrophil senescence by microRNAs.

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    Jon R Ward

    2011-01-01

    Full Text Available Neutrophils are rapidly recruited to sites of tissue injury or infection, where they protect against invading pathogens. Neutrophil functions are limited by a process of neutrophil senescence, which renders the cells unable to respond to chemoattractants, carry out respiratory burst, or degranulate. In parallel, aged neutrophils also undergo spontaneous apoptosis, which can be delayed by factors such as GMCSF. This is then followed by their subsequent removal by phagocytic cells such as macrophages, thereby preventing unwanted inflammation and tissue damage. Neutrophils translate mRNA to make new proteins that are important in maintaining functional longevity. We therefore hypothesised that neutrophil functions and lifespan might be regulated by microRNAs expressed within human neutrophils. Total RNA from highly purified neutrophils was prepared and subjected to microarray analysis using the Agilent human miRNA microarray V3. We found human neutrophils expressed a selected repertoire of 148 microRNAs and that 6 of these were significantly upregulated after a period of 4 hours in culture, at a time when the contribution of apoptosis is negligible. A list of predicted targets for these 6 microRNAs was generated from http://mirecords.biolead.org and compared to mRNA species downregulated over time, revealing 83 genes targeted by at least 2 out of the 6 regulated microRNAs. Pathway analysis of genes containing binding sites for these microRNAs identified the following pathways: chemokine and cytokine signalling, Ras pathway, and regulation of the actin cytoskeleton. Our data suggest that microRNAs may play a role in the regulation of neutrophil senescence and further suggest that manipulation of microRNAs might represent an area of future therapeutic interest for the treatment of inflammatory disease.

  9. MicroRNAs expression profile in solid and unicystic ameloblastomas

    Science.gov (United States)

    Setién-Olarra, A.; Bediaga, N. G.; Aguirre-Echebarria, P.; Aguirre-Urizar, J. M.; Mosqueda-Taylor, A.

    2017-01-01

    Objectives Odontogenic tumors (OT) represent a specific pathological category that includes some lesions with unpredictable biological behavior. Although most of these lesions are benign, some, such as the ameloblastoma, exhibit local aggressiveness and high recurrence rates. The most common types of ameloblastoma are the solid/multicystic (SA) and the unicystic ameloblastoma (UA); the latter considered a much less aggressive entity as compared to the SA. The microRNA system regulates the expression of many human genes while its deregulation has been associated with neoplastic development. The aim of the current study was to determine the expression profiles of microRNAs present in the two most common types of ameloblastomas. Material & methods MicroRNA expression profiles were assessed using TaqMan® Low Density Arrays (TLDAs) in 24 samples (8 SA, 8 UA and 8 control samples). The findings were validated using quantitative RTqPCR in an independent cohort of 19 SA, 8 UA and 19 dentigerous cysts as controls. Results We identified 40 microRNAs differentially regulated in ameloblastomas, which are related to neoplastic development and differentiation, and with the osteogenic process. Further validation of the top ranked microRNAs revealed significant differences in the expression of 6 of them in relation to UA, 7 in relation to SA and 1 (miR-489) that was related to both types. Conclusion We identified a new microRNA signature for the ameloblastoma and for its main types, which may be useful to better understand the etiopathogenesis of this neoplasm. In addition, we identified a microRNA (miR-489) that is suggestive of differentiating among solid from unicystic ameloblastoma. PMID:29053755

  10. New Ir Bis-Carbonyl Precursor for Water Oxidation Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Daria L. [Department of Chemistry, Yale University, 225; Beltrán-Suito, Rodrigo [Department of Chemistry, Yale University, 225; Thomsen, Julianne M. [Department of Chemistry, Yale University, 225; Hashmi, Sara M. [Department of Chemical and Environmental; Materna, Kelly L. [Department of Chemistry, Yale University, 225; Sheehan, Stafford W. [Catalytic Innovations LLC, 70 Crandall; Mercado, Brandon Q. [Department of Chemistry, Yale University, 225; Brudvig, Gary W. [Department of Chemistry, Yale University, 225; Crabtree, Robert H. [Department of Chemistry, Yale University, 225

    2016-02-05

    This paper introduces IrI(CO)2(pyalc) (pyalc = (2-pyridyl)-2-propanoate) as an atom-efficient precursor for Ir-based homogeneous oxidation catalysis. This compound was chosen to simplify analysis of the water oxidation catalyst species formed by the previously reported Cp*IrIII(pyalc)OH water oxidation precatalyst. Here, we present a comparative study on the chemical and catalytic properties of these two precursors. Previous studies show that oxidative activation of Cp*Ir-based precursors with NaIO4 results in formation of a blue IrIV species. This activation is concomitant with the loss of the placeholder Cp* ligand which oxidatively degrades to form acetic acid, iodate, and other obligatory byproducts. The activation process requires substantial amounts of primary oxidant, and the degradation products complicate analysis of the resulting IrIV species. The species formed from oxidation of the Ir(CO)2(pyalc) precursor, on the other hand, lacks these degradation products (the CO ligands are easily lost upon oxidation) which allows for more detailed examination of the resulting Ir(pyalc) active species both catalytically and spectroscopically, although complete structural analysis is still elusive. Once Ir(CO)2(pyalc) is activated, the system requires acetic acid or acetate to prevent the formation of nanoparticles. Investigation of the activated bis-carbonyl complex also suggests several Ir(pyalc) isomers may exist in solution. By 1H NMR, activated Ir(CO)2(pyalc) has fewer isomers than activated Cp*Ir complexes, allowing for advanced characterization. Future research in this direction is expected to contribute to a better structural understanding of the active species. A diol crystallization agent was needed for the structure determination of 3.

  11. Radiochemical Means of Investigating Delayed Neutron Precursors

    International Nuclear Information System (INIS)

    Marmol, P. del

    1968-01-01

    Fast radiochemical methods used now for the determination of delayed neutron precursors are classified and reviewed: precipitations, solvent extractions, range experiments, milking, gas sweeping, isotopic and ion exchange, hot atom reactions and diffusion loss. Advantages and limitations of irradiation systems with respect to fast separations are discussed: external beams which allow faster separations only have low neutron fluxes, internal beams which are mostly fit for gaseous reactions; and rabbits for solution irradiations. Future prospects of radiochemical procedures are presented; among these, studies should be mostly oriented towards gaseous reactions which offer possibilities of isolating very short-lived delayed neutron precursors. Chemical procedures for delayed neutron precursor detection are compared with mass spectrometric and isotope separator techniques; it is concluded that the methods are complementary. (author)

  12. Radiochemical Means of Investigating Delayed Neutron Precursors

    International Nuclear Information System (INIS)

    Marmol, P. del

    1968-01-01

    Fast radiochemical methods used now for the determination of delayed neutron precursors are classified and reviewed: precipitations, solvent extractions, range experiments, milking, gas sweeping, isotopic and ion exchange, hot-atom reactions and diffusion loss. Advantages and limitations of irradiation systems with respect to fast separations are discussed: external beams which allow faster separations only have low neutron fluxes, internal beams which are mostly fit for gaseous reactions; and rabbits for solution irradiations. Future prospects of radiochemical procedures are presented; among these, studies should be mostly oriented towards gaseous reactions which offer possibilities of isolating very short-lived delayed neutron precursors. Chemical procedures for delayed neutron precursor detection are compared with mass spectrometric and isotope-separator techniques; it is concluded that the methods are complementary. (author)

  13. Quantification of microRNA-21 and microRNA-125b in melanoma tissue

    DEFF Research Database (Denmark)

    Wandler, Anne; Riber-Hansen, Rikke; Hager, Henrik

    2017-01-01

    Although microRNAs (miRNAs) have emerged as potent mediators of melanoma development and progression, a precise understanding of their oncogenic role remains unclear. In this study, we analysed formalin-fixed and paraffin-embedded tissues from two separate melanoma cohorts and from a series...... the important involvement of different miRNAs in melanoma biology and may serve as solid basics for further miRNA investigations in melanoma formalin-fixed and paraffin-embedded tissue. In particular, there is increased expression of miR-21 in melanomas compared with benign nevi....

  14. Analysis of host microRNA function uncovers a role for miR-29b-2-5p in Shigella capture by filopodia.

    Science.gov (United States)

    Sunkavalli, Ushasree; Aguilar, Carmen; Silva, Ricardo Jorge; Sharan, Malvika; Cruz, Ana Rita; Tawk, Caroline; Maudet, Claire; Mano, Miguel; Eulalio, Ana

    2017-04-01

    MicroRNAs play an important role in the interplay between bacterial pathogens and host cells, participating as host defense mechanisms, as well as exploited by bacteria to subvert host cellular functions. Here, we show that microRNAs modulate infection by Shigella flexneri, a major causative agent of bacillary dysentery in humans. Specifically, we characterize the dual regulatory role of miR-29b-2-5p during infection, showing that this microRNA strongly favors Shigella infection by promoting both bacterial binding to host cells and intracellular replication. Using a combination of transcriptome analysis and targeted high-content RNAi screening, we identify UNC5C as a direct target of miR-29b-2-5p and show its pivotal role in the modulation of Shigella binding to host cells. MiR-29b-2-5p, through repression of UNC5C, strongly enhances filopodia formation thus increasing Shigella capture and promoting bacterial invasion. The increase of filopodia formation mediated by miR-29b-2-5p is dependent on RhoF and Cdc42 Rho-GTPases. Interestingly, the levels of miR-29b-2-5p, but not of other mature microRNAs from the same precursor, are decreased upon Shigella replication at late times post-infection, through degradation of the mature microRNA by the exonuclease PNPT1. While the relatively high basal levels of miR-29b-2-5p at the start of infection ensure efficient Shigella capture by host cell filopodia, dampening of miR-29b-2-5p levels later during infection may constitute a bacterial strategy to favor a balanced intracellular replication to avoid premature cell death and favor dissemination to neighboring cells, or alternatively, part of the host response to counteract Shigella infection. Overall, these findings reveal a previously unappreciated role of microRNAs, and in particular miR-29b-2-5p, in the interaction of Shigella with host cells.

  15. Analysis of host microRNA function uncovers a role for miR-29b-2-5p in Shigella capture by filopodia.

    Directory of Open Access Journals (Sweden)

    Ushasree Sunkavalli

    2017-04-01

    Full Text Available MicroRNAs play an important role in the interplay between bacterial pathogens and host cells, participating as host defense mechanisms, as well as exploited by bacteria to subvert host cellular functions. Here, we show that microRNAs modulate infection by Shigella flexneri, a major causative agent of bacillary dysentery in humans. Specifically, we characterize the dual regulatory role of miR-29b-2-5p during infection, showing that this microRNA strongly favors Shigella infection by promoting both bacterial binding to host cells and intracellular replication. Using a combination of transcriptome analysis and targeted high-content RNAi screening, we identify UNC5C as a direct target of miR-29b-2-5p and show its pivotal role in the modulation of Shigella binding to host cells. MiR-29b-2-5p, through repression of UNC5C, strongly enhances filopodia formation thus increasing Shigella capture and promoting bacterial invasion. The increase of filopodia formation mediated by miR-29b-2-5p is dependent on RhoF and Cdc42 Rho-GTPases. Interestingly, the levels of miR-29b-2-5p, but not of other mature microRNAs from the same precursor, are decreased upon Shigella replication at late times post-infection, through degradation of the mature microRNA by the exonuclease PNPT1. While the relatively high basal levels of miR-29b-2-5p at the start of infection ensure efficient Shigella capture by host cell filopodia, dampening of miR-29b-2-5p levels later during infection may constitute a bacterial strategy to favor a balanced intracellular replication to avoid premature cell death and favor dissemination to neighboring cells, or alternatively, part of the host response to counteract Shigella infection. Overall, these findings reveal a previously unappreciated role of microRNAs, and in particular miR-29b-2-5p, in the interaction of Shigella with host cells.

  16. Precursors prior to type IIn supernova explosions are common: Precursor rates, properties, and correlations

    Energy Technology Data Exchange (ETDEWEB)

    Ofek, Eran O.; Steinbok, Aviram; Arcavi, Iair; Gal-Yam, Avishay; Tal, David; Ben-Ami, Sagi; Yaron, Ofer [Benoziyo Center for Astrophysics, Weizmann Institute of Science, 76100 Rehovot (Israel); Sullivan, Mark [School of Physics and Astronomy, University of Southampton, Southampton SO17 1BJ (United Kingdom); Shaviv, Nir J. [Racah Institute of Physics, The Hebrew University, 91904 Jerusalem (Israel); Kulkarni, Shrinivas R. [Cahill Center for Astronomy and Astrophysics, California Institute of Technology, Pasadena, CA 91125 (United States); Nugent, Peter E. [Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Kasliwal, Mansi M. [Observatories of the Carnegie Institution for Science, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Cenko, S. Bradley [Astrophysics Science Division, NASA/Goddard Space Flight Center, Mail Code 661, Greenbelt, MD 20771 (United States); Laher, Russ; Surace, Jason [Spitzer Science Center, California Institute of Technology, M/S 314-6, Pasadena, CA 91125 (United States); Bloom, Joshua S.; Filippenko, Alexei V. [Department of Astronomy, University of California, Berkeley, CA 94720-3411 (United States); Silverman, Jeffrey M. [Department of Astronomy, University of Texas, Austin, TX 78712 (United States)

    2014-07-10

    There is a growing number of Type IIn supernovae (SNe) which present an outburst prior to their presumably final explosion. These precursors may affect the SN display, and are likely related to poorly charted phenomena in the final stages of stellar evolution. By coadding Palomar Transient Factory (PTF) images taken prior to the explosion, here we present a search for precursors in a sample of 16 Type IIn SNe. We find five SNe IIn that likely have at least one possible precursor event (PTF 10bjb, SN 2010mc, PTF 10weh, SN 2011ht, and PTF 12cxj), three of which are reported here for the first time. For each SN we calculate the control time. We find that precursor events among SNe IIn are common: at the one-sided 99% confidence level, >50% of SNe IIn have at least one pre-explosion outburst that is brighter than 3 × 10{sup 7} L{sub ☉} taking place up to 1/3 yr prior to the SN explosion. The average rate of such precursor events during the year prior to the SN explosion is likely ≳ 1 yr{sup –1}, and fainter precursors are possibly even more common. Ignoring the two weakest precursors in our sample, the precursors rate we find is still on the order of one per year. We also find possible correlations between the integrated luminosity of the precursor and the SN total radiated energy, peak luminosity, and rise time. These correlations are expected if the precursors are mass-ejection events, and the early-time light curve of these SNe is powered by interaction of the SN shock and ejecta with optically thick circumstellar material.

  17. Profile of cerebrospinal microRNAs in fibromyalgia.

    Directory of Open Access Journals (Sweden)

    Jan L Bjersing

    Full Text Available Fibromyalgia (FM is characterized by chronic pain and reduced pain threshold. The pathophysiology involves disturbed neuroendocrine function, including impaired function of the growth hormone/insulin-like growth factor-1 axis. Recently, microRNAs have been shown to be important regulatory factors in a number of diseases. The aim of this study was to try to identify cerebrospinal microRNAs with expression specific for FM and to determine their correlation to pain and fatigue.The genome-wide profile of microRNAs in cerebrospinal fluid was assessed in ten women with FM and eight healthy controls using real-time quantitative PCR. Pain thresholds were examined by algometry. Levels of pain (FIQ pain were rated on a 0-100 mm scale (fibromyalgia impact questionnaire, FIQ. Levels of fatigue (FIQ fatigue were rated on a 0-100 mm scale using FIQ and by multidimensional fatigue inventory (MFI-20 general fatigue (MFIGF.Expression levels of nine microRNAs were significantly lower in patients with FM patients compared to healthy controls. The microRNAs identified were miR-21-5p, miR-145-5p, miR-29a-3p, miR-99b-5p, miR-125b-5p, miR-23a-3p, 23b-3p, miR-195-5p, miR-223-3p. The identified microRNAs with significantly lower expression in FM were assessed with regard to pain and fatigue. miR-145-5p correlated positively with FIQ pain (r=0.709, p=0.022, n=10 and with FIQ fatigue (r=0.687, p=0.028, n=10.To our knowledge, this is the first study to show a disease-specific pattern of cerebrospinal microRNAs in FM. We have identified nine microRNAs in cerebrospinal fluid that differed between FM patients and healthy controls. One of the identified microRNAs, miR-145 was associated with the cardinal symptoms of FM, pain and fatigue.

  18. Profile of cerebrospinal microRNAs in fibromyalgia.

    Science.gov (United States)

    Bjersing, Jan L; Lundborg, Christopher; Bokarewa, Maria I; Mannerkorpi, Kaisa

    2013-01-01

    Fibromyalgia (FM) is characterized by chronic pain and reduced pain threshold. The pathophysiology involves disturbed neuroendocrine function, including impaired function of the growth hormone/insulin-like growth factor-1 axis. Recently, microRNAs have been shown to be important regulatory factors in a number of diseases. The aim of this study was to try to identify cerebrospinal microRNAs with expression specific for FM and to determine their correlation to pain and fatigue. The genome-wide profile of microRNAs in cerebrospinal fluid was assessed in ten women with FM and eight healthy controls using real-time quantitative PCR. Pain thresholds were examined by algometry. Levels of pain (FIQ pain) were rated on a 0-100 mm scale (fibromyalgia impact questionnaire, FIQ). Levels of fatigue (FIQ fatigue) were rated on a 0-100 mm scale using FIQ and by multidimensional fatigue inventory (MFI-20) general fatigue (MFIGF). Expression levels of nine microRNAs were significantly lower in patients with FM patients compared to healthy controls. The microRNAs identified were miR-21-5p, miR-145-5p, miR-29a-3p, miR-99b-5p, miR-125b-5p, miR-23a-3p, 23b-3p, miR-195-5p, miR-223-3p. The identified microRNAs with significantly lower expression in FM were assessed with regard to pain and fatigue. miR-145-5p correlated positively with FIQ pain (r=0.709, p=0.022, n=10) and with FIQ fatigue (r=0.687, p=0.028, n=10). To our knowledge, this is the first study to show a disease-specific pattern of cerebrospinal microRNAs in FM. We have identified nine microRNAs in cerebrospinal fluid that differed between FM patients and healthy controls. One of the identified microRNAs, miR-145 was associated with the cardinal symptoms of FM, pain and fatigue.

  19. Functions of microRNA in response to cocaine stimulation.

    Science.gov (United States)

    Xu, L-F; Wang, J; Lv, F B; Song, Q

    2013-12-04

    MicroRNAs (miRNAs) are a type of non-protein-coding single-stranded RNA, which are typically 20-25 nt in length. miRNAs play important roles in various biological processes, including development, cell proliferation, differentiation, and apoptosis. We aimed to detect the miRNA response to cocaine stimulations and their target genes. Using the miRNA expression data GSE21901 downloaded from the Gene Expression Omnibus database, we screened out the differentially expressed miRNA after short-term (1 h) and longer-term (6 h) cocaine stimulations based on the fold change >1.2. Target genes of differentially expressed miRNAs were retrieved from TargetScan database with the context score -0.3. Functional annotation enrichment analysis was performed for all the target genes with DAVID. A total of 121 differentially expressed miRNAs between the 1-h treatment and the control samples, 58 between the 6-h treatment and the control samples, and 69 between the 1-h and the 6-h treatment samples. Among them, miR-212 results of particular interest, since its expression level was constantly elevated responding to cocaine treatment. After functional and pathway annotations of target genes, we proved that miR-212 was a critical element in cocaine-addiction, because of its involvement in regulating several important cell cycle events. The results may pave the way for further understanding the regulatory mechanisms of cocaine-response in human bodies.

  20. MicroRNA and Pathogenesis of Enterovirus Infection.

    Science.gov (United States)

    Ho, Bing-Ching; Yang, Pan-Chyr; Yu, Sung-Liang

    2016-01-06

    There are no currently available specific antiviral therapies for non-polio Enterovirus infections. Although several vaccines have entered clinical trials, the efficacy requires further evaluation, particularly for cross-strain protective activity. Curing patients with viral infections is a public health problem due to antigen alterations and drug resistance caused by the high genomic mutation rate. To conquer these limits in the development of anti-Enterovirus treatments, a comprehensive understanding of the interactions between Enterovirus and host cells is urgently needed. MicroRNA (miRNA) constitutes the biggest family of gene regulators in mammalian cells and regulates almost a half of all human genes. The roles of miRNAs in Enterovirus pathogenesis have recently begun to be noted. In this review, we shed light on recent advances in the understanding of Enterovirus infection-modulated miRNAs. The impacts of altered host miRNAs on cellular processes, including immune escape, apoptosis, signal transduction, shutdown of host protein synthesis and viral replication, are discussed. Finally, miRNA-based medication provides a promising strategy for the development of antiviral therapy.

  1. Function and evolution of microRNAs in eusocial Hymenoptera

    Directory of Open Access Journals (Sweden)

    Eirik eSovik

    2015-05-01

    Full Text Available The emergence of eusociality (true sociality in several insect lineages represents one of the most successful evolutionary adaptations in the animal kingdom in terms of species richness and global biomass. In contrast to solitary insects, eusocial insects evolved a set of unique behavioral and physiological traits such as reproductive division of labor and cooperative brood care, which likely played a major role in their ecological success. The molecular mechanisms that support the social regulation of behavior in eusocial insects, and their evolution, are mostly unknown. The recent whole-genome sequencing of several eusocial insect species set the stage for deciphering the molecular and genetic bases of eusociality, and the possible evolutionary modifications that led to it. Studies of mRNA expression patterns in the brains of diverse eusocial insect species have indicated that specific social behavioral states of individual workers and queens are often associated with particular tissue-specific transcriptional profiles. Here we discuss recent findings that highlight the role of non-coding microRNAs (miRNAs in modulating traits associated with reproductive and behavioral divisions of labor in eusocial insects. We provide bioinformatic and phylogenetic data, which suggest that some Hymenoptera-specific miRNA may have contributed to the evolution of traits important for the evolution of eusociality in this group.

  2. Capillary electrophoresis methods for microRNAs assays: A review

    Energy Technology Data Exchange (ETDEWEB)

    Ban, Eunmi; Song, Eun Joo, E-mail: ejsong@kist.re.kr

    2014-12-10

    Highlights: • A review of CE analysis of miRNAs. • Summary of developments and applications of CE systems in miRNA studies. • Applications and development of microchip-based CE for rapid analysis of miRNA. - Abstract: MicroRNAs (miRNAs) are short noncoding RNAs that conduct important roles in many cellular processes such as development, proliferation, differentiation, and apoptosis. In particular, circulating miRNAs have been proposed as biomarkers for cancer, diabetes, cardiovascular disease, and other illnesses. Therefore, determination of miRNA expression levels in various biofluids is important for the investigation of biological processes in health and disease and for discovering their potential as new biomarkers and drug targets. Capillary electrophoresis (CE) is emerging as a useful analytical tool for analyzing miRNA because of its simple sample preparation steps and efficient resolution of a diverse size range of compounds. In particular, CE with laser-induced fluorescence detection is a promising and relatively rapidly developing tool with the potential to provide high sensitivity and specificity in the analysis of miRNAs. This paper covers a short overview of the recent developments and applications of CE systems in miRNA studies in biological and biomedical areas.

  3. Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.

    Science.gov (United States)

    Vitsios, Dimitrios M; Kentepozidou, Elissavet; Quintais, Leonor; Benito-Gutiérrez, Elia; van Dongen, Stijn; Davis, Matthew P; Enright, Anton J

    2017-12-01

    The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large numbers of miRNAs that are expressed in very particular cell types and remain elusive. Sequencing allows us to quickly and accurately identify the expression of known miRNAs from small RNA-Seq data. The biogenesis of miRNAs leads to very specific characteristics observed in their sequences. In brief, miRNAs usually have a well-defined 5' end and a more flexible 3' end with the possibility of 3' tailing events, such as uridylation. Previous approaches to the prediction of novel miRNAs usually involve the analysis of structural features of miRNA precursor hairpin sequences obtained from genome sequence. We surmised that it may be possible to identify miRNAs by using these biogenesis features observed directly from sequenced reads, solely or in addition to structural analysis from genome data. To this end, we have developed mirnovo, a machine learning based algorithm, which is able to identify known and novel miRNAs in animals and plants directly from small RNA-Seq data, with or without a reference genome. This method performs comparably to existing tools, however is simpler to use with reduced run time. Its performance and accuracy has been tested on multiple datasets, including species with poorly assembled genomes, RNaseIII (Drosha and/or Dicer) deficient samples and single cells (at both embryonic and adult stage). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Improvement of the design and generation of highly specific plant knockdown lines using primary synthetic microRNAs (pri-smiRNAs

    Directory of Open Access Journals (Sweden)

    Alves Leonardo

    2010-03-01

    Full Text Available Abstract Background microRNAs (miRNAs are endogenous small non-coding RNAs that post-transcriptionally regulate gene expression. In plants, they typically show high complementarity to a single sequence motif within their target mRNAs and act by catalyzing specific mRNA cleavage and degradation. miRNAs are processed from much longer primary transcripts via precursor miRNAs containing fold-back structures. Leaving these secondary structures intact, miRNAs can be re-designed experimentally to target mRNAs of choice. Results We designed primary synthetic miRNAs (pri-smiRNAs on the basis of the primary transcript of the Arabidopsis MIR159A gene by replacing the original miR159a and the corresponding miR159a* with novel sequences, keeping the overall secondary structure as predicted by the program RNAfold. We used the program RNAhybrid to optimize smiRNA design and to screen the complete Arabidopsis transcriptome for potential off-targets. To improve the molecular cloning of the pri-smiRNA we inserted restriction sites in the original MIR159A primary transcript to easily accommodate the smiRNA/smiRNA* DNA fragment. As a proof-of-concept, we targeted the single gene encoding chalcone synthase (CHS in Arabidopsis. We demonstrate smiRNA(CHS expression and CHS mRNA cleavage in different transgenic lines. Phenotypic changes in these lines were observed for seed color and flavonol derivatives, and quantified with respect to anthocyanin content. We also tested the effect of mismatches and excess G:U base pairs on knockdown efficiency. Conclusions RNAhybrid-assisted design of smiRNAs and generation of pri-smiRNAs using a novel vector containing restriction sites greatly improves specificity and speed of the generation of stable knockdown lines for functional analyses in plants.

  5. MicroRNAs in Cardiometabolic Diseases

    Directory of Open Access Journals (Sweden)

    Anna Meiliana

    2013-08-01

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are ~22-nucleotide noncoding RNAs with critical functions in multiple physiological and pathological processes. An explosion of reports on the discovery and characterization of different miRNA species and their involvement in almost every aspect of cardiac biology and diseases has established an exciting new dimension in gene regulation networks for cardiac development and pathogenesis. CONTENT: Alterations in the metabolic control of lipid and glucose homeostasis predispose an individual to develop cardiometabolic diseases, such as type 2 diabetes mellitus and atherosclerosis. Work over the last years has suggested that miRNAs play an important role in regulating these physiological processes. Besides a cell-specific transcription factor profile, cell-specific miRNA-regulated gene expression is integral to cell fate and activation decisions. Thus, the cell types involved in atherosclerosis, vascular disease, and its myocardial sequelae may be differentially regulated by distinct miRNAs, thereby controlling highly complex processes, for example, smooth muscle cell phenotype and inflammatory responses of endothelial cells or macrophages. The recent advancements in using miRNAs as circulating biomarkers or therapeutic modalities, will hopefully be able to provide a strong basis for future research to further expand our insights into miRNA function in cardiovascular biology. SUMMARY: MiRNAs are small, noncoding RNAs that function as post-transcriptional regulators of gene expression. They are potent modulators of diverse biological processes and pathologies. Recent findings demonstrated the importance of miRNAs in the vasculature and the orchestration of lipid metabolism and glucose homeostasis. MiRNA networks represent an additional layer of regulation for gene expression that absorbs perturbations and ensures the robustness of biological systems. A detailed understanding of the molecular and cellular mechanisms of mi

  6. Intra-tumor heterogeneity of microRNA-92a, microRNA-375 and microRNA-424 in colorectal cancer

    DEFF Research Database (Denmark)

    Jepsen, Rikke Karlin; Novotny, Guy Wayne; Klarskov, Louise Laurberg

    2016-01-01

    Various microRNAs (miRNAs) have been investigated in order to improve diagnostics and risk assessment in colorectal cancer (CRC). To clarify the potential of miRNA profiling in CRC, knowledge of intra-tumor heterogeneity in expression levels is crucial. The study aim was to estimate the intra...

  7. PRECOMBUSTION REMOVAL OF HAZARDOUS AIR POLLUTANT PRECURSORS

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    2000-10-09

    In response to growing environmental concerns reflected in the 1990 Clean Air Act Amendment (CAAA), the United States Department of Energy (DOE) sponsored several research and development projects in late 1995 as part of an initiative entitled Advanced Environmental Control Technologies for Coal-Based Power Systems. The program provided cost-shared support for research and development projects that could accelerate the commercialization of affordable, high-efficiency, low-emission, coal-fueled electric generating technologies. Clean coal technologies developed under this program would serve as prototypes for later generations of technologies to be implemented in the industrial sector. In order to identify technologies with the greatest potential for commercial implementation, projects funded under Phase I of this program were subject to competitive review by DOE before being considered for continuation funding under Phase II. One of the primary topical areas identified under the DOE initiative relates to the development of improved technologies for reducing the emissions of air toxics. Previous studies have suggested that many of the potentially hazardous air pollutant precursors (HAPPs) occur as trace elements in the mineral matter of run-of-mine coals. As a result, these elements have the potential to be removed prior to combustion at the mine site by physical coal cleaning processes (i.e., coal preparation). Unfortunately, existing coal preparation plants are generally limited in their ability to remove HAPPs due to incomplete liberation of the mineral matter and high organic associations of some trace elements. In addition, existing physical coal cleaning plants are not specifically designed or optimized to ensure that high trace element rejections may be achieved.

  8. On important precursor of singular optics (tutorial)

    Science.gov (United States)

    Polyanskii, Peter V.; Felde, Christina V.; Bogatyryova, Halina V.; Konovchuk, Alexey V.

    2018-01-01

    The rise of singular optics is usually associated with the seminal paper by J. F. Nye and M. V. Berry [Proc. R. Soc. Lond. A, 336, 165-189 (1974)]. Intense development of this area of modern photonics has started since the early eighties of the XX century due to invention of the interfrence technique for detection and diagnostics of phase singularities, such as optical vortices in complex speckle-structured light fields. The next powerful incentive for formation of singular optics into separate area of the science on light was connectected with discovering of very practical technique for creation of singular optical beams of various kinds on the base of computer-generated holograms. In the eghties and ninetieth of the XX century, singular optics evolved, almost entirely, under the approximation of complete coherency of light field. Only at the threshold of the XXI century, it has been comprehended that the singular-optics approaches can be fruitfully expanded onto partially spatially coherent, partially polarized and polychromatic light fields supporting singularities of new kinds, that has been resulted in establishing of correlation singular optics. Here we show that correlation singular optics has much deeper roots, ascending to "pre-singular" and even pre-laser epoch and associated with the concept of partial coherence and polarization. It is remarcable that correlation singular optics in its present interpretation has forestalled the standard coherent singular optics. This paper is timed to the sixtieth anniversary of the most profound precursor of modern correlation singular optics [J. Opt. Soc. Am., 47, 895-902 (1957)].

  9. Degradation of Highly Alloyed Metal Halide Perovskite Precursor Inks: Mechanism and Storage Solutions

    Energy Technology Data Exchange (ETDEWEB)

    Dou, Benjia [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Wheeler, Lance M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Christians, Jeffrey A [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Moore, David [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Harvey, Steven P [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Berry, Joseph J [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Van Hest, Marinus F [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Barnes, Frank S. [University of Colorado; Shaheen, Sean E. [University of Colorado

    2018-03-02

    Whereas the promise of metal halide perovskite (MHP) photovoltaics (PV) is that they can combine high efficiency with solution-processability, the chemistry occurring in precursor inks is largely unexplored. Herein, we investigate the degradation of MHP solutions based on the most widely used solvents, dimethylformamide (DMF) and dimethyl sulfoxide (DMSO). For the MHP inks studied, which contain formamidinium (FA+), methylammonium (MA+), cesium (Cs+), lead (Pb2+), bromide (Br-), and iodide (I-), dramatic compositional changes are observed following storage of the inks in nitrogen in the dark. We show that hydrolysis of DMF in the precursor solution forms dimethylammonium formate, which subsequently incorporates into the MHP film to compromise the ability of Cs+ and MA+ to stabilize FA+-based MHP. The changes in solution chemistry lead to a modification of the perovskite film stoichiometry, band gap, and structure. The solid precursor salts are stable when ball-milled into a powder, allowing for the storage of large quantities of stoichiometric precursor materials.

  10. Development of techniques for tagging precursor and essential chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Swansiger, W.A.; Shepodd, T.J. [Sandia National Labs., Livermore, CA (United States); Phillips, M.L.F. [Sandia National Labs., Albuquerque, NM (United States)

    1994-01-01

    The ability to identify the manufacturers and distributors of chemicals seized in raids of illicit drug labs would be of great value in controlling the diversion of these chemicals. We developed a tagging scheme based on the addition of sub-ppM concentrations of various combinations of rare-earth elements to the target chemicals and evaluated a number of techniques for detecting the tags. We developed soluble tags for tagging liquids and selected Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) as the preferred detection technique. We developed insoluble tags for tagging solids and developed methods to analyze them and mix them into solid precursors. We have successfully demonstrated the tagging of several solvents and two of the precursor chemicals used in one of the most popular clandestine methamphetamine syntheses (ephedrine reacting with hydriodic acid/red phosphorus). The tagging scheme is capable of yielding tens of thousands of signatures (using holmium as an internal standard and up to 9 rare-earths at up to 3 concentrations yields 3{sup 9} {minus} 1 = 19,682 signatures) and is applicable to most of the chemicals on the precursor and essential chemicals list. In the concentrations employed, the tags are safe enough to be added to pharmaceuticals and cheap enough to tag tanker loads of chemicals.

  11. Thermogravimetric evaluation of the suitability of precursors for MOCVD

    International Nuclear Information System (INIS)

    Kunte, G V; Shivashankar, S A; Umarji, A M

    2008-01-01

    A method based on the Langmuir equation for the estimation of vapour pressure and enthalpy of sublimation of subliming compounds is described. The variable temperature thermogravimetric/differential thermogravimetric (TG/DTG) curve of benzoic acid is used to arrive at the instrument parameters. Employing these parameters, the vapour pressure–temperature curves are derived for salicylic acid and camphor from their TG/DTG curves. The values match well with vapour pressure data in the literature, obtained by effusion methods. By employing the Clausius–Clapeyron equation, the enthalpy of sublimation could be calculated. Extending the method further, two precursors for metal-organic chemical vapour deposition (MOCVD) of titanium oxide bis-isopropyl bis tert-butyl 2-oxobutanoato titanium, Ti(O i Pr) 2 (tbob) 2 , and bis-oxo-bis-tertbutyl 2-oxobutanoato titanium, [TiO(tbob) 2 ] 2 , have been evaluated. The complex Ti(O i Pr) 2 (tbob) 2 is found to be a more suitable precursor. This approach can be helpful in quickly screening for the suitability of a compound as a CVD precursor

  12. Earthquake prediction the ory and its relation to precursors

    International Nuclear Information System (INIS)

    Negarestani, A.; Setayeshi, S.; Ghannadi-Maragheh, M.; Akasheh, B.

    2001-01-01

    Since we don't have enough knowledge about the Physics of earthquakes. therefore. the study of seismic precursors plays an important role in earthquake prediction. Earthquake prediction is a science which discusses about precursory phenomena during seismogenic process, and then investigates the correlation and association among them and the intrinsic relation between precursors and the seismogenic process. ar the end judges comprehensively the seismic status and finally makes earthquake prediction. There are two ways for predicting earthquake prediction. The first is to study the physics of seismogenic process and to determine the parameters in the process based on the source theories and the second way is to use seismic precursors. In this paper the theory of earthquake is reviewed. We also study theory of earthquake using models of earthquake origin, the relation between seismogenic process and various accompanying precursory phenomena. The earthquake prediction is divided into three categories: long-term, medium-term and short-term. We study seismic anomalous behavior. electric field, crustal deformation, gravity. magnetism of earth. change of groundwater variation. groundwater geochemistry and change of Radon gas emission. Finally, it is concluded the there is a correlation between Radon gas emission and earthquake phenomena. Meanwhile, there are some samples from actual processing in this area

  13. Precursor Wave Emission Enhanced by Weibel Instability in Relativistic Shocks

    Science.gov (United States)

    Iwamoto, Masanori; Amano, Takanobu; Hoshino, Masahiro; Matsumoto, Yosuke

    2018-05-01

    We investigated the precursor wave emission efficiency in magnetized purely perpendicular relativistic shocks in pair plasmas. We extended our previous study to include the dependence of upstream magnetic field orientations. We performed two-dimensional particle-in-cell simulations and focused on two magnetic field orientations: the magnetic field in the simulation plane (i.e., in-plane configuration) and that perpendicular to the simulation plane (i.e., out-of-plane configuration). Our simulations in the in-plane configuration demonstrated that not only extraordinary but also ordinary mode waves are excited. We quantified the emission efficiency as a function of the magnetization parameter σ e and found that the large-amplitude precursor waves are emitted for a wide range of σ e . We found that especially at low σ e , the magnetic field generated by Weibel instability amplifies the ordinary mode wave power. The amplitude is large enough to perturb the upstream plasma, and transverse density filaments are generated as in the case of the out-of-plane configuration investigated in the previous study. We confirmed that our previous conclusion holds regardless of upstream magnetic field orientations with respect to the two-dimensional simulation plane. We discuss the precursor wave emission in three dimensions and the feasibility of wakefield acceleration in relativistic shocks based on our results.

  14. Spectroscopy Study of Synthetic Forsterite Obtained from Zeolite Precursors

    Directory of Open Access Journals (Sweden)

    Subotić, B.

    2008-02-01

    Full Text Available Important ceramics materials are prepared from aluminosilicate based precursors using novel methods, offering at the same time a better control over many important properties. Forsterite, due to its good refractoriness with melting point at 2163 K, excellent electrical insulation properties even at high temperatures, low dielectric permittivity, thermal expansion and chemical stability, is a material of interest to engineers and designers especially as an active medium for tuneable laser and is also a material of interest to SOFC (Solid oxide fuel cells manufacturers. The aim of this study is to investigate the synthesis of crystalline forsterite using different zeolite precursors previously activated by ball milling. Synthetic forsterite was synthesized from different zeolite precursors and MgO combining highenergy ball milling and thermal treatment of the mixture under determined conditions of time and temperature for each operation. In this research are studied the solid-state phase transformations taking place at temperatures below 1273 K. The obtained products were characterized using different spectroscopy techniques in comparison with surface analysis method and X-ray diffraction.

  15. Differential expression of microRNA-675, microRNA-139-3p and microRNA-335 in benign and malignant adrenocortical tumours

    Science.gov (United States)

    Helwig, J; Bertram, S; Sheu, S Y; Suttorp, A C; Seggewiß, J; Willscher, E; Walz, M K; Worm, K; Schmid, K W

    2011-01-01

    Background For the clinical management of adrenocortical neoplasms it is crucial to correctly distinguish between benign and malignant tumours. Even histomorphologically based scoring systems do not allow precise separation in single lesions, thus novel parameters are desired which offer a more accurate differentiation. The tremendous potential of microRNAs (miRNAs) as diagnostic biomarkers in surgical pathology has recently been shown in a broad variety of tumours. Methods In order to elucidate the diagnostic impact of miRNA expression in adrenocortical neoplasms, a cohort of 20 adrenocortical specimens including normal adrenal tissue (n=4), adrenocortical adenomas (ACAs) (n=9), adrenocortical carcinomas (ACCs) (n=4) and metastases (n=3) was analysed using TaqMan low density arrays to identify specific miRNA profiles in order to distinguish between benign and malignant adrenocortical lesions. Results were validated in a validation cohort (n=16). Results Concerning the differential diagnosis of ACAs and ACCs, 159 out of 667 miRNAs were up- and 89 were down-regulated in ACAs. Using real-time PCR analysis of three of the most significantly expressed single key miRNAs allowed separation of ACAs from ACCs. ACCs exhibited significantly lower levels of miR-139-3p (up to 8.49-fold, p<0.001), miR-675 (up to 23.25-fold, p<0.001) and miR-335 (up to 5.25-fold, p<0.001). A validation cohort of 16 specimen with known Weiss score showed up-regulation of miR-335 and miR-675 in the majority of cases with probable malignant course, although overlapping values exist. Conclusion miRNA profiling of miR-675 and miR-335 helps in discriminating ACCs from ACAs. miRNA analysis may indicate malignant behaviour in cases with indeterminate malignant potential. PMID:21471143

  16. MicroRNAs in cancer therapeutics: "from the bench to the bedside".

    Science.gov (United States)

    Monroig-Bosque, Paloma del C; Rivera, Carlos A; Calin, George A

    2015-01-01

    MicroRNAs (miRNAs) are non-coding RNA transcripts that regulate physiological processes by targeting proteins directly. Their involvement in research has been robust, and evidence of their regulative functions has granted them the title: master regulators of the human genome. In cancer, they are considered important therapeutic agents, due to the fact that their aberrant expression contributes to disease development, progression, metastasis, therapeutic response and patient overall survival. This has endeavored fields of biomedical sciences to invest in developing and exploiting miRNA-based therapeutics thoroughly. Herein we highlight relevant ongoing/open clinical trials involving miRNAs and cancer.

  17. MicroRNA silencing in primates: towards development of novel therapeutics

    DEFF Research Database (Denmark)

    Petri, Andreas; Lindow, Morten; Kauppinen, Sakari

    2009-01-01

    MicroRNAs (miRNA) comprise an abundant class of small noncoding RNAs that act as important posttranscriptional regulators of gene expression. Accumulating evidence showing that aberrantly expressed miRNAs play important roles in human cancers underscores them as potential targets for therapeutic ...... intervention. Recent reports on efficient miRNA silencing in rodents and nonhuman primates using high-affinity targeting by chemically modified antisense oligonucleotides highlight the utility of such compounds in the development of miRNA-based cancer therapeutics....

  18. Conductance of single microRNAs chains related to the autism spectrum disorder

    Science.gov (United States)

    Oliveira, J. I. N.; Albuquerque, E. L.; Fulco, U. L.; Mauriz, P. W.; Sarmento, R. G.; Caetano, E. W. S.; Freire, V. N.

    2014-09-01

    The charge transport properties of single-stranded microRNAs (miRNAs) chains associated to autism disorder were investigated. The computations were performed within a tight-binding model, together with a transfer matrix technique, with ionization energies and hopping parameters obtained by quantum chemistry method. Current-voltage (I× V) curves of twelve miRNA chains related to the autism spectrum disorders were calculated and analysed. We have obtained both semiconductor and insulator behavior, and a relationship between the current intensity and the autism-related miRNA bases sequencies, suggesting that a kind of electronic biosensor can be developed to distinguish different profiles of autism disorders.

  19. Tissue-specific regulation of mouse MicroRNA genes in endoderm-derived tissues

    OpenAIRE

    Gao, Yan; Schug, Jonathan; McKenna, Lindsay B.; Le Lay, John; Kaestner, Klaus H.; Greenbaum, Linda E.

    2010-01-01

    MicroRNAs fine-tune the activity of hundreds of protein-coding genes. The identification of tissue-specific microRNAs and their promoters has been constrained by the limited sensitivity of prior microRNA quantification methods. Here, we determine the entire microRNAome of three endoderm-derived tissues, liver, jejunum and pancreas, using ultra-high throughput sequencing. Although many microRNA genes are expressed at comparable levels, 162 microRNAs exhibited striking tissue-specificity. After...

  20. MicroRNA mimicry blocks pulmonary fibrosis

    Science.gov (United States)

    Montgomery, Rusty L; Yu, Guoying; Latimer, Paul A; Stack, Christianna; Robinson, Kathryn; Dalby, Christina M; Kaminski, Naftali; van Rooij, Eva

    2014-01-01

    Over the last decade, great enthusiasm has evolved for microRNA (miRNA) therapeutics. Part of the excitement stems from the fact that a miRNA often regulates numerous related mRNAs. As such, modulation of a single miRNA allows for parallel regulation of multiple genes involved in a particular disease. While many studies have shown therapeutic efficacy using miRNA inhibitors, efforts to restore or increase the function of a miRNA have been lagging behind. The miR-29 family has gained a lot of attention for its clear function in tissue fibrosis. This fibroblast-enriched miRNA family is downregulated in fibrotic diseases which induces a coordinate increase of many extracellular matrix genes. Here, we show that intravenous injection of synthetic RNA duplexes can increase miR-29 levels in vivo for several days. Moreover, therapeutic delivery of these miR-29 mimics during bleomycin-induced pulmonary fibrosis restores endogenous miR-29 function whereby decreasing collagen expression and blocking and reversing pulmonary fibrosis. Our data support the feasibility of using miRNA mimics to therapeutically increase miRNAs and indicate miR-29 to be a potent therapeutic miRNA for treating pulmonary fibrosis. PMID:25239947

  1. MicroRNAs regulate osteogenesis and chondrogenesis

    International Nuclear Information System (INIS)

    Dong, Shiwu; Yang, Bo; Guo, Hongfeng; Kang, Fei

    2012-01-01

    Highlights: ► To focus on the role of miRNAs in chondrogenesis and osteogenesis. ► Involved in the regulation of miRNAs in osteoarthritis. ► To speculate some therapeutic targets for bone diseases. -- Abstract: MicroRNAs (miRNAs) are a class of small molecules and non-coding single strand RNAs that regulate gene expression at the post-transcriptional level by binding to specific sequences within target genes. miRNAs have been recognized as important regulatory factors in organism development and disease expression. Some miRNAs regulate the proliferation and differentiation of osteoblasts, osteoclasts and chondrocytes, eventually influencing metabolism and bone formation. miRNAs are expected to provide potential gene therapy targets for the clinical treatment of metabolic bone diseases and bone injuries. Here, we review the recent research progress on the regulation of miRNAs in bone biology, with a particular focus on the miRNA-mediated control mechanisms of bone and cartilage formation.

  2. MicroRNAs horizon in retinoblastoma.

    Directory of Open Access Journals (Sweden)

    Mojgan Mirakholi

    2013-12-01

    Full Text Available In the retinoblastoma research, it is of great interest to identify molecular markers associated with the genetics of tumorigenesis. microRNAs (miRNAs are small non-coding RNA molecules that play a regulatory role in many crucial cellular pathways such as differentiation, cell cycle progression, and apoptosis. A body of evidences showed dysregulation of miRNAs in tumor biology and many diseases. They potentially play a significant role in tumorigenesis processes and have been the subject of research in many types of cancers including retinal tumorigenesis. miRNA expression profiling was found to be associated with tumor development, progression and treatment. These associations demonstrate the putative applications of miRNAs in monitoring of different aspect of tumors consisting diagnostic, prognostic and therapeutic. Herein, we review the current literature concerning to the study of miRNA target recognition, function to tumorigenesis and treatment in retinoblastoma. Identification the specific miRNA biomarkers associated with retinoblastoma cancer may help to establish new therapeutic approaches for salvage affected eyes in patients.

  3. MicroRNAs in addiction: adaptation's middlemen?

    Science.gov (United States)

    Li, M D; van der Vaart, A D

    2011-12-01

    A central question in addiction is how drug-induced changes in synaptic signaling are converted into long-term neuroadaptations. Emerging evidence reveals that microRNAs (miRNAs) have a distinct role in this process through rapid response to cellular signals and dynamic regulation of local mRNA transcripts. Because each miRNA can target hundreds of mRNAs, relative changes in the expression of miRNAs can greatly impact cellular responsiveness, synaptic plasticity and transcriptional events. These diverse consequences of miRNA action occur through coordination with genes implicated in addictions, the most compelling of these being the neurotrophin BDNF, the transcription factor cAMP-responsive element-binding protein (CREB) and the DNA-binding methyl CpG binding protein 2 (MeCP2). In this study, we review the recent progress in the understanding of miRNAs in general mechanisms of plasticity and neuroadaptation and then focus on specific examples of miRNA regulation in the context of addiction. We conclude that miRNA-mediated gene regulation is a conserved means of converting environmental signals into neuronal response, which holds significant implications for addiction and other psychiatric illnesses.

  4. MicroRNAs regulate osteogenesis and chondrogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Shiwu, E-mail: shiwudong@gmail.com [Laboratory of Biomechanics, Department of Anatomy, The Third Military Medical University, Chongqing (China); Yang, Bo; Guo, Hongfeng; Kang, Fei [Laboratory of Biomechanics, Department of Anatomy, The Third Military Medical University, Chongqing (China)

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer To focus on the role of miRNAs in chondrogenesis and osteogenesis. Black-Right-Pointing-Pointer Involved in the regulation of miRNAs in osteoarthritis. Black-Right-Pointing-Pointer To speculate some therapeutic targets for bone diseases. -- Abstract: MicroRNAs (miRNAs) are a class of small molecules and non-coding single strand RNAs that regulate gene expression at the post-transcriptional level by binding to specific sequences within target genes. miRNAs have been recognized as important regulatory factors in organism development and disease expression. Some miRNAs regulate the proliferation and differentiation of osteoblasts, osteoclasts and chondrocytes, eventually influencing metabolism and bone formation. miRNAs are expected to provide potential gene therapy targets for the clinical treatment of metabolic bone diseases and bone injuries. Here, we review the recent research progress on the regulation of miRNAs in bone biology, with a particular focus on the miRNA-mediated control mechanisms of bone and cartilage formation.

  5. Electrophysiological precursors of social conformity

    Science.gov (United States)

    Rieskamp, Jörg; Tugin, Sergey; Ossadtchi, Alexey; Krutitskaya, Janina; Klucharev, Vasily

    2013-01-01

    Humans often change their beliefs or behavior due to the behavior or opinions of others. This study explored, with the use of human event-related potentials (ERPs), whether social conformity is based on a general performance-monitoring mechanism. We tested the hypothesis that conflicts with a normative group opinion evoke a feedback-related negativity (FRN) often associated with performance monitoring and subsequent adjustment of behavior. The experimental results show that individual judgments of facial attractiveness were adjusted in line with a normative group opinion. A mismatch between individual and group opinions triggered a frontocentral negative deflection with the maximum at 200 ms, similar to FRN. Overall, a conflict with a normative group opinion triggered a cascade of neuronal responses: from an earlier FRN response reflecting a conflict with the normative opinion to a later ERP component (peaking at 380 ms) reflecting a conforming behavioral adjustment. These results add to the growing literature on neuronal mechanisms of social influence by disentangling the conflict-monitoring signal in response to the perceived violation of social norms and the neural signal of a conforming behavioral adjustment. PMID:22683703

  6. Sol-gel precursors and products thereof

    Science.gov (United States)

    Warren, Scott C.; DiSalvo, Jr., Francis J.; Weisner, Ulrich B.

    2017-02-14

    The present invention provides a generalizable single-source sol-gel precursor capable of introducing a wide range of functionalities to metal oxides such as silica. The sol-gel precursor facilitates a one-molecule, one-step approach to the synthesis of metal-silica hybrids with combinations of biological, catalytic, magnetic, and optical functionalities. The single-source precursor also provides a flexible route for simultaneously incorporating functional species of many different types. The ligands employed for functionalizing the metal oxides are derived from a library of amino acids, hydroxy acids, or peptides and a silicon alkoxide, allowing many biological functionalities to be built into silica hybrids. The ligands can coordinate with a wide range of metals via a carboxylic acid, thereby allowing direct incorporation of inorganic functionalities from across the periodic table. Using the single-source precursor a wide range of functionalized nanostructures such as monolith structures, mesostructures, multiple metal gradient mesostructures and Stober-type nanoparticles can be synthesized. ##STR00001##

  7. Precursor Dependent Structural Properties and Antibacterial Activity ...

    Indian Academy of Sciences (India)

    71

    10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30 ... absorption spectroscopy, Scanning electron microscopy (SEM) and Zeta ... The antibacterial activity of the synthesized CuO were studied against human .... Sample d : Copper oxide synthesized with cupric sulphate as precursor ...... Chem.4 86.

  8. Biochemical Removal of HAP Precursors from Coal

    Energy Technology Data Exchange (ETDEWEB)

    Olson, Gregory J

    1997-05-12

    Column biooxidation tests with Kentucky coal confirmed results of earlier shake flask tests showing significant removal from the coal of arsenic, selenium, cobalt, manganese, nickel and cadmium. Rates of pyrite biooxidation in Kentucky coal were only slightly more than half the rates found previously for Indiana and Pittsburgh coals. Removal of pyrite from Pittsburgh coal by ferric ion oxidation slows markedly as ferrous ions accumulate in solution, requiring maintenance of high redox potentials in processes designed for removal of pyrite and hazardous air pollutant (HAP) precursors by circulation of ferric solutions through coal. The pyrite oxidation rates obtained in these tests were used by Unifield Engineering to support the conceptual designs for alternative pyrite and HAP precursor bioleaching processes for the phase 2 pilot plant. Thermophilic microorganisms were tested to determine if mercury could be mobilized from coal under elevated growth temperatures. There was no evidence for mercury removal from coal under these conditions. However, the activity of the organisms may have liberated mercury physically. It is also possible that the organisms dissolved mercury and it readsorbed to the clay preferentially. Both of these possibilities are undergoing further testing. The Idaho National Engineering and Environmental Laboratory's (INEEL) slurry column reactor was operated and several batches of feed coal, product coal, waste solids and leach solutions were submitted to LBL for HAP precursor analysis. Results to date indicate significant removal of mercury, arsenic and other HAP precursors in the combined physical-biological process.

  9. Transcriptome dynamics of the microRNA inhibition response

    DEFF Research Database (Denmark)

    Wen, Jiayu; Leucci, Elenora; Vendramin, Roberto

    2015-01-01

    We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line-the first such dynamic study of the microRNA inhibition response-revealing both general and specific aspects of the physiological response. We show...... validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods...... of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies....

  10. Expression of Hormonal Carcinogenesis Genes and Related Regulatory microRNAs in Uterus and Ovaries of DDT-Treated Female Rats.

    Science.gov (United States)

    Kalinina, T S; Kononchuk, V V; Gulyaeva, L F

    2017-10-01

    The insecticide dichlorodiphenyltrichloroethane (DDT) is a nonmutagenic xenobiotic compound able to exert estrogen-like effects resulting in activation of estrogen receptor-α (ERα) followed by changed expression of its downstream target genes. In addition, studies performed over recent years suggest that DDT may also influence expression of microRNAs. However, an impact of DDT on expression of ER, microRNAs, and related target genes has not been fully elucidated. Here, using real-time PCR, we assessed changes in expression of key genes involved in hormonal carcinogenesis as well as potentially related regulatory oncogenic/tumor suppressor microRNAs and their target genes in the uterus and ovaries of female Wistar rats during single and chronic multiple-dose DDT exposure. We found that applying DDT results in altered expression of microRNAs-221, -222, -205, -126a, and -429, their target genes (Pten, Dicer1), as well as genes involved in hormonal carcinogenesis (Esr1, Pgr, Ccnd1, Cyp19a1). Notably, Cyp19a1 expression seems to be also regulated by microRNAs-221, -222, and -205. The data suggest that epigenetic effects induced by DDT as a potential carcinogen may be based on at least two mechanisms: (i) activation of ERα followed by altered expression of the target genes encoding receptor Pgr and Ccnd1 as well as impaired expression of Cyp19a1, affecting, thereby, cell hormone balance; and (ii) changed expression of microRNAs resulting in impaired expression of related target genes including reduced level of Cyp19a1 mRNA.

  11. Detection of plant microRNAs in honey.

    Directory of Open Access Journals (Sweden)

    Angelo Gismondi

    Full Text Available For the first time in the literature, our group has managed to demonstrate the existence of plant RNAs in honey samples. In particular, in our work, different RNA extraction procedures were performed in order to identify a purification method for nucleic acids from honey. Purity, stability and integrity of the RNA samples were evaluated by spectrophotometric, PCR and electrophoretic analyses. Among all honey RNAs, we specifically revealed the presence of both plastidial and nuclear plant transcripts: RuBisCO large subunit mRNA, maturase K messenger and 18S ribosomal RNA. Surprisingly, nine plant microRNAs (miR482b, miR156a, miR396c, miR171a, miR858, miR162a, miR159c, miR395a and miR2118a were also detected and quantified by qPCR. In this context, a comparison between microRNA content in plant samples (i.e. flowers, nectars and their derivative honeys was carried out. In addition, peculiar microRNA profiles were also identified in six different monofloral honeys. Finally, the same plant microRNAs were investigated in other plant food products: tea, cocoa and coffee. Since plant microRNAs introduced by diet have been recently recognized as being able to modulate the consumer's gene expression, our research suggests that honey's benefits for human health may be strongly correlated to the bioactivity of plant microRNAs contained in this matrix.

  12. Small Molecule, Big Prospects: MicroRNA in Pregnancy and Its Complications

    Directory of Open Access Journals (Sweden)

    Meng Cai

    2017-01-01

    Full Text Available MicroRNAs are small, noncoding RNA molecules that regulate target gene expression in the posttranscriptional level. Unlike siRNA, microRNAs are “fine-tuners” rather than “switches” in the regulation of gene expression; thus they play key roles in maintaining tissue homeostasis. The aberrant microRNA expression is implicated in the disease process. To date, numerous studies have demonstrated the regulatory roles of microRNAs in various pathophysiological conditions. In contrast, the study of microRNA in pregnancy and its associated complications, such as preeclampsia (PE, fetal growth restriction (FGR, and preterm labor, is a young field. Over the last decade, the knowledge of pregnancy-related microRNAs has increased and the molecular mechanisms by which microRNAs regulate pregnancy or its associated complications are emerging. In this review, we focus on the recent advances in the research of pregnancy-related microRNAs, especially their function in pregnancy-associated complications and the potential clinical applications. Here microRNAs that associate with pregnancy are classified as placenta-specific, placenta-associated, placenta-derived circulating, and uterine microRNA according to their localization and origin. MicroRNAs offer a great potential for developing diagnostic and therapeutic targets in pregnancy-related disorders.

  13. Expression of MicroRNA-146a and MicroRNA-155 in Placental Villi in Early- and Late-Onset Preeclampsia.

    Science.gov (United States)

    Nizyaeva, N V; Kulikova, G V; Nagovitsyna, M N; Kan, N E; Prozorovskaya, K N; Shchegolev, A I; Sukhikh, G T

    2017-07-01

    We studied the expression of microRNA-146a and microRNA-155 in placental villi from 18 women (26-39 weeks of gestation) of reproductive age with early- or late-onset preeclampsia. The reference group consisted of women with physiological pregnancy and full-term gestation and with preterm birth after caesarian section on gestation week 26-31. MicroRNA-146a and microRNA-155 were detected by in situ hybridization with digoxigenin on paraffin sections. It was found that the expression of microRNA-146a in both syncytiotrophoblast of the intermediate villi and syncytial knots was lower at late-onset preeclampsia than at physiologic pregnancy of full-term period (p=0.037 and p=0.001 respectively). The expression of microRNA-155 in syncytiotrophoblast of intermediate placental villi in early-onset preeclampsia was higher than in group with preterm delivery (p=0.003). However, in syncytiotrophoblast of intermediate villi and in syncytial knots, the expression of microRNA-155 was lower at late-onset preeclampsia in comparison with full-term physiological pregnancy (p=0.005). In addition, the expression of microRNA-146a and microRNA-155 did not increase in the later terms in preeclampsia, while in the reference groups demonstrating gradual increase in the expression of these markers with increasing gestational age. Expression microRNA-146a and microRNA-155 little differed in early- and late-onset preeclampsia. These findings suggest that different variants of preeclampsia are probably characterized by common pathogenetic pathways. Damaged trophoblast cannot maintain of microRNAs synthesis at the required level, which determines the formation of a vicious circle in preeclampsia and further progression of the disease.

  14. miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.

    Science.gov (United States)

    Gupta, Samir; Ross, Karen E; Tudor, Catalina O; Wu, Cathy H; Schmidt, Carl J; Vijay-Shanker, K

    2016-04-29

    MicroRNAs are increasingly being appreciated as critical players in human diseases, and questions concerning the role of microRNAs arise in many areas of biomedical research. There are several manually curated databases of microRNA-disease associations gathered from the biomedical literature; however, it is difficult for curators of these databases to keep up with the explosion of publications in the microRNA-disease field. Moreover, automated literature mining tools that assist manual curation of microRNA-disease associations currently capture only one microRNA property (expression) in the context of one disease (cancer). Thus, there is a clear need to develop more sophisticated automated literature mining tools that capture a variety of microRNA properties and relations in the context of multiple diseases to provide researchers with fast access to the most recent published information and to streamline and accelerate manual curation. We have developed miRiaD (microRNAs in association with Disease), a text-mining tool that automatically extracts associations between microRNAs and diseases from the literature. These associations are often not directly linked, and the intermediate relations are often highly informative for the biomedical researcher. Thus, miRiaD extracts the miR-disease pairs together with an explanation for their association. We also developed a procedure that assigns scores to sentences, marking their informativeness, based on the microRNA-disease relation observed within the sentence. miRiaD was applied to the entire Medline corpus, identifying 8301 PMIDs with miR-disease associations. These abstracts and the miR-disease associations are available for browsing at http://biotm.cis.udel.edu/miRiaD . We evaluated the recall and precision of miRiaD with respect to information of high interest to public microRNA-disease database curators (expression and target gene associations), obtaining a recall of 88.46-90.78. When we expanded the evaluation to

  15. Identification of a novel FGFRL1 MicroRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies

    NARCIS (Netherlands)

    T. Niu (Tianhua); N. Liu (Ning); M. Zhao (Ming); G. Xie (Guie); L. Zhang (Lei); J. Li (Jian); Y.-F. Pei (Yu-Fang); H. Shen (Hui); X. Fu (Xiaoying); H. He (Hao); S. Lu (Shan); X. Chen (Xiangding); L. Tan (Lijun); T.-L. Yang (Tie-Lin); Y. Guo (Yan); P.J. Leo (Paul); E.L. Duncan (Emma); J. Shen (Jie); Y.-F. Guo (Yan-fang); G.C. Nicholson (Geoffrey); R.L. Prince (Richard L.); J.A. Eisman (John); G. Jones (Graeme); P.N. Sambrook (Philip); X. Hu (Xiang); P.M. Das (Partha M.); Q. Tian (Qing); X.-Z. Zhu (Xue-Zhen); C.J. Papasian (Christopher J.); M.A. Brown (Matthew); A.G. Uitterlinden (André); Y.-P. Wang (Yu-Ping); S. Xiang (Shuanglin); H.-W. Deng

    2015-01-01

    textabstractMicroRNAs (miRNAs) are critical post-transcriptional regulators. Based on a previous genome-wide association (GWA) scan, we conducted a polymorphism in microRNAs' Target Sites (poly-miRTS)-centric multistage meta-analysis for lumbar spine (LS)-, total hip (HIP)-, and femoral neck

  16. Artificial microRNAs and their applications in plant molecular biology

    Directory of Open Access Journals (Sweden)

    Pérez-Quintero Álvaro Luis

    2010-11-01

    Full Text Available

    Artificial microRNAs (amiRNAs are modified endogenous microRNA precursors in which the miRNA:miRNA* duplex is replaced with sequences designed to silence any desired gene. amiRNAs are used as part of new genetic transformation techniques in eukaryotes and have proven to be effective and to excel over other RNA-mediated gene silencing methods in both specificity and stability. amiRNAs can be designed to silence single or multiple genes, it is also possible to construct dimeric amiRNA precursors to silence two non-related genes simultaneously. amiRNA expression is quantitative and allows using constitutive, inducible, or tissue-specific promoters. One main application of amiRNAs is gene functional validation and to this end they have been mostly used in model plants; however, their use can be extended to any species or variety. amiRNA-mediated antiviral defense is another important application with great potential for plant molecular biology and crop improvement, but it still needs to be optimized to prevent the escape of viruses from the silencing mechanism. Furthermore, amiRNAs have propelled research in related areas allowing the development of similar tools like artificial trans-acting small interference RNAs (tasiARNs and artificial target mimicry. In this review, some applications and advantages of amiRNAs in plant molecular biology are analyzed. 

  17. Transcriptome-wide identification of Rauvolfia serpentina microRNAs and prediction of their potential targets.

    Science.gov (United States)

    Prakash, Pravin; Rajakani, Raja; Gupta, Vikrant

    2016-04-01

    MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 19-24 nucleotides (nt) in length and considered as potent regulators of gene expression at transcriptional and post-transcriptional levels. Here we report the identification and characterization of 15 conserved miRNAs belonging to 13 families from Rauvolfia serpentina through in silico analysis of available nucleotide dataset. The identified mature R. serpentina miRNAs (rse-miRNAs) ranged between 20 and 22nt in length, and the average minimal folding free energy index (MFEI) value of rse-miRNA precursor sequences was found to be -0.815 kcal/mol. Using the identified rse-miRNAs as query, their potential targets were predicted in R. serpentina and other plant species. Gene Ontology (GO) annotation showed that predicted targets of rse-miRNAs include transcription factors as well as genes involved in diverse biological processes such as primary and secondary metabolism, stress response, disease resistance, growth, and development. Few rse-miRNAs were predicted to target genes of pharmaceutically important secondary metabolic pathways such as alkaloids and anthocyanin biosynthesis. Phylogenetic analysis showed the evolutionary relationship of rse-miRNAs and their precursor sequences to homologous pre-miRNA sequences from other plant species. The findings under present study besides giving first hand information about R. serpentina miRNAs and their targets, also contributes towards the better understanding of miRNA-mediated gene regulatory processes in plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. MicroRNA-142 is mutated in about 20% of diffuse large B-cell lymphoma

    International Nuclear Information System (INIS)

    Kwanhian, Wiyada; Lenze, Dido; Alles, Julia; Motsch, Natalie; Barth, Stephanie; Döll, Celina; Imig, Jochen; Hummel, Michael; Tinguely, Marianne; Trivedi, Pankaj; Lulitanond, Viraphong; Meister, Gunter; Renner, Christoph; Grässer, Friedrich A

    2012-01-01

    MicroRNAs (miRNAs) are short 18–23 nucleotide long noncoding RNAs that posttranscriptionally regulate gene expression by binding to mRNA. Our previous miRNA profiling of diffuse large B-cell lymphoma (DLBCL) revealed a mutation in the seed sequence of miR-142-3p. Further analysis now showed that miR-142 was mutated in 11 (19.64%) of the 56 DLBCL cases. Of these, one case had a mutation in both alleles, with the remainder being heterozygous. Four mutations were found in the mature miR-142-5p, four in the mature miR-142-3p, and three mutations affected the miR-142 precursor. Two mutations in the seed sequence redirected miR-142-3p to the mRNA of the transcriptional repressor ZEB2 and one of them also targeted the ZEB1 mRNA. However, the other mutations in the mature miR-142-3p did not influence either the ZEB1 or ZEB2 3′ untranslated region (3′ UTR). On the other hand, the mutations affecting the seed sequence of miR-142-3p resulted in a loss of responsiveness in the 3′ UTR of the known miR-142-3p targets RAC1 and ADCY9. In contrast to the mouse p300 gene, the human p300 gene was not found to be a target for miR-142-5p. In one case with a mutation of the precursor, we observed aberrant processing of the miR-142-5p. Our data suggest that the mutations in miR-142 probably lead to a loss rather than a gain of function. This is the first report describing mutations of a miRNA gene in a large percentage of a distinct lymphoma subtype

  19. Modulation of microRNA editing, expression and processing by ADAR2 deaminase in glioblastoma.

    Science.gov (United States)

    Tomaselli, Sara; Galeano, Federica; Alon, Shahar; Raho, Susanna; Galardi, Silvia; Polito, Vinicia Assunta; Presutti, Carlo; Vincenti, Sara; Eisenberg, Eli; Locatelli, Franco; Gallo, Angela

    2015-01-13

    ADAR enzymes convert adenosines to inosines within double-stranded RNAs, including microRNA (miRNA) precursors, with important consequences on miRNA retargeting and expression. ADAR2 activity is impaired in glioblastoma and its rescue has anti-tumoral effects. However, how ADAR2 activity may impact the miRNome and the progression of glioblastoma is not known. By integrating deep-sequencing and array approaches with bioinformatics analyses and molecular studies, we show that ADAR2 is essential to edit a small number of mature miRNAs and to significantly modulate the expression of about 90 miRNAs in glioblastoma cells. Specifically, the rescue of ADAR2 activity in cancer cells recovers the edited miRNA population lost in glioblastoma cell lines and tissues, and rebalances expression of onco-miRNAs and tumor suppressor miRNAs to the levels observed in normal human brain. We report that the major effect of ADAR2 is to reduce the expression of a large number of miRNAs, most of which act as onco-miRNAs. ADAR2 can edit miR-222/221 and miR-21 precursors and decrease the expression of the corresponding mature onco-miRNAs in vivo and in vitro, with important effects on cell proliferation and migration. Our findings disclose an additional layer of complexity in miRNome regulation and provide information to better understand the impact of ADAR2 editing enzyme in glioblastoma. We propose that ADAR2 is a key factor for maintaining edited-miRNA population and balancing the expression of several essential miRNAs involved in cancer.

  20. MicroRNAs and potential target interactions in psoriasis

    DEFF Research Database (Denmark)

    Zibert, John Robert; Løvendorf, Marianne B.; Litman, Thomas

    2010-01-01

    BACKGROUND: Psoriasis is a chronic inflammatory skin disease often seen in patients with a genetic susceptibility. MicroRNAs (miRNA) are endogenous, short RNA molecules that can bind to parts of mRNA target genes, thus inhibiting their translation and causing accelerated turnover or transcript...... degradation. MicroRNAs are important in the pathogenesis of human diseases such as immunological disorders, as they regulate a broad range of biological processes. OBJECTIVE: We investigated miRNA-mRNA interactions in involved (PP) and non-involved (PN) psoriatic skin compared with healthy skin (NN). METHODS...

  1. MicroRNA in oral cancer research: future prospects.

    Science.gov (United States)

    Sarode, Sachin C; Sarode, Gargi S; Patil, Shankargouda

    2014-09-01

    MicroRNA (miRNA) and related therapeutic approaches hold great promise in the field of cancer managements. Various studies on epithelial malignancies have shown encouraging results on various fronts. Its association with invasion, tumor growth, epithelial mesenchymal transition (EMT), angiogenesis, cancer stem cells (CSCs), metastasis and refects the diversified role of miRNA. Moreover, miRNA plays an important role in determining the prognosis of the patients. MicroRNAs interactions with each other and with external factors [human papilloma virus (HPV) (like oncoproteins)] intrigue us to explore more deep into this fascinating world.(1.)

  2. MicroRNAs as potential therapeutic targets in kidney disease

    Science.gov (United States)

    Gomez, Ivan G; Grafals, Monica; Portilla, Didier; Duffield, Jeremy S

    2014-01-01

    One cornerstone of Chronic Kidney Disease (CKD) is fibrosis, as kidneys are susceptible due to their high vascularity and predisposition to ischemia. Presently, only therapies targeting the angiotensin receptor are used in clinical practice to retard the progression of CKD. Thus, there is a pressing need for new therapies designed to treat the damaged kidney. Several independent laboratories have identified a number of microRNAs that are dysregulated in human and animal models of CKD. We will explore the evidence suggesting that by blocking the activity of such dysregulated microRNAs, new therapeutics could be developed to treat the progression of CKD. PMID:23660218

  3. MicroRNA-21 Increases Proliferation and Cisplatin Sensitivity of Osteosarcoma-Derived Cells.

    Directory of Open Access Journals (Sweden)

    Vanita Vanas

    Full Text Available Osteosarcoma is the most common primary bone tumor and poor prognosis for osteosarcoma patients is mainly due to chemotherapy resistance. MicroRNAs are important to maintain pathophysiological mechanisms of cancer and influence cell sensitivity to chemotherapy. In this study, we tested the functions of microRNA-21 for malignant features as well as for drug resistance of osteosarcoma. We used Northern blot to measure microRNA-21 levels in osteosarcoma-derived cell lines. MicroRNA-21 activity was modulated by either expressing a sponge to decrease its activity in an osteosarcoma-derived cell line expressing high levels of microRNA-21 or by introducing pri-microRNA-21 in a cell line with low endogenous levels. Cell migration was determined in a scratch assay and cell proliferation was measured by performing growth curve analysis. Sensitivity of the cells towards chemotherapeutics was investigated by performing cell viability assays and calculating the IC50 values. While cell migration was unaffected by modulated microRNA-21 levels, microRNA-21 inhibition slowed proliferation and exogenously expressed microRNA-21 promoted this process. Modulated microRNA-21 activity failed to effect sensitivity of osteosarcoma-derived cell lines to doxorubicin or methotrexate. Contrarily, reduction of microRNA-21 activity resulted in enhanced resistance towards cisplatin while ectopic expression of microRNA-21 showed the opposite effect. Increased microRNA-21 levels repressed the expression of Sprouty2 and ectopic expression of Sprouty2 was able to largely rescue the observed effects of microRNA-21 in osteosarcoma. In summary, our data indicate that in osteosarcoma microRNA-21 expression is an important component for regulation of cell proliferation and for determining sensitivity to cisplatin.

  4. MicroRNAs associated with exercise and diet: a systematic review.

    Science.gov (United States)

    Flowers, Elena; Won, Gloria Y; Fukuoka, Yoshimi

    2015-01-01

    MicroRNAs are posttranscriptional regulators of gene expression. MicroRNAs reflect individual biologic adaptation to exposures in the environment. As such, measurement of circulating microRNAs presents an opportunity to evaluate biologic changes associated with behavioral interventions (i.e., exercise, diet) for weight loss. The aim of this study was to perform a systematic review of the literature to summarize what is known about circulating microRNAs associated with exercise, diet, and weight loss. We performed a systematic review of three scientific databases. We included studies reporting on circulating microRNAs associated with exercise, diet, and weight loss in humans. Of 1,219 studies identified in our comprehensive database search, 14 were selected for inclusion. Twelve reported on microRNAs associated with exercise, and two reported on microRNAs associated with diet and weight loss. The majority of studies used a quasiexperimental, cross-sectional design. There were numerous differences in the type and intensity of exercise and dietary interventions, the biologic source of microRNAs, and the methodological approaches used quantitate microRNAs. Data from several studies support an association between circulating microRNAs and exercise. The evidence for an association between circulating microRNAs and diet is weaker because of a small number of studies. Additional research is needed to validate previous observations using methodologically rigorous approaches to microRNA quantitation to determine the specific circulating microRNA signatures associated with behavioral approaches to weight loss. Future directions include longitudinal studies to determine if circulating microRNAs are predictive of response to behavioral interventions. Copyright © 2015 the American Physiological Society.

  5. Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance.

    Science.gov (United States)

    Niu, Qi-Wen; Lin, Shih-Shun; Reyes, Jose Luis; Chen, Kuan-Chun; Wu, Hui-Wen; Yeh, Shyi-Dong; Chua, Nam-Hai

    2006-11-01

    Plant microRNAs (miRNAs) regulate the abundance of target mRNAs by guiding their cleavage at the sequence complementary region. We have modified an Arabidopsis thaliana miR159 precursor to express artificial miRNAs (amiRNAs) targeting viral mRNA sequences encoding two gene silencing suppressors, P69 of turnip yellow mosaic virus (TYMV) and HC-Pro of turnip mosaic virus (TuMV). Production of these amiRNAs requires A. thaliana DICER-like protein 1. Transgenic A. thaliana plants expressing amiR-P69(159) and amiR-HC-Pro(159) are specifically resistant to TYMV and TuMV, respectively. Expression of amiR-TuCP(159) targeting TuMV coat protein sequences also confers specific TuMV resistance. However, transgenic plants that express both amiR-P69(159) and amiR-HC-Pro(159) from a dimeric pre-amiR-P69(159)/amiR-HC-Pro(159) transgene are resistant to both viruses. The virus resistance trait is displayed at the cell level and is hereditable. More important, the resistance trait is maintained at 15 degrees C, a temperature that compromises small interfering RNA-mediated gene silencing. The amiRNA-mediated approach should have broad applicability for engineering multiple virus resistance in crop plants.

  6. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias

    Science.gov (United States)

    Calin, George Adrian; Liu, Chang-Gong; Sevignani, Cinzia; Ferracin, Manuela; Felli, Nadia; Dumitru, Calin Dan; Shimizu, Masayoshi; Cimmino, Amelia; Zupo, Simona; Dono, Mariella; Dell'Aquila, Marie L.; Alder, Hansjuerg; Rassenti, Laura; Kipps, Thomas J.; Bullrich, Florencia; Negrini, Massimo; Croce, Carlo M.

    2004-01-01

    Little is known about the expression levels or function of micro-RNAs (miRNAs) in normal and neoplastic cells, although it is becoming clear that miRNAs play important roles in the regulation of gene expression during development [Ambros, V. (2003) Cell 113, 673–676; McManus, M. T. (2003) Semin. Cancer Biol. 13, 253–258]. We now report the genomewide expression profiling of miRNAs in human B cell chronic lymphocytic leukemia (CLL) by using a microarray containing hundreds of human precursor and mature miRNA oligonucleotide probes. This approach allowed us to identify significant differences in miRNome expression between CLL samples and normal CD5+ B cells; data were confirmed by Northern blot analyses and real-time RT-PCR. At least two distinct clusters of CLL samples can be identified that were associated with the presence or absence of Zap-70 expression, a predictor of early disease progression. Two miRNA signatures were associated with the presence or absence of mutations in the expressed Ig variableregion genes or with deletions at 13q14, respectively. These data suggest that miRNA expression patterns have relevance to the biological and clinical behavior of this leukemia. PMID:15284443

  7. Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

    Science.gov (United States)

    Feng, Yue; Feng, Yue-Mei; Feng, Yang; Lu, Caixia; Liu, Li; Sun, Xiaomei; Dai, Jiejie; Xia, Xueshan

    2015-10-01

    Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection. This study aimed to construct a liver microRNA (miRNA) data of the tree shrew. Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing. A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction. According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

  8. Characterisation of microRNA expression in post-natal mouse mammary gland development

    Directory of Open Access Journals (Sweden)

    Karagavriilidou Konstantina

    2009-11-01

    Full Text Available Abstract Background The differential expression pattern of microRNAs (miRNAs during mammary gland development might provide insights into their role in regulating the homeostasis of the mammary epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development. We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained. Results One third (n = 102 of all murine miRNAs analysed were detected during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show changes, we observed inverse patterns of miRNA and target expression. The data sets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research. Conclusion MicroRNAs were expressed in likely co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation provide new avenues for research into mammary gland biology and generate candidates for functional validation.

  9. Human embryos secrete microRNAs into culture media--a potential biomarker for implantation.

    Science.gov (United States)

    Rosenbluth, Evan M; Shelton, Dawne N; Wells, Lindsay M; Sparks, Amy E T; Van Voorhis, Bradley J

    2014-05-01

    To determine whether human blastocysts secrete microRNA (miRNAs) into culture media and whether these reflect embryonic ploidy status and can predict in vitro fertilization (IVF) outcomes. Experimental study of human embryos and IVF culture media. Academic IVF program. 91 donated, cryopreserved embryos that developed into 28 tested blastocysts, from 13 couples who had previously completed IVF cycles. None. Relative miRNA expression in IVF culture media. Blastocysts were assessed by chromosomal comparative genomic hybridization analysis, and the culture media from 55 single-embryo transfer cycles was tested for miRNA expression using an array-based quantitative real-time polymerase chain reaction analysis. The expression of the identified miRNA was correlated with pregnancy outcomes. Ten miRNA were identified in the culture media; two were specific to spent media (miR-191 and miR-372), and one was only present in media before the embryos had been cultured (miR-645). MicroRNA-191 was more highly concentrated in media from aneuploid embryos, and miR-191, miR-372, and miR-645 were more highly concentrated in media from failed IVF/non-intracytoplasmic sperm injection cycles. Additionally, miRNA were found to be more highly concentrated in ICSI and day-5 media samples when compared with regularly inseminated and day-4 samples, respectively. MicroRNA can be detected in IVF culture media. Some of these miRNA are differentially expressed according to the fertilization method, chromosomal status, and pregnancy outcome, which makes them potential biomarkers for predicting IVF success. Copyright © 2014 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  10. MicroRNAs and Periodontal Homeostasis.

    Science.gov (United States)

    Luan, X; Zhou, X; Trombetta-eSilva, J; Francis, M; Gaharwar, A K; Atsawasuwan, P; Diekwisch, T G H

    2017-05-01

    MicroRNAs (miRNAs) are a group of small RNAs that control gene expression in all aspects of eukaryotic life, primarily through RNA silencing mechanisms. The purpose of the present review is to introduce key miRNAs involved in periodontal homeostasis, summarize the mechanisms by which they affect downstream genes and tissues, and provide an introduction into the therapeutic potential of periodontal miRNAs. In general, miRNAs function synergistically to fine-tune the regulation of biological processes and to remove expression noise rather than by causing drastic changes in expression levels. In the periodontium, miRNAs play key roles in development and periodontal homeostasis and during the loss of periodontal tissue integrity as a result of periodontal disease. As part of the anabolic phase of periodontal homeostasis and periodontal development, miRNAs direct periodontal fibroblasts toward alveolar bone lineage differentiation and new bone formation through WNT, bone morphogenetic protein, and Notch signaling pathways. miRNAs contribute equally to the catabolic aspect of periodontal homeostasis as they affect osteoclastogenesis and osteoclast function, either by directly promoting osteoclast activity or by inhibiting osteoclast signaling intermediaries or through negative feedback loops. Their small size and ability to target multiple regulatory networks of related sets of genes have predisposed miRNAs to become ideal candidates for drug delivery and tissue regeneration. To address the immense therapeutic potential of miRNAs and their antagomirs, an ever growing number of delivery approaches toward clinical applications have been developed, including nanoparticle carriers and secondary structure interference inhibitor systems. However, only a fraction of the miRNAs involved in periodontal health and disease are known today. It is anticipated that continued research will lead to a more comprehensive understanding of the periodontal miRNA world, and a systematic

  11. microRNA expression during trophectoderm specification.

    Directory of Open Access Journals (Sweden)

    Srinivas R Viswanathan

    2009-07-01

    Full Text Available Segregation of the trophectoderm from the inner cell mass of the embryo represents the first cell-fate decision of mammalian development. Transcription factors essential for specifying trophectoderm have been identified, but the role of microRNAs (miRNAs in modulating this fate-choice has been largely unexplored. We have compared miRNA expression in embryonic stem cell (ESC-derived trophectoderm and in staged murine embryos to identify a set of candidate miRNAs likely to be involved in trophectoderm specification.We profiled embryonic stem cells (ESCs as they were induced to differentiate into trophectodermal cells by ectopic expression of HRas/Q61L. We also profiled murine embryos at progressive stages of preimplantation development (zygote, 2-cell, 4-cell, 8-cell, morula, and blastocyst, which includes the time window in which the trophectoderm is specified in vivo Q61L/H.We describe miRNA expression changes that occur during trophectoderm specification and validate that our in vitro system faithfully recapitulates trophectoderm specification in vivo. By comparing our in vitro and in vivo datasets, we have identified a minimal set of candidate miRNAs likely to play a role in trophectoderm specification. These miRNAs are predicted to regulate a host of development-associated target genes, and many of these miRNAs have previously reported roles in development and differentiation. Additionally, we highlight a number of miRNAs whose tight developmental regulation may reflect a functional role in other stages of embryogenesis. Our embryo profiling data may be useful to investigators studying trophectoderm specification and other stages of preimplantation development.

  12. NPK macronutrients and microRNA homeostasis.

    Science.gov (United States)

    Kulcheski, Franceli R; Côrrea, Régis; Gomes, Igor A; de Lima, Júlio C; Margis, Rogerio

    2015-01-01

    Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.

  13. Understanding the Thermal Properties of Precursor-Ionomers to Optimize Fabrication Processes for Ionic Polymer-Metal Composites (IPMCs

    Directory of Open Access Journals (Sweden)

    Sarah Trabia

    2018-04-01

    Full Text Available Ionic polymer-metal composites (IPMCs are one of many smart materials and have ionomer bases with a noble metal plated on the surface. The ionomer is usually Nafion, but recently Aquivion has been shown to be a promising alternative. Ionomers are available in the form of precursor pellets. This is an un-activated form that is able to melt, unlike the activated form. However, there is little study on the thermal characteristics of these precursor ionomers. This lack of knowledge causes issues when trying to fabricate ionomer shapes using methods such as extrusion, hot-pressing, and more recently, injection molding and 3D printing. To understand the two precursor-ionomers, a set of tests were conducted to measure the thermal degradation temperature, viscosity, melting temperature, and glass transition. The results have shown that the precursor Aquivion has a higher melting temperature (240 °C than precursor Nafion (200 °C and a larger glass transition range (32–65°C compared with 21–45 °C. The two have the same thermal degradation temperature (~400 °C. Precursor Aquivion is more viscous than precursor Nafion as temperature increases. Based on the results gathered, it seems that the precursor Aquivion is more stable as temperature increases, facilitating the manufacturing processes. This paper presents the data collected to assist researchers in thermal-based fabrication processes.

  14. MMPM - Mars MetNet Precursor Mission

    Science.gov (United States)

    Harri, A.-M.; Schmidt, W.; Pichkhadze, K.; Linkin, V.; Vazquez, L.; Uspensky, M.; Polkko, J.; Genzer, M.; Lipatov, A.; Guerrero, H.; Alexashkin, S.; Haukka, H.; Savijarvi, H.; Kauhanen, J.

    2008-09-01

    We are developing a new kind of planetary exploration mission for Mars - MetNet in situ observation network based on a new semi-hard landing vehicle called the Met-Net Lander (MNL). The eventual scope of the MetNet Mission is to deploy some 20 MNLs on the Martian surface using inflatable descent system structures, which will be supported by observations from the orbit around Mars. Currently we are working on the MetNet Mars Precursor Mission (MMPM) to deploy one MetNet Lander to Mars in the 2009/2011 launch window as a technology and science demonstration mission. The MNL will have a versatile science payload focused on the atmospheric science of Mars. Detailed characterization of the Martian atmospheric circulation patterns, boundary layer phenomena, and climatology cycles, require simultaneous in-situ measurements by a network of observation posts on the Martian surface. The scientific payload of the MetNet Mission encompasses separate instrument packages for the atmospheric entry and descent phase and for the surface operation phase. The MetNet mission concept and key probe technologies have been developed and the critical subsystems have been qualified to meet the Martian environmental and functional conditions. Prototyping of the payload instrumentation with final dimensions was carried out in 2003-2006.This huge development effort has been fulfilled in collaboration between the Finnish Meteorological Institute (FMI), the Russian Lavoschkin Association (LA) and the Russian Space Research Institute (IKI) since August 2001. Currently the INTA (Instituto Nacional de Técnica Aeroespacial) from Spain is also participating in the MetNet payload development. To understand the behavior and dynamics of the Martian atmosphere, a wealth of simultaneous in situ observations are needed on varying types of Martian orography, terrain and altitude spanning all latitudes and longitudes. This will be performed by the Mars MetNet Mission. In addition to the science aspects the

  15. Understanding Animal Detection of Precursor Earthquake Sounds.

    Science.gov (United States)

    Garstang, Michael; Kelley, Michael C

    2017-08-31

    We use recent research to provide an explanation of how animals might detect earthquakes before they occur. While the intrinsic value of such warnings is immense, we show that the complexity of the process may result in inconsistent responses of animals to the possible precursor signal. Using the results of our research, we describe a logical but complex sequence of geophysical events triggered by precursor earthquake crustal movements that ultimately result in a sound signal detectable by animals. The sound heard by animals occurs only when metal or other surfaces (glass) respond to vibrations produced by electric currents induced by distortions of the earth's electric fields caused by the crustal movements. A combination of existing measurement systems combined with more careful monitoring of animal response could nevertheless be of value, particularly in remote locations.

  16. Metabolic Precursors to Amphetamine and Methamphetamine.

    Science.gov (United States)

    Cody, J D

    1993-12-01

    Analysis and interpretation of amphetamine results is a challenging process made difficult by a number of factors. One of the complications comes from determination of the origin of amphetamine or methamphetamine in a sample. Given the relatively rare occasions that either of these two drugs are prescribed, legal prescription of one of these drugs is seldom a reason for positive findings. A number of other precursor compounds are metabolized by the body to amphetamine or methamphetamine, many of which could be used for legitimate reasons. Fourteen different metabolic precursors of amphetamine or methamphetamine are included in this review. They are amphetaminil, benzphetamine, clobenzorex, deprenyl, dimethylamphetamine, ethylamphetamine, famprofazone, fencamine, fenethylline, fenproporex, furfenorex, mefenorex, mesocarb, and prenylamine. Medical use, metabolism, analysis, and interpretation are described to afford sufficient information to evaluate the possible involvement of these drugs in positive amphetamine or methamphetamine results. Copyright © 1993 Central Police University.

  17. Investigations on precursor measures for aeroelastic flutter

    Science.gov (United States)

    Venkatramani, J.; Sarkar, Sunetra; Gupta, Sayan

    2018-04-01

    Wind tunnel experiments carried out on a pitch-plunge aeroelastic system in the presence of fluctuating flows reveal that flutter instability is presaged by a regime of intermittency. It is observed that as the flow speed gradually increases towards the flutter speed, there appears intermittent bursts of periodic oscillations which become more frequent as the wind speed increases and eventually the dynamics transition into fully developed limit cycle oscillations, marking the onset of flutter. The signature from these intermittent oscillations are exploited to develop measures that forewarn a transition to flutter and can serve as precursors. This study investigates a suite of measures that are obtained directly from the time history of measurements and are hence model independent. The dependence of these precursors on the size of the measured data set and the time required for their computation is investigated. These measures can be useful in structural health monitoring of aeroelastic structures.

  18. Comparison exercise of probabilistic precursor analysis

    International Nuclear Information System (INIS)

    Fauchille, V.; Babst, S.

    2004-01-01

    From 2000 up to 2003, a comparison exercise concerning accident precursor programs was performed by IRSN, GRS, and NUPEC (Japan). The objective of this exercise was to compare the methodologies used to quantify conditional core damage probability related to incidents which can be considered as accident precursors. This exercise provided interesting results concerning the interpretation of such events. Generally, the participants identified similar scenarios of potential degradation. However, for several dominant sequences, differences in the results were noticed. The differences can be attributed to variations in the plant design, the strategy of management and in the methodological approach. For many reasons, comparison of human reliability analysis was difficult and perhaps another exercise in the future could provide more information about this subject. On the other hand, interesting outcomes have been obtained from the quantification of both common cause failures and potential common cause failures. (orig.)

  19. Functional Nanoporous Polymers from Block Copolymer Precursors

    DEFF Research Database (Denmark)

    Guo, Fengxiao

    Abstract Self-assembly of block copolymers provides well-defined morphologies with characteristic length scales in the nanometer range. Nanoporous polymers prepared by selective removal of one block from self-assembled block copolymers offer great technological promise due to their many potential...... functionalities remains a great challenge due to the limitation of available polymer synthesis and the nanoscale confinement of the porous cavities. The main topic of this thesis is to develop methods for fabrication of functional nanoporous polymers from block copolymer precursors. A method has been developed......, where living anionic polymerization and atom transfer radical polymerization (ATRP) are combined to synthesize a polydimethylsiloxane-b-poly(tert-butyl acrylate)-b-polystyrene (PDMS-b-PtBA-b-PS) triblock copolymer precursor. By using either anhydrous hydrogen fluoride or trifluoroacetic acid, PtBA block...

  20. PRECURSORS OF EARTHQUAKES: VLF SIGNALSIONOSPHERE IONOSPHERE RELATION

    Directory of Open Access Journals (Sweden)

    Mustafa ULAS

    2013-01-01

    Full Text Available lot of people have died because of earthquakes every year. Therefore It is crucial to predict the time of the earthquakes reasonable time before it had happed. This paper presents recent information published in the literature about precursors of earthquakes. The relationships between earthquakes and ionosphere are targeted to guide new researches in order to study further to find novel prediction methods.

  1. High-Throughput Sequencing of MicroRNAs in Adenovirus Type 3 Infected Human Laryngeal Epithelial Cells

    Directory of Open Access Journals (Sweden)

    Yuhua Qi

    2010-01-01

    Full Text Available Adenovirus infection can cause various illnesses depending on the infecting serotype, such as gastroenteritis, conjunctivitis, cystitis, and rash illness, but the infection mechanism is still unknown. MicroRNAs (miRNA have been reported to play essential roles in cell proliferation, cell differentiation, and pathogenesis of human diseases including viral infections. We analyzed the miRNA expression profiles from adenovirus type 3 (AD3 infected Human laryngeal epithelial (Hep2 cells using a SOLiD deep sequencing. 492 precursor miRNAs were identified in the AD3 infected Hep2 cells, and 540 precursor miRNAs were identified in the control. A total of 44 miRNAs demonstrated high expression and 36 miRNAs showed lower expression in the AD3 infected cells than control. The biogenesis of miRNAs has been analyzed, and some of the SOLiD results were confirmed by Quantitative PCR analysis. The present studies may provide a useful clue for the biological function research into AD3 infection.

  2. Subgenomic analysis of microRNAs in polyploid wheat

    Czech Academy of Sciences Publication Activity Database

    Kantar, M.; Akpinar, B. A.; Valárik, Miroslav; Lucas, S. J.; Doležel, Jaroslav; Hernandez, P.; Budak, H.

    2012-01-01

    Roč. 12, č. 3 (2012), s. 465-479 ISSN 1438-793X Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511 Keywords : Triticum aestivum * microRNA * miRNA prediction Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.292, year: 2012

  3. Bioavailability of transgenic microRNAs in genetically modified plants

    Science.gov (United States)

    Transgenic expression of small RNAs is a prevalent approach in agrobiotechnology for the global enhancement of plant foods. Meanwhile, emerging studies have, on the one hand, emphasized the potential of transgenic microRNAs (miRNAs) as novel dietary therapeutics and, on the other, suggested potentia...

  4. MicroRNA-449a deficiency promotes colon carcinogenesis.

    Science.gov (United States)

    Niki, Masanori; Nakajima, Kohei; Ishikawa, Daichi; Nishida, Jun; Ishifune, Chieko; Tsukumo, Shin-Ichi; Shimada, Mitsuo; Nagahiro, Shinji; Mitamura, Yoshinori; Yasutomo, Koji

    2017-09-06

    MicroRNAs have broad roles in tumorigenesis and cell differentiation through regulation of target genes. Notch signaling also controls cell differentiation and tumorigenesis. However, the mechanisms through which Notch mediates microRNA expression are still unclear. In this study, we aimed to identify microRNAs regulated by Notch signaling. Our analysis found that microRNA-449a (miR-449a) was indirectly regulated by Notch signaling. Although miR-449a-deficient mice did not show any Notch-dependent defects in immune cell development, treatment of miR-449a-deficient mice with azoxymethane (AOM) or dextran sodium sulfate (DSS) increased the numbers and sizes of colon tumors. These effects were associated with an increase in intestinal epithelial cell proliferation following AOM/DSS treatment. In patients with colon cancer, miR-449a expression was inversely correlated with disease-free survival and histological scores and was positively correlated with the expression of MLH1 for which loss-of function mutations have been shown to be involved in colon cancer. Colon tissues of miR-449a-deficient mice showed reduced Mlh1 expression compared with those of wild-type mice. Thus, these data suggested that miR-449a acted as a key regulator of colon tumorigenesis by controlling the proliferation of intestinal epithelial cells. Additionally, activation of miR-449a may represent an effective therapeutic strategy and prognostic marker in colon cancer.

  5. Circulating microRNAs as diagnostic biomarkers for cardiovascular diseases

    NARCIS (Netherlands)

    Tijsen, Anke J.; Pinto, Yigal M.; Creemers, Esther E.

    2012-01-01

    Tijsen AJ, Pinto YM, Creemers EE. Circulating microRNAs as diagnostic biomarkers for cardiovascular diseases. Am J Physiol Heart Circ Physiol 303: H1085-H1095, 2012. First published August 31, 2012; doi:10.1152/ajpheart.00191.2012.-One of the major challenges in cardiovascular disease is the

  6. Aberrant microRNA expression in multiple myeloma

    DEFF Research Database (Denmark)

    Dimopoulos, Konstantinos; Gimsing, Peter; Grønbæk, Kirsten

    2013-01-01

    Multiple myeloma (MM) is a devastating disease with a complex biology, and in spite of improved survivability by novel treatment strategies over the last decade, MM is still incurable by current therapy. MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression at a post...

  7. microRNA-101 is a potent inhibitor of autophagy

    DEFF Research Database (Denmark)

    Frankel, Lisa B; Wen, Jiayu; Lees, Michael

    2011-01-01

    performed a functional screen in search of microRNAs (miRNAs), which regulate the autophagic flux in breast cancer cells. In this study, we identified the tumour suppressive miRNA, miR-101, as a potent inhibitor of basal, etoposide- and rapamycin-induced autophagy. Through transcriptome profiling, we...

  8. The therapeutic potential of MicroRNAs in cancer

    DEFF Research Database (Denmark)

    Thorsen, Stine Buch; Obad, Susanna; Jensen, Niels Frank

    2012-01-01

    MicroRNAs (miRNAs) have been uncovered as important posttranscriptional regulators of nearly every biological process in the cell. Furthermore, mounting evidence implies that miRNAs play key roles in the pathogenesis of cancer and that many miRNAs can function either as oncogenes or tumor...

  9. Pharmacogenomics genes show varying perceptibility to microRNA regulation

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Vinther, Jeppe; Shomron, Noam

    2011-01-01

    The aim of pharmacogenomics is to identify individual differences in genome and transcriptome composition and their effect on drug efficacy. MicroRNAs (miRNAs) are short noncoding RNAs that negatively regulate expression of the majority of animal genes, including many genes involved in drug...

  10. Brain expressed microRNAs implicated in schizophrenia etiology

    DEFF Research Database (Denmark)

    Hansen, Thomas; Olsen, Line; Lindow, Morten

    2007-01-01

    Protein encoding genes have long been the major targets for research in schizophrenia genetics. However, with the identification of regulatory microRNAs (miRNAs) as important in brain development and function, miRNAs genes have emerged as candidates for schizophrenia-associated genetic factors...

  11. Strategies to identify microRNA targets: New advances

    Science.gov (United States)

    MicroRNAs (miRNAs) are small regulatory RNA molecules functioning to modulate gene expression at the post-transcriptional level, and playing an important role in many developmental and physiological processes. Ten thousand miRNAs have been discovered in various organisms. Although considerable progr...

  12. MicroRNAs, the DNA damage response and cancer

    International Nuclear Information System (INIS)

    Wouters, Maikel D.; Gent, Dik C. van; Hoeijmakers, Jan H.J.; Pothof, Joris

    2011-01-01

    Many carcinogenic agents such as ultra-violet light from the sun and various natural and man-made chemicals act by damaging the DNA. To deal with these potentially detrimental effects of DNA damage, cells induce a complex DNA damage response (DDR) that includes DNA repair, cell cycle checkpoints, damage tolerance systems and apoptosis. This DDR is a potent barrier against carcinogenesis and defects within this response are observed in many, if not all, human tumors. DDR defects fuel the evolution of precancerous cells to malignant tumors, but can also induce sensitivity to DNA damaging agents in cancer cells, which can be therapeutically exploited by the use of DNA damaging treatment modalities. Regulation of and coordination between sub-pathways within the DDR is important for maintaining genome stability. Although regulation of the DDR has been extensively studied at the transcriptional and post-translational level, less is known about post-transcriptional gene regulation by microRNAs, the topic of this review. More specifically, we highlight current knowledge about DNA damage responsive microRNAs and microRNAs that regulate DNA damage response genes. We end by discussing the role of DNA damage response microRNAs in cancer etiology and sensitivity to ionizing radiation and other DNA damaging therapeutic agents.

  13. The Potential of MicroRNAs as Prostate Cancer Biomarkers

    NARCIS (Netherlands)

    L. Fabris (Linda); Y. Ceder (Yvonne); A.M. Chinnaiyan (Arul); G.W. Jenster (Guido); K.D. Sorensen (Karina D.); S.A. Tomlins (Scott A); T. Visakorpi (Tapio); G.A. Calin (George)

    2016-01-01

    textabstractContext: Short noncoding RNAs known as microRNAs (miRNAs) control protein expression through the degradation of RNA or the inhibition of protein translation. The miRNAs influence a wide range of biologic processes and are often deregulated in cancer. This family of small RNAs constitutes

  14. MicroRNA related polymorphisms and breast cancer risk

    NARCIS (Netherlands)

    S. Khan (Sofia); D. Greco (Dario); K. Michailidou (Kyriaki); R.L. Milne (Roger); T.A. Muranen (Taru); T. Heikkinen (Tuomas); K. Aaltonen (Kirsimari); J. Dennis (Joe); M.K. Bolla (Manjeet); J. Liu (Jianjun); P. Hall (Per); A. Irwanto (Astrid); M.K. Humphreys (Manjeet); J. Li (Jingmei); K. Czene (Kamila); J. Chang-Claude (Jenny); R. Hein (Rebecca); A. Rudolph (Anja); P. Seibold (Petra); D. Flesch-Janys (Dieter); O. Fletcher (Olivia); J. Peto (Julian); I. dos Santos Silva (Isabel); N. Johnson (Nichola); L.J. Gibson (Lorna); A. Aitken; J.L. Hopper (John); H. Tsimiklis (Helen); M. Bui (Minh); E. Makalic (Enes); D.F. Schmidt (Daniel); M.C. Southey (Melissa); C. Apicella (Carmel); J. Stone (Jennifer);